HEADER TRANSFERASE 25-JAN-17 5MY8
TITLE CRYSTAL STRUCTURE OF SRPK1 IN COMPLEX WITH SPHINX31
COMPND MOL_ID: 1;
COMPND 2 MOLECULE: SRSF PROTEIN KINASE 1,SRSF PROTEIN KINASE 1;
COMPND 3 CHAIN: A;
COMPND 4 SYNONYM: SFRS PROTEIN KINASE 1,SERINE/ARGININE-RICH PROTEIN-SPECIFIC
COMPND 5 KINASE 1,SR-PROTEIN-SPECIFIC KINASE 1,SFRS PROTEIN KINASE 1,
COMPND 6 SERINE/ARGININE-RICH PROTEIN-SPECIFIC KINASE 1,SR-PROTEIN-SPECIFIC
COMPND 7 KINASE 1;
COMPND 8 EC: 2.7.11.1,2.7.11.1;
COMPND 9 ENGINEERED: YES
SOURCE MOL_ID: 1;
SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS;
SOURCE 3 ORGANISM_COMMON: HUMAN;
SOURCE 4 ORGANISM_TAXID: 9606;
SOURCE 5 GENE: SRPK1;
SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3);
SOURCE 7 EXPRESSION_SYSTEM_TAXID: 469008;
SOURCE 8 EXPRESSION_SYSTEM_VARIANT: R3-PRARE2;
SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID;
SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PNIC28-BSA4
KEYWDS TRANSFERASE, SPLICING KINASE, INHIBITOR, STRUCTURAL GENOMICS,
KEYWDS 2 STRUCTURAL GENOMICS CONSORTIUM, SGC
EXPDTA X-RAY DIFFRACTION
AUTHOR A.CHAIKUAD,F.VON DELFT,C.BOUNTRA,C.H.ARROWSMITH,A.M.EDWARDS,S.KNAPP,
AUTHOR 2 STRUCTURAL GENOMICS CONSORTIUM (SGC)
REVDAT 1 10-MAY-17 5MY8 0
JRNL AUTH J.BATSON,H.D.TOOP,C.REDONDO,R.BABAEI-JADIDI,A.CHAIKUAD,
JRNL AUTH 2 S.F.WEARMOUTH,B.GIBBONS,C.ALLEN,C.TALLANT,J.ZHANG,C.DU,
JRNL AUTH 3 J.C.HANCOX,T.HAWTREY,J.DA ROCHA,R.GRIFFITH,S.KNAPP,
JRNL AUTH 4 D.O.BATES,J.C.MORRIS
JRNL TITL DEVELOPMENT OF POTENT, SELECTIVE SRPK1 INHIBITORS AS
JRNL TITL 2 POTENTIAL TOPICAL THERAPEUTICS FOR NEOVASCULAR EYE DISEASE.
JRNL REF ACS CHEM. BIOL. V. 12 825 2017
JRNL REFN ESSN 1554-8937
JRNL PMID 28135068
JRNL DOI 10.1021/ACSCHEMBIO.6B01048
REMARK 2
REMARK 2 RESOLUTION. 1.70 ANGSTROMS.
REMARK 3
REMARK 3 REFINEMENT.
REMARK 3 PROGRAM : REFMAC 5.8.0131
REMARK 3 AUTHORS : MURSHUDOV,VAGIN,DODSON
REMARK 3
REMARK 3 REFINEMENT TARGET : NULL
REMARK 3
REMARK 3 DATA USED IN REFINEMENT.
REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.70
REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 28.74
REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL
REMARK 3 COMPLETENESS FOR RANGE (%) : 99.4
REMARK 3 NUMBER OF REFLECTIONS : 54679
REMARK 3
REMARK 3 FIT TO DATA USED IN REFINEMENT.
REMARK 3 CROSS-VALIDATION METHOD : THROUGHOUT
REMARK 3 FREE R VALUE TEST SET SELECTION : RANDOM
REMARK 3 R VALUE (WORKING + TEST SET) : 0.166
REMARK 3 R VALUE (WORKING SET) : 0.164
REMARK 3 FREE R VALUE : 0.200
REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000
REMARK 3 FREE R VALUE TEST SET COUNT : 2893
REMARK 3
REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN.
REMARK 3 TOTAL NUMBER OF BINS USED : 20
REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 1.70
REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.74
REMARK 3 REFLECTION IN BIN (WORKING SET) : 3892
REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 98.56
REMARK 3 BIN R VALUE (WORKING SET) : 0.2510
REMARK 3 BIN FREE R VALUE SET COUNT : 218
REMARK 3 BIN FREE R VALUE : 0.2780
REMARK 3
REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT.
REMARK 3 PROTEIN ATOMS : 2874
REMARK 3 NUCLEIC ACID ATOMS : 0
REMARK 3 HETEROGEN ATOMS : 140
REMARK 3 SOLVENT ATOMS : 396
REMARK 3
REMARK 3 B VALUES.
REMARK 3 FROM WILSON PLOT (A**2) : 20.90
REMARK 3 MEAN B VALUE (OVERALL, A**2) : 32.39
REMARK 3 OVERALL ANISOTROPIC B VALUE.
REMARK 3 B11 (A**2) : 0.25000
REMARK 3 B22 (A**2) : 0.25000
REMARK 3 B33 (A**2) : -0.80000
REMARK 3 B12 (A**2) : 0.12000
REMARK 3 B13 (A**2) : 0.00000
REMARK 3 B23 (A**2) : 0.00000
REMARK 3
REMARK 3 ESTIMATED OVERALL COORDINATE ERROR.
REMARK 3 ESU BASED ON R VALUE (A): 0.084
REMARK 3 ESU BASED ON FREE R VALUE (A): 0.088
REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.060
REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 3.621
REMARK 3
REMARK 3 CORRELATION COEFFICIENTS.
REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.970
REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.958
REMARK 3
REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT
REMARK 3 BOND LENGTHS REFINED ATOMS (A): 3181 ; 0.016 ; 0.019
REMARK 3 BOND LENGTHS OTHERS (A): 3112 ; 0.002 ; 0.020
REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 4287 ; 1.648 ; 1.963
REMARK 3 BOND ANGLES OTHERS (DEGREES): 7168 ; 0.935 ; 3.000
REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 381 ; 5.893 ; 5.000
REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 141 ;34.918 ;24.113
REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 555 ;13.355 ;15.000
REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 16 ;24.384 ;15.000
REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 465 ; 0.109 ; 0.200
REMARK 3 GENERAL PLANES REFINED ATOMS (A): 3604 ; 0.009 ; 0.020
REMARK 3 GENERAL PLANES OTHERS (A): 722 ; 0.002 ; 0.020
REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): NULL ; NULL ; NULL
REMARK 3 NON-BONDED CONTACTS OTHERS (A): NULL ; NULL ; NULL
REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): NULL ; NULL ; NULL
REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL
REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): NULL ; NULL ; NULL
REMARK 3 H-BOND (X...Y) OTHERS (A): NULL ; NULL ; NULL
REMARK 3 POTENTIAL METAL-ION REFINED ATOMS (A): NULL ; NULL ; NULL
REMARK 3 POTENTIAL METAL-ION OTHERS (A): NULL ; NULL ; NULL
REMARK 3 SYMMETRY VDW REFINED ATOMS (A): NULL ; NULL ; NULL
REMARK 3 SYMMETRY VDW OTHERS (A): NULL ; NULL ; NULL
REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): NULL ; NULL ; NULL
REMARK 3 SYMMETRY H-BOND OTHERS (A): NULL ; NULL ; NULL
REMARK 3 SYMMETRY METAL-ION REFINED ATOMS (A): NULL ; NULL ; NULL
REMARK 3 SYMMETRY METAL-ION OTHERS (A): NULL ; NULL ; NULL
REMARK 3
REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT
REMARK 3 MAIN-CHAIN BOND REFINED ATOMS (A**2): 1459 ; 1.551 ; 2.032
REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): 1460 ; 1.551 ; 2.032
REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 1829 ; 2.457 ; 3.032
REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): 1829 ; 2.458 ; 3.032
REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 1722 ; 2.315 ; 2.486
REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): 1723 ; 2.314 ; 2.487
REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL
REMARK 3 SIDE-CHAIN ANGLE OTHER ATOMS (A**2): 2447 ; 3.680 ; 3.507
REMARK 3 LONG RANGE B REFINED ATOMS (A**2): 3934 ; 8.183 ;19.179
REMARK 3 LONG RANGE B OTHER ATOMS (A**2): 3932 ; 8.186 ;19.170
REMARK 3
REMARK 3 ANISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT
REMARK 3 RIGID-BOND RESTRAINTS (A**2): NULL ; NULL ; NULL
REMARK 3 SPHERICITY; FREE ATOMS (A**2): NULL ; NULL ; NULL
REMARK 3 SPHERICITY; BONDED ATOMS (A**2): NULL ; NULL ; NULL
REMARK 3
REMARK 3 NCS RESTRAINTS STATISTICS
REMARK 3 NUMBER OF DIFFERENT NCS GROUPS : NULL
REMARK 3
REMARK 3 TLS DETAILS
REMARK 3 NUMBER OF TLS GROUPS : 1
REMARK 3
REMARK 3 TLS GROUP : 1
REMARK 3 NUMBER OF COMPONENTS GROUP : 1
REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI
REMARK 3 RESIDUE RANGE : A 64 A 655
REMARK 3 ORIGIN FOR THE GROUP (A): 19.6780 46.5970 19.8650
REMARK 3 T TENSOR
REMARK 3 T11: 0.0940 T22: 0.0629
REMARK 3 T33: 0.0140 T12: -0.0679
REMARK 3 T13: 0.0139 T23: -0.0064
REMARK 3 L TENSOR
REMARK 3 L11: 0.2655 L22: 0.6193
REMARK 3 L33: 0.8355 L12: -0.2062
REMARK 3 L13: -0.1204 L23: 0.2749
REMARK 3 S TENSOR
REMARK 3 S11: 0.0182 S12: 0.0332 S13: 0.0007
REMARK 3 S21: 0.0219 S22: -0.0974 S23: 0.0038
REMARK 3 S31: -0.0650 S32: 0.0365 S33: 0.0792
REMARK 3
REMARK 3 BULK SOLVENT MODELLING.
REMARK 3 METHOD USED : NULL
REMARK 3 PARAMETERS FOR MASK CALCULATION
REMARK 3 VDW PROBE RADIUS : 1.20
REMARK 3 ION PROBE RADIUS : 0.80
REMARK 3 SHRINKAGE RADIUS : 0.80
REMARK 3
REMARK 3 OTHER REFINEMENT REMARKS: HYDROGENS HAVE BEEN ADDED IN THE RIDING
REMARK 3 POSITIONS
REMARK 4
REMARK 4 5MY8 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11
REMARK 100
REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 26-JAN-17.
REMARK 100 THE DEPOSITION ID IS D_1200003235.
REMARK 200
REMARK 200 EXPERIMENTAL DETAILS
REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION
REMARK 200 DATE OF DATA COLLECTION : 17-JAN-16
REMARK 200 TEMPERATURE (KELVIN) : 100.0
REMARK 200 PH : 5.5
REMARK 200 NUMBER OF CRYSTALS USED : 1
REMARK 200
REMARK 200 SYNCHROTRON (Y/N) : Y
REMARK 200 RADIATION SOURCE : DIAMOND
REMARK 200 BEAMLINE : I02
REMARK 200 X-RAY GENERATOR MODEL : NULL
REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M
REMARK 200 WAVELENGTH OR RANGE (A) : 0.97949
REMARK 200 MONOCHROMATOR : NULL
REMARK 200 OPTICS : NULL
REMARK 200
REMARK 200 DETECTOR TYPE : PIXEL
REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS 6M
REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS
REMARK 200 DATA SCALING SOFTWARE : SCALA
REMARK 200
REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 57614
REMARK 200 RESOLUTION RANGE HIGH (A) : 1.700
REMARK 200 RESOLUTION RANGE LOW (A) : 28.740
REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL
REMARK 200
REMARK 200 OVERALL.
REMARK 200 COMPLETENESS FOR RANGE (%) : 99.2
REMARK 200 DATA REDUNDANCY : 7.600
REMARK 200 R MERGE (I) : 0.07800
REMARK 200 R SYM (I) : NULL
REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 14.2000
REMARK 200
REMARK 200 IN THE HIGHEST RESOLUTION SHELL.
REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.70
REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.79
REMARK 200 COMPLETENESS FOR SHELL (%) : 99.0
REMARK 200 DATA REDUNDANCY IN SHELL : 7.90
REMARK 200 R MERGE FOR SHELL (I) : 0.79900
REMARK 200 R SYM FOR SHELL (I) : NULL
REMARK 200 <I/SIGMA(I)> FOR SHELL : 2.700
REMARK 200
REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH
REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT
REMARK 200 SOFTWARE USED: PHASER
REMARK 200 STARTING MODEL: NULL
REMARK 200
REMARK 200 REMARK: NULL
REMARK 280
REMARK 280 CRYSTAL
REMARK 280 SOLVENT CONTENT, VS (%): 57.27
REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.88
REMARK 280
REMARK 280 CRYSTALLIZATION CONDITIONS: 22% BROAD-MOLECULAR-WEIGHT PEG SMEARS
REMARK 280 (BMW PEG SMEARS) AND 0.1 M CITRATE, PH 5.5, VAPOR DIFFUSION,
REMARK 280 SITTING DROP, TEMPERATURE 277.15K
REMARK 290
REMARK 290 CRYSTALLOGRAPHIC SYMMETRY
REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 65 2 2
REMARK 290
REMARK 290 SYMOP SYMMETRY
REMARK 290 NNNMMM OPERATOR
REMARK 290 1555 X,Y,Z
REMARK 290 2555 -Y,X-Y,Z+2/3
REMARK 290 3555 -X+Y,-X,Z+1/3
REMARK 290 4555 -X,-Y,Z+1/2
REMARK 290 5555 Y,-X+Y,Z+1/6
REMARK 290 6555 X-Y,X,Z+5/6
REMARK 290 7555 Y,X,-Z+2/3
REMARK 290 8555 X-Y,-Y,-Z
REMARK 290 9555 -X,-X+Y,-Z+1/3
REMARK 290 10555 -Y,-X,-Z+1/6
REMARK 290 11555 -X+Y,Y,-Z+1/2
REMARK 290 12555 X,X-Y,-Z+5/6
REMARK 290
REMARK 290 WHERE NNN -> OPERATOR NUMBER
REMARK 290 MMM -> TRANSLATION VECTOR
REMARK 290
REMARK 290 CRYSTALLOGRAPHIC SYMMETRY TRANSFORMATIONS
REMARK 290 THE FOLLOWING TRANSFORMATIONS OPERATE ON THE ATOM/HETATM
REMARK 290 RECORDS IN THIS ENTRY TO PRODUCE CRYSTALLOGRAPHICALLY
REMARK 290 RELATED MOLECULES.
REMARK 290 SMTRY1 1 1.000000 0.000000 0.000000 0.00000
REMARK 290 SMTRY2 1 0.000000 1.000000 0.000000 0.00000
REMARK 290 SMTRY3 1 0.000000 0.000000 1.000000 0.00000
REMARK 290 SMTRY1 2 -0.500000 -0.866025 0.000000 0.00000
REMARK 290 SMTRY2 2 0.866025 -0.500000 0.000000 0.00000
REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 206.75267
REMARK 290 SMTRY1 3 -0.500000 0.866025 0.000000 0.00000
REMARK 290 SMTRY2 3 -0.866025 -0.500000 0.000000 0.00000
REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 103.37633
REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 0.00000
REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 0.00000
REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 155.06450
REMARK 290 SMTRY1 5 0.500000 0.866025 0.000000 0.00000
REMARK 290 SMTRY2 5 -0.866025 0.500000 0.000000 0.00000
REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 51.68817
REMARK 290 SMTRY1 6 0.500000 -0.866025 0.000000 0.00000
REMARK 290 SMTRY2 6 0.866025 0.500000 0.000000 0.00000
REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 258.44083
REMARK 290 SMTRY1 7 -0.500000 0.866025 0.000000 0.00000
REMARK 290 SMTRY2 7 0.866025 0.500000 0.000000 0.00000
REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 206.75267
REMARK 290 SMTRY1 8 1.000000 0.000000 0.000000 0.00000
REMARK 290 SMTRY2 8 0.000000 -1.000000 0.000000 0.00000
REMARK 290 SMTRY3 8 0.000000 0.000000 -1.000000 0.00000
REMARK 290 SMTRY1 9 -0.500000 -0.866025 0.000000 0.00000
REMARK 290 SMTRY2 9 -0.866025 0.500000 0.000000 0.00000
REMARK 290 SMTRY3 9 0.000000 0.000000 -1.000000 103.37633
REMARK 290 SMTRY1 10 0.500000 -0.866025 0.000000 0.00000
REMARK 290 SMTRY2 10 -0.866025 -0.500000 0.000000 0.00000
REMARK 290 SMTRY3 10 0.000000 0.000000 -1.000000 51.68817
REMARK 290 SMTRY1 11 -1.000000 0.000000 0.000000 0.00000
REMARK 290 SMTRY2 11 0.000000 1.000000 0.000000 0.00000
REMARK 290 SMTRY3 11 0.000000 0.000000 -1.000000 155.06450
REMARK 290 SMTRY1 12 0.500000 0.866025 0.000000 0.00000
REMARK 290 SMTRY2 12 0.866025 -0.500000 0.000000 0.00000
REMARK 290 SMTRY3 12 0.000000 0.000000 -1.000000 258.44083
REMARK 290
REMARK 290 REMARK: NULL
REMARK 300
REMARK 300 BIOMOLECULE: 1
REMARK 300 SEE REMARK 350 FOR THE AUTHOR PROVIDED AND/OR PROGRAM
REMARK 300 GENERATED ASSEMBLY INFORMATION FOR THE STRUCTURE IN
REMARK 300 THIS ENTRY. THE REMARK MAY ALSO PROVIDE INFORMATION ON
REMARK 300 BURIED SURFACE AREA.
REMARK 350
REMARK 350 COORDINATES FOR A COMPLETE MULTIMER REPRESENTING THE KNOWN
REMARK 350 BIOLOGICALLY SIGNIFICANT OLIGOMERIZATION STATE OF THE
REMARK 350 MOLECULE CAN BE GENERATED BY APPLYING BIOMT TRANSFORMATIONS
REMARK 350 GIVEN BELOW. BOTH NON-CRYSTALLOGRAPHIC AND
REMARK 350 CRYSTALLOGRAPHIC OPERATIONS ARE GIVEN.
REMARK 350
REMARK 350 BIOMOLECULE: 1
REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC
REMARK 350 SOFTWARE USED: PISA
REMARK 350 TOTAL BURIED SURFACE AREA: 4180 ANGSTROM**2
REMARK 350 SURFACE AREA OF THE COMPLEX: 17690 ANGSTROM**2
REMARK 350 CHANGE IN SOLVENT FREE ENERGY: 53.0 KCAL/MOL
REMARK 350 APPLY THE FOLLOWING TO CHAINS: A
REMARK 350 BIOMT1 1 1.000000 0.000000 0.000000 0.00000
REMARK 350 BIOMT2 1 0.000000 1.000000 0.000000 0.00000
REMARK 350 BIOMT3 1 0.000000 0.000000 1.000000 0.00000
REMARK 375
REMARK 375 SPECIAL POSITION
REMARK 375 THE FOLLOWING ATOMS ARE FOUND TO BE WITHIN 0.15 ANGSTROMS
REMARK 375 OF A SYMMETRY RELATED ATOM AND ARE ASSUMED TO BE ON SPECIAL
REMARK 375 POSITIONS.
REMARK 375
REMARK 375 ATOM RES CSSEQI
REMARK 375 C3 CIT A 701 LIES ON A SPECIAL POSITION.
REMARK 375 HOH A1188 LIES ON A SPECIAL POSITION.
REMARK 465
REMARK 465 MISSING RESIDUES
REMARK 465 THE FOLLOWING RESIDUES WERE NOT LOCATED IN THE
REMARK 465 EXPERIMENT. (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN
REMARK 465 IDENTIFIER; SSSEQ=SEQUENCE NUMBER; I=INSERTION CODE.)
REMARK 465
REMARK 465 M RES C SSSEQI
REMARK 465 SER A 56
REMARK 465 MET A 57
REMARK 465 ASP A 58
REMARK 465 PRO A 59
REMARK 465 ASN A 60
REMARK 465 ASP A 61
REMARK 465 TYR A 62
REMARK 465 CYS A 63
REMARK 465 SER A 458
REMARK 465 GLY A 459
REMARK 465 ALA A 460
REMARK 465 PRO A 461
REMARK 465 PRO A 462
REMARK 465 PRO A 463
REMARK 465 SER A 464
REMARK 465 GLY A 465
REMARK 465 SER A 466
REMARK 465 ALA A 467
REMARK 465 VAL A 468
REMARK 465 SER A 469
REMARK 465 THR A 470
REMARK 465 ALA A 471
REMARK 465 PRO A 472
REMARK 465 ALA A 473
REMARK 465 THR A 474
REMARK 465 ALA A 475
REMARK 465 GLY A 476
REMARK 465 ASN A 477
REMARK 470
REMARK 470 MISSING ATOM
REMARK 470 THE FOLLOWING RESIDUES HAVE MISSING ATOMS (M=MODEL NUMBER;
REMARK 470 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER;
REMARK 470 I=INSERTION CODE):
REMARK 470 M RES CSSEQI ATOMS
REMARK 470 LYS A 64 CG CD CE NZ
REMARK 470 GLU A 237 CG CD OE1 OE2
REMARK 470 GLN A 239 CG CD OE1 NE2
REMARK 470 ARG A 240 CG CD NE CZ NH1 NH2
REMARK 500
REMARK 500 GEOMETRY AND STEREOCHEMISTRY
REMARK 500 SUBTOPIC: COVALENT BOND LENGTHS
REMARK 500
REMARK 500 THE STEREOCHEMICAL PARAMETERS OF THE FOLLOWING RESIDUES
REMARK 500 HAVE VALUES WHICH DEVIATE FROM EXPECTED VALUES BY MORE
REMARK 500 THAN 6*RMSD (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN
REMARK 500 IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE).
REMARK 500
REMARK 500 STANDARD TABLE:
REMARK 500 FORMAT: (10X,I3,1X,2(A3,1X,A1,I4,A1,1X,A4,3X),1X,F6.3)
REMARK 500
REMARK 500 EXPECTED VALUES PROTEIN: ENGH AND HUBER, 1999
REMARK 500 EXPECTED VALUES NUCLEIC ACID: CLOWNEY ET AL 1996
REMARK 500
REMARK 500 M RES CSSEQI ATM1 RES CSSEQI ATM2 DEVIATION
REMARK 500 GLU A 622 CD GLU A 622 OE1 0.069
REMARK 500
REMARK 500 REMARK: NULL
REMARK 500
REMARK 500 GEOMETRY AND STEREOCHEMISTRY
REMARK 500 SUBTOPIC: COVALENT BOND ANGLES
REMARK 500
REMARK 500 THE STEREOCHEMICAL PARAMETERS OF THE FOLLOWING RESIDUES
REMARK 500 HAVE VALUES WHICH DEVIATE FROM EXPECTED VALUES BY MORE
REMARK 500 THAN 6*RMSD (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN
REMARK 500 IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE).
REMARK 500
REMARK 500 STANDARD TABLE:
REMARK 500 FORMAT: (10X,I3,1X,A3,1X,A1,I4,A1,3(1X,A4,2X),12X,F5.1)
REMARK 500
REMARK 500 EXPECTED VALUES PROTEIN: ENGH AND HUBER, 1999
REMARK 500 EXPECTED VALUES NUCLEIC ACID: CLOWNEY ET AL 1996
REMARK 500
REMARK 500 M RES CSSEQI ATM1 ATM2 ATM3
REMARK 500 ARG A 141 NE - CZ - NH1 ANGL. DEV. = 3.3 DEGREES
REMARK 500 ARG A 141 NE - CZ - NH2 ANGL. DEV. = -4.1 DEGREES
REMARK 500 ARG A 649 NE - CZ - NH1 ANGL. DEV. = -3.9 DEGREES
REMARK 500
REMARK 500 REMARK: NULL
REMARK 500
REMARK 500 GEOMETRY AND STEREOCHEMISTRY
REMARK 500 SUBTOPIC: TORSION ANGLES
REMARK 500
REMARK 500 TORSION ANGLES OUTSIDE THE EXPECTED RAMACHANDRAN REGIONS:
REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER;
REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE).
REMARK 500
REMARK 500 STANDARD TABLE:
REMARK 500 FORMAT:(10X,I3,1X,A3,1X,A1,I4,A1,4X,F7.2,3X,F7.2)
REMARK 500
REMARK 500 EXPECTED VALUES: GJ KLEYWEGT AND TA JONES (1996). PHI/PSI-
REMARK 500 CHOLOGY: RAMACHANDRAN REVISITED. STRUCTURE 4, 1395 - 1400
REMARK 500
REMARK 500 M RES CSSEQI PSI PHI
REMARK 500 ARG A 79 -40.65 -154.30
REMARK 500 ASP A 135 87.46 -151.15
REMARK 500 LEU A 168 -97.75 -123.28
REMARK 500 THR A 212 -9.50 74.15
REMARK 500 ASP A 213 50.62 -145.37
REMARK 500 ASP A 497 98.46 44.68
REMARK 500 GLN A 513 140.15 79.84
REMARK 500 ASN A 529 -159.12 -155.70
REMARK 500
REMARK 500 REMARK: NULL
REMARK 800
REMARK 800 SITE
REMARK 800 SITE_IDENTIFIER: AC1
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: binding site for residue CIT A 701
REMARK 800
REMARK 800 SITE_IDENTIFIER: AC2
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: binding site for residue GOL A 702
REMARK 800
REMARK 800 SITE_IDENTIFIER: AC3
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: binding site for residue DMS A 703
REMARK 800
REMARK 800 SITE_IDENTIFIER: AC4
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: binding site for residue EDO A 704
REMARK 800
REMARK 800 SITE_IDENTIFIER: AC5
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: binding site for residue EDO A 705
REMARK 800
REMARK 800 SITE_IDENTIFIER: AC6
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: binding site for residue EDO A 706
REMARK 800
REMARK 800 SITE_IDENTIFIER: AC7
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: binding site for residue EDO A 708
REMARK 800
REMARK 800 SITE_IDENTIFIER: AC8
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: binding site for residue EDO A 709
REMARK 800
REMARK 800 SITE_IDENTIFIER: AC9
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: binding site for residue EDO A 710
REMARK 800
REMARK 800 SITE_IDENTIFIER: AD1
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: binding site for residue EDO A 711
REMARK 800
REMARK 800 SITE_IDENTIFIER: AD2
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: binding site for residue EDO A 712
REMARK 800
REMARK 800 SITE_IDENTIFIER: AD3
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: binding site for residue EDO A 713
REMARK 800
REMARK 800 SITE_IDENTIFIER: AD4
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: binding site for residue EDO A 714
REMARK 800
REMARK 800 SITE_IDENTIFIER: AD5
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: binding site for residue EDO A 715
REMARK 800
REMARK 800 SITE_IDENTIFIER: AD6
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: binding site for residue EDO A 716
REMARK 800
REMARK 800 SITE_IDENTIFIER: AD7
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: binding site for residue EDO A 718
REMARK 800
REMARK 800 SITE_IDENTIFIER: AD8
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: binding site for residue EDO A 719
REMARK 800
REMARK 800 SITE_IDENTIFIER: AD9
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: binding site for residue EDO A 720
REMARK 800
REMARK 800 SITE_IDENTIFIER: AE1
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: binding site for residue EDO A 721
REMARK 800
REMARK 800 SITE_IDENTIFIER: AE2
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: binding site for residue EDO A 722
REMARK 800
REMARK 800 SITE_IDENTIFIER: AE3
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: binding site for residue EDO A 723
REMARK 800
REMARK 800 SITE_IDENTIFIER: AE4
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: binding site for residue RXZ A 724
DBREF 5MY8 A 58 472 UNP Q96SB4 SRPK1_HUMAN 58 255
DBREF 5MY8 A 474 655 UNP Q96SB4 SRPK1_HUMAN 474 655
SEQADV 5MY8 SER A 56 UNP Q96SB4 EXPRESSION TAG
SEQADV 5MY8 MET A 57 UNP Q96SB4 EXPRESSION TAG
SEQADV 5MY8 ALA A 473 UNP Q96SB4 LINKER
SEQRES 1 A 383 SER MET ASP PRO ASN ASP TYR CYS LYS GLY GLY TYR HIS
SEQRES 2 A 383 LEU VAL LYS ILE GLY ASP LEU PHE ASN GLY ARG TYR HIS
SEQRES 3 A 383 VAL ILE ARG LYS LEU GLY TRP GLY HIS PHE SER THR VAL
SEQRES 4 A 383 TRP LEU SER TRP ASP ILE GLN GLY LYS LYS PHE VAL ALA
SEQRES 5 A 383 MET LYS VAL VAL LYS SER ALA GLU HIS TYR THR GLU THR
SEQRES 6 A 383 ALA LEU ASP GLU ILE ARG LEU LEU LYS SER VAL ARG ASN
SEQRES 7 A 383 SER ASP PRO ASN ASP PRO ASN ARG GLU MET VAL VAL GLN
SEQRES 8 A 383 LEU LEU ASP ASP PHE LYS ILE SER GLY VAL ASN GLY THR
SEQRES 9 A 383 HIS ILE CYS MET VAL PHE GLU VAL LEU GLY HIS HIS LEU
SEQRES 10 A 383 LEU LYS TRP ILE ILE LYS SER ASN TYR GLN GLY LEU PRO
SEQRES 11 A 383 LEU PRO CYS VAL LYS LYS ILE ILE GLN GLN VAL LEU GLN
SEQRES 12 A 383 GLY LEU ASP TYR LEU HIS THR LYS CYS ARG ILE ILE HIS
SEQRES 13 A 383 THR ASP ILE LYS PRO GLU ASN ILE LEU LEU SER VAL ASN
SEQRES 14 A 383 GLU GLN TYR ILE ARG ARG LEU ALA ALA GLU ALA THR GLU
SEQRES 15 A 383 TRP GLN ARG SER GLY ALA PRO PRO PRO SER GLY SER ALA
SEQRES 16 A 383 VAL SER THR ALA PRO ALA THR ALA GLY ASN PHE LEU VAL
SEQRES 17 A 383 ASN PRO LEU GLU PRO LYS ASN ALA GLU LYS LEU LYS VAL
SEQRES 18 A 383 LYS ILE ALA ASP LEU GLY ASN ALA CYS TRP VAL HIS LYS
SEQRES 19 A 383 HIS PHE THR GLU ASP ILE GLN THR ARG GLN TYR ARG SER
SEQRES 20 A 383 LEU GLU VAL LEU ILE GLY SER GLY TYR ASN THR PRO ALA
SEQRES 21 A 383 ASP ILE TRP SER THR ALA CYS MET ALA PHE GLU LEU ALA
SEQRES 22 A 383 THR GLY ASP TYR LEU PHE GLU PRO HIS SER GLY GLU GLU
SEQRES 23 A 383 TYR THR ARG ASP GLU ASP HIS ILE ALA LEU ILE ILE GLU
SEQRES 24 A 383 LEU LEU GLY LYS VAL PRO ARG LYS LEU ILE VAL ALA GLY
SEQRES 25 A 383 LYS TYR SER LYS GLU PHE PHE THR LYS LYS GLY ASP LEU
SEQRES 26 A 383 LYS HIS ILE THR LYS LEU LYS PRO TRP GLY LEU PHE GLU
SEQRES 27 A 383 VAL LEU VAL GLU LYS TYR GLU TRP SER GLN GLU GLU ALA
SEQRES 28 A 383 ALA GLY PHE THR ASP PHE LEU LEU PRO MET LEU GLU LEU
SEQRES 29 A 383 ILE PRO GLU LYS ARG ALA THR ALA ALA GLU CYS LEU ARG
SEQRES 30 A 383 HIS PRO TRP LEU ASN SER
HET CIT A 701 13
HET GOL A 702 6
HET DMS A 703 4
HET EDO A 704 4
HET EDO A 705 4
HET EDO A 706 4
HET EDO A 707 4
HET EDO A 708 8
HET EDO A 709 4
HET EDO A 710 4
HET EDO A 711 4
HET EDO A 712 4
HET EDO A 713 4
HET EDO A 714 4
HET EDO A 715 4
HET EDO A 716 4
HET EDO A 717 4
HET EDO A 718 4
HET EDO A 719 4
HET EDO A 720 4
HET EDO A 721 4
HET EDO A 722 4
HET EDO A 723 4
HET RXZ A 724 37
HETNAM CIT CITRIC ACID
HETNAM GOL GLYCEROL
HETNAM DMS DIMETHYL SULFOXIDE
HETNAM EDO 1,2-ETHANEDIOL
HETNAM RXZ SPHINX31
HETSYN GOL GLYCERIN; PROPANE-1,2,3-TRIOL
HETSYN EDO ETHYLENE GLYCOL
FORMUL 2 CIT C6 H8 O7
FORMUL 3 GOL C3 H8 O3
FORMUL 4 DMS C2 H6 O S
FORMUL 5 EDO 20(C2 H6 O2)
FORMUL 25 RXZ C27 H24 F3 N5 O2
FORMUL 26 HOH *396(H2 O)
HELIX 1 AA1 ALA A 114 SER A 134 1 21
HELIX 2 AA2 ASP A 138 VAL A 144 5 7
HELIX 3 AA3 HIS A 171 SER A 179 1 9
HELIX 4 AA4 PRO A 185 LYS A 206 1 22
HELIX 5 AA5 LYS A 215 GLU A 217 5 3
HELIX 6 AA6 ASN A 224 GLN A 239 1 16
HELIX 7 AA7 GLU A 484 LEU A 491 5 8
HELIX 8 AA8 THR A 514 ARG A 518 5 5
HELIX 9 AA9 SER A 519 GLY A 525 1 7
HELIX 10 AB1 THR A 530 GLY A 547 1 18
HELIX 11 AB2 THR A 560 GLY A 574 1 15
HELIX 12 AB3 PRO A 577 GLY A 584 1 8
HELIX 13 AB4 TYR A 586 PHE A 590 5 5
HELIX 14 AB5 GLY A 607 LYS A 615 1 9
HELIX 15 AB6 SER A 619 LEU A 631 1 13
HELIX 16 AB7 PRO A 632 GLU A 635 5 4
HELIX 17 AB8 ILE A 637 ARG A 641 5 5
HELIX 18 AB9 THR A 643 ARG A 649 1 7
HELIX 19 AC1 HIS A 650 SER A 655 5 6
SHEET 1 AA1 6 LEU A 75 PHE A 76 0
SHEET 2 AA1 6 TYR A 80 TRP A 88 -1 O TYR A 80 N PHE A 76
SHEET 3 AA1 6 SER A 92 ASP A 99 -1 O LEU A 96 N ARG A 84
SHEET 4 AA1 6 LYS A 104 VAL A 111 -1 O LYS A 104 N ASP A 99
SHEET 5 AA1 6 THR A 159 GLU A 166 -1 O MET A 163 N LYS A 109
SHEET 6 AA1 6 LEU A 147 SER A 154 -1 N LEU A 148 O VAL A 164
SHEET 1 AA2 2 ILE A 209 ILE A 210 0
SHEET 2 AA2 2 CYS A 502 TRP A 503 -1 O CYS A 502 N ILE A 210
SHEET 1 AA3 2 ILE A 219 LEU A 221 0
SHEET 2 AA3 2 VAL A 493 ILE A 495 -1 O LYS A 494 N LEU A 220
SITE 1 AC1 6 ARG A 515 ARG A 518 ARG A 561 GOL A 702
SITE 2 AC1 6 HOH A 801 HOH A 829
SITE 1 AC2 10 ASP A 213 ASN A 500 ASP A 511 GLN A 513
SITE 2 AC2 10 ARG A 518 ARG A 561 CIT A 701 HOH A 801
SITE 3 AC2 10 HOH A 813 HOH A1071
SITE 1 AC3 6 TYR A 549 TRP A 606 LYS A 615 TYR A 616
SITE 2 AC3 6 EDO A 714 HOH A 987
SITE 1 AC4 2 GLY A 87 TRP A 88
SITE 1 AC5 5 LEU A 648 HIS A 650 PRO A 651 ASN A 654
SITE 2 AC5 5 HOH A 806
SITE 1 AC6 2 THR A 205 HOH A 811
SITE 1 AC7 8 ASP A 138 ASN A 140 ASP A 201 TYR A 202
SITE 2 AC7 8 THR A 205 LYS A 206 HOH A 847 HOH A 874
SITE 1 AC8 4 ASN A 529 PRO A 531 GLU A 639 HOH A 833
SITE 1 AC9 2 VAL A 582 ALA A 583
SITE 1 AD1 3 TYR A 586 HOH A 842 HOH A 995
SITE 1 AD2 4 TRP A 618 GLU A 622 HOH A 868 HOH A1031
SITE 1 AD3 6 ASN A 140 GLN A 198 HOH A 815 HOH A 819
SITE 2 AD3 6 HOH A 823 HOH A 911
SITE 1 AD4 3 TRP A 606 LYS A 615 DMS A 703
SITE 1 AD5 3 ASN A 157 LYS A 615 HOH A 910
SITE 1 AD6 4 LEU A 86 HIS A 170 TYR A 227 RXZ A 724
SITE 1 AD7 3 ARG A 208 HIS A 505 HOH A1048
SITE 1 AD8 7 LYS A 640 ALA A 642 GLU A 646 EDO A 722
SITE 2 AD8 7 HOH A 844 HOH A 878 HOH A 959
SITE 1 AD9 4 HIS A 554 TYR A 559 ASP A 564 HOH A 861
SITE 1 AE1 4 GLU A 510 GLU A 557 THR A 560 HOH A 817
SITE 1 AE2 8 ASP A 628 PRO A 632 HIS A 650 EDO A 719
SITE 2 AE2 8 HOH A 878 HOH A 901 HOH A 934 HOH A 994
SITE 1 AE3 5 SER A 130 CYS A 207 TRP A 503 HOH A1007
SITE 2 AE3 5 HOH A1027
SITE 1 AE4 21 LEU A 86 TRP A 88 GLY A 89 SER A 92
SITE 2 AE4 21 VAL A 94 ALA A 107 LYS A 109 PHE A 165
SITE 3 AE4 21 GLU A 166 VAL A 167 LEU A 168 GLY A 169
SITE 4 AE4 21 HIS A 170 LEU A 220 VAL A 223 TYR A 227
SITE 5 AE4 21 ILE A 228 LEU A 231 ALA A 496 EDO A 716
SITE 6 AE4 21 HOH A 971
CRYST1 74.883 74.883 310.129 90.00 90.00 120.00 P 65 2 2 12
ORIGX1 1.000000 0.000000 0.000000 0.00000
ORIGX2 0.000000 1.000000 0.000000 0.00000
ORIGX3 0.000000 0.000000 1.000000 0.00000
SCALE1 0.013354 0.007710 0.000000 0.00000
SCALE2 0.000000 0.015420 0.000000 0.00000
SCALE3 0.000000 0.000000 0.003224 0.00000
(ATOM LINES ARE NOT SHOWN.)
END
