HEADER PROTEIN/DNA 20-NOV-15 5EW2
TITLE HUMAN THROMBIN SANDWICHED BETWEEN TWO DNA APTAMERS: HD22 AND HD1-
TITLE 2 DELTAT12
COMPND MOL_ID: 1;
COMPND 2 MOLECULE: THROMBIN LIGHT CHAIN;
COMPND 3 CHAIN: L;
COMPND 4 SYNONYM: COAGULATION FACTOR II;
COMPND 5 EC: 3.4.21.5;
COMPND 6 MOL_ID: 2;
COMPND 7 MOLECULE: THROMBIN HEAVY CHAIN;
COMPND 8 CHAIN: H;
COMPND 9 SYNONYM: COAGULATION FACTOR II;
COMPND 10 EC: 3.4.21.5;
COMPND 11 MOL_ID: 3;
COMPND 12 MOLECULE: HD22 (27MER);
COMPND 13 CHAIN: D;
COMPND 14 ENGINEERED: YES;
COMPND 15 MOL_ID: 4;
COMPND 16 MOLECULE: HD1-DELTAT12;
COMPND 17 CHAIN: E;
COMPND 18 ENGINEERED: YES;
COMPND 19 OTHER_DETAILS: HD1 VARIANT IN WHICH NUCLEOBASE OF T12 HAS BEEN
COMPND 20 DELETED
SOURCE MOL_ID: 1;
SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS;
SOURCE 3 ORGANISM_COMMON: HUMAN;
SOURCE 4 ORGANISM_TAXID: 9606;
SOURCE 5 MOL_ID: 2;
SOURCE 6 ORGANISM_SCIENTIFIC: HOMO SAPIENS;
SOURCE 7 ORGANISM_COMMON: HUMAN;
SOURCE 8 ORGANISM_TAXID: 9606;
SOURCE 9 MOL_ID: 3;
SOURCE 10 SYNTHETIC: YES;
SOURCE 11 ORGANISM_SCIENTIFIC: HOMO SAPIENS;
SOURCE 12 ORGANISM_COMMON: HUMAN;
SOURCE 13 ORGANISM_TAXID: 9606;
SOURCE 14 MOL_ID: 4;
SOURCE 15 SYNTHETIC: YES;
SOURCE 16 ORGANISM_SCIENTIFIC: HOMO SAPIENS;
SOURCE 17 ORGANISM_COMMON: HUMAN;
SOURCE 18 ORGANISM_TAXID: 9606
KEYWDS PROTEIN-DNA COMPLEX, BLOOD COAGULATION, DNA APTAMER, DNA-INHIBITOR,
KEYWDS 2 G-QUADRUPLEX, DUPLEX-QUADRUPLEX JUNCTION, SERINE PROTEASE,
KEYWDS 3 HYDROLASE, ABASIC FURAN, HYDROLASE-DNA COMPLEX
EXPDTA X-RAY DIFFRACTION
AUTHOR A.PICA,I.RUSSO KRAUSS,V.PARENTE,F.SICA
REVDAT 5 29-JUL-20 5EW2 1 COMPND REMARK HETNAM SITE
REVDAT 4 18-JAN-17 5EW2 1 JRNL
REVDAT 3 21-DEC-16 5EW2 1 REMARK
REVDAT 2 14-DEC-16 5EW2 1 JRNL
REVDAT 1 30-NOV-16 5EW2 0
JRNL AUTH A.PICA,I.RUSSO KRAUSS,V.PARENTE,H.TATEISHI-KARIMATA,
JRNL AUTH 2 S.NAGATOISHI,K.TSUMOTO,N.SUGIMOTO,F.SICA
JRNL TITL THROUGH-BOND EFFECTS IN THE TERNARY COMPLEXES OF THROMBIN
JRNL TITL 2 SANDWICHED BY TWO DNA APTAMERS.
JRNL REF NUCLEIC ACIDS RES. V. 45 461 2017
JRNL REFN ESSN 1362-4962
JRNL PMID 27899589
JRNL DOI 10.1093/NAR/GKW1113
REMARK 1
REMARK 1 REFERENCE 1
REMARK 1 AUTH I.RUSSO KRAUSS,A.PICA,A.MERLINO,L.MAZZARELLA,F.SICA
REMARK 1 TITL DUPLEX-QUADRUPLEX MOTIFS IN A PECULIAR STRUCTURAL
REMARK 1 TITL 2 ORGANIZATION COOPERATIVELY CONTRIBUTE TO THROMBIN BINDING OF
REMARK 1 TITL 3 A DNA APTAMER.
REMARK 1 REF ACTA CRYSTALLOGR. D BIOL. V. 69 2403 2013
REMARK 1 REF 2 CRYSTALLOGR.
REMARK 1 REFN ESSN 1399-0047
REMARK 1 PMID 24311581
REMARK 1 DOI 10.1107/S0907444913022269
REMARK 1 REFERENCE 2
REMARK 1 AUTH A.PICA,I.RUSSO KRAUSS,A.MERLINO,S.NAGATOISHI,N.SUGIMOTO,
REMARK 1 AUTH 2 F.SICA
REMARK 1 TITL DISSECTING THE CONTRIBUTION OF THROMBIN EXOSITE I IN THE
REMARK 1 TITL 2 RECOGNITION OF THROMBIN BINDING APTAMER.
REMARK 1 REF FEBS J. V. 280 6581 2013
REMARK 1 REFN ISSN 1742-4658
REMARK 1 PMID 24128303
REMARK 1 DOI 10.1111/FEBS.12561
REMARK 2
REMARK 2 RESOLUTION. 3.59 ANGSTROMS.
REMARK 3
REMARK 3 REFINEMENT.
REMARK 3 PROGRAM : REFMAC 5.8.0135
REMARK 3 AUTHORS : MURSHUDOV,SKUBAK,LEBEDEV,PANNU,STEINER,
REMARK 3 : NICHOLLS,WINN,LONG,VAGIN
REMARK 3
REMARK 3 REFINEMENT TARGET : MAXIMUM LIKELIHOOD
REMARK 3
REMARK 3 DATA USED IN REFINEMENT.
REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 3.59
REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 50.00
REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL
REMARK 3 COMPLETENESS FOR RANGE (%) : 90.8
REMARK 3 NUMBER OF REFLECTIONS : 5167
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) : 0.212
REMARK 3 R VALUE (WORKING SET) : 0.208
REMARK 3 FREE R VALUE : 0.268
REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000
REMARK 3 FREE R VALUE TEST SET COUNT : 271
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) : 3.59
REMARK 3 BIN RESOLUTION RANGE LOW (A) : 3.68
REMARK 3 REFLECTION IN BIN (WORKING SET) : 219
REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 49.89
REMARK 3 BIN R VALUE (WORKING SET) : 0.2850
REMARK 3 BIN FREE R VALUE SET COUNT : 9
REMARK 3 BIN FREE R VALUE : 0.3050
REMARK 3
REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT.
REMARK 3 PROTEIN ATOMS : 2260
REMARK 3 NUCLEIC ACID ATOMS : 832
REMARK 3 HETEROGEN ATOMS : 47
REMARK 3 SOLVENT ATOMS : 7
REMARK 3
REMARK 3 B VALUES.
REMARK 3 FROM WILSON PLOT (A**2) : NULL
REMARK 3 MEAN B VALUE (OVERALL, A**2) : 70.00
REMARK 3 OVERALL ANISOTROPIC B VALUE.
REMARK 3 B11 (A**2) : -0.99000
REMARK 3 B22 (A**2) : 1.49000
REMARK 3 B33 (A**2) : -0.26000
REMARK 3 B12 (A**2) : 0.00000
REMARK 3 B13 (A**2) : -0.47000
REMARK 3 B23 (A**2) : 0.00000
REMARK 3
REMARK 3 ESTIMATED OVERALL COORDINATE ERROR.
REMARK 3 ESU BASED ON R VALUE (A): NULL
REMARK 3 ESU BASED ON FREE R VALUE (A): NULL
REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.570
REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): NULL
REMARK 3
REMARK 3 CORRELATION COEFFICIENTS.
REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.895
REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.859
REMARK 3
REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT
REMARK 3 BOND LENGTHS REFINED ATOMS (A): 3299 ; 0.015 ; 0.017
REMARK 3 BOND LENGTHS OTHERS (A): 2695 ; 0.003 ; 0.020
REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 4640 ; 1.855 ; 1.724
REMARK 3 BOND ANGLES OTHERS (DEGREES): 6247 ; 1.237 ; 3.000
REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 276 ; 6.534 ; 5.000
REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 110 ;33.375 ;23.273
REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 417 ;16.483 ;15.000
REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 20 ;10.740 ;15.000
REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 452 ; 0.118 ; 0.200
REMARK 3 GENERAL PLANES REFINED ATOMS (A): 3096 ; 0.009 ; 0.021
REMARK 3 GENERAL PLANES OTHERS (A): 737 ; 0.003 ; 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): 1116 ; 1.569 ; 3.836
REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): 1117 ; 1.568 ; 3.836
REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 1388 ; 2.734 ; 5.752
REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): 1389 ; 2.733 ; 5.751
REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 2183 ; 2.073 ; 4.332
REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): 2182 ; 2.074 ; 4.332
REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL
REMARK 3 SIDE-CHAIN ANGLE OTHER ATOMS (A**2): 3253 ; 3.603 ; 6.478
REMARK 3 LONG RANGE B REFINED ATOMS (A**2): 14184 ; 7.595 ;39.907
REMARK 3 LONG RANGE B OTHER ATOMS (A**2): 14183 ; 7.590 ;39.908
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 : 4
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 : L 1 L 14
REMARK 3 ORIGIN FOR THE GROUP (A): -12.5517 29.6449 26.5447
REMARK 3 T TENSOR
REMARK 3 T11: 0.1401 T22: 0.2637
REMARK 3 T33: 1.0309 T12: -0.1408
REMARK 3 T13: -0.0519 T23: -0.2887
REMARK 3 L TENSOR
REMARK 3 L11: 5.9265 L22: 2.2683
REMARK 3 L33: 3.8518 L12: 1.2961
REMARK 3 L13: -0.6886 L23: -1.1844
REMARK 3 S TENSOR
REMARK 3 S11: -0.2949 S12: -0.2269 S13: 1.6795
REMARK 3 S21: -0.1198 S22: 0.3894 S23: -0.6251
REMARK 3 S31: -0.1524 S32: 0.0437 S33: -0.0945
REMARK 3
REMARK 3 TLS GROUP : 2
REMARK 3 NUMBER OF COMPONENTS GROUP : 1
REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI
REMARK 3 RESIDUE RANGE : H 16 H 246
REMARK 3 ORIGIN FOR THE GROUP (A): -25.1854 15.5941 23.9870
REMARK 3 T TENSOR
REMARK 3 T11: 0.0549 T22: 0.0950
REMARK 3 T33: 0.0489 T12: -0.0189
REMARK 3 T13: 0.0111 T23: -0.0262
REMARK 3 L TENSOR
REMARK 3 L11: 5.7149 L22: 3.3266
REMARK 3 L33: 2.5072 L12: 0.0246
REMARK 3 L13: 0.5818 L23: 0.3858
REMARK 3 S TENSOR
REMARK 3 S11: -0.2540 S12: 0.0162 S13: 0.1101
REMARK 3 S21: 0.1565 S22: 0.4006 S23: 0.0425
REMARK 3 S31: 0.0191 S32: 0.0472 S33: -0.1466
REMARK 3
REMARK 3 TLS GROUP : 3
REMARK 3 NUMBER OF COMPONENTS GROUP : 1
REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI
REMARK 3 RESIDUE RANGE : D 2 D 26
REMARK 3 ORIGIN FOR THE GROUP (A): -48.2681 19.7699 16.2639
REMARK 3 T TENSOR
REMARK 3 T11: 0.1083 T22: 0.2909
REMARK 3 T33: 0.6444 T12: -0.1085
REMARK 3 T13: -0.0900 T23: 0.1598
REMARK 3 L TENSOR
REMARK 3 L11: 4.7521 L22: 2.6528
REMARK 3 L33: 5.7599 L12: -0.5379
REMARK 3 L13: 0.1815 L23: -1.1933
REMARK 3 S TENSOR
REMARK 3 S11: -0.4809 S12: 0.3790 S13: 0.6995
REMARK 3 S21: -0.1250 S22: 0.4201 S23: 0.6893
REMARK 3 S31: -0.1411 S32: -0.7463 S33: 0.0607
REMARK 3
REMARK 3 TLS GROUP : 4
REMARK 3 NUMBER OF COMPONENTS GROUP : 1
REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI
REMARK 3 RESIDUE RANGE : E 1 E 15
REMARK 3 ORIGIN FOR THE GROUP (A): -4.0337 6.1274 44.8645
REMARK 3 T TENSOR
REMARK 3 T11: 0.6983 T22: 0.9732
REMARK 3 T33: 0.2971 T12: 0.3153
REMARK 3 T13: -0.2201 T23: -0.0430
REMARK 3 L TENSOR
REMARK 3 L11: 4.6085 L22: 3.9519
REMARK 3 L33: 0.6521 L12: 2.7805
REMARK 3 L13: 0.4233 L23: -0.5020
REMARK 3 S TENSOR
REMARK 3 S11: 0.3555 S12: -0.9524 S13: -0.8502
REMARK 3 S21: 0.5931 S22: -0.2629 S23: -0.8318
REMARK 3 S31: 0.2829 S32: 0.2820 S33: -0.0926
REMARK 3
REMARK 3 BULK SOLVENT MODELLING.
REMARK 3 METHOD USED : MASK
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 5EW2 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11
REMARK 100
REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 20-NOV-15.
REMARK 100 THE DEPOSITION ID IS D_1000215521.
REMARK 200
REMARK 200 EXPERIMENTAL DETAILS
REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION
REMARK 200 DATE OF DATA COLLECTION : 13-NOV-13
REMARK 200 TEMPERATURE (KELVIN) : 100
REMARK 200 PH : NULL
REMARK 200 NUMBER OF CRYSTALS USED : 1
REMARK 200
REMARK 200 SYNCHROTRON (Y/N) : N
REMARK 200 RADIATION SOURCE : ROTATING ANODE
REMARK 200 BEAMLINE : NULL
REMARK 200 X-RAY GENERATOR MODEL : RIGAKU MICROMAX-007 HF
REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M
REMARK 200 WAVELENGTH OR RANGE (A) : 1.5418
REMARK 200 MONOCHROMATOR : NULL
REMARK 200 OPTICS : NULL
REMARK 200
REMARK 200 DETECTOR TYPE : CCD
REMARK 200 DETECTOR MANUFACTURER : RIGAKU SATURN 944
REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000
REMARK 200 DATA SCALING SOFTWARE : HKL-2000
REMARK 200
REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 5755
REMARK 200 RESOLUTION RANGE HIGH (A) : 3.580
REMARK 200 RESOLUTION RANGE LOW (A) : 50.000
REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL
REMARK 200
REMARK 200 OVERALL.
REMARK 200 COMPLETENESS FOR RANGE (%) : 96.4
REMARK 200 DATA REDUNDANCY : 2.800
REMARK 200 R MERGE (I) : 0.12000
REMARK 200 R SYM (I) : NULL
REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 5.9000
REMARK 200
REMARK 200 IN THE HIGHEST RESOLUTION SHELL.
REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 3.58
REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 3.71
REMARK 200 COMPLETENESS FOR SHELL (%) : 95.7
REMARK 200 DATA REDUNDANCY IN SHELL : 2.60
REMARK 200 R MERGE FOR SHELL (I) : 0.46600
REMARK 200 R SYM FOR SHELL (I) : NULL
REMARK 200 <I/SIGMA(I)> FOR SHELL : NULL
REMARK 200
REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH
REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT
REMARK 200 SOFTWARE USED: PHASER 2.5.7, PHASER
REMARK 200 STARTING MODEL: NULL
REMARK 200
REMARK 200 REMARK: NULL
REMARK 280
REMARK 280 CRYSTAL
REMARK 280 SOLVENT CONTENT, VS (%): 53.24
REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.63
REMARK 280
REMARK 280 CRYSTALLIZATION CONDITIONS: 18% PEG 3350, 0.2 M SODIUM FORMATE, 2%
REMARK 280 ACETONITRILE, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 298K
REMARK 290
REMARK 290 CRYSTALLOGRAPHIC SYMMETRY
REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: C 1 2 1
REMARK 290
REMARK 290 SYMOP SYMMETRY
REMARK 290 NNNMMM OPERATOR
REMARK 290 1555 X,Y,Z
REMARK 290 2555 -X,Y,-Z
REMARK 290 3555 X+1/2,Y+1/2,Z
REMARK 290 4555 -X+1/2,Y+1/2,-Z
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 -1.000000 0.000000 0.000000 0.00000
REMARK 290 SMTRY2 2 0.000000 1.000000 0.000000 0.00000
REMARK 290 SMTRY3 2 0.000000 0.000000 -1.000000 0.00000
REMARK 290 SMTRY1 3 1.000000 0.000000 0.000000 58.54450
REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 20.64800
REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000
REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 58.54450
REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 20.64800
REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000
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: TETRAMERIC
REMARK 350 SOFTWARE USED: PISA
REMARK 350 TOTAL BURIED SURFACE AREA: 5880 ANGSTROM**2
REMARK 350 SURFACE AREA OF THE COMPLEX: 17280 ANGSTROM**2
REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -31.0 KCAL/MOL
REMARK 350 APPLY THE FOLLOWING TO CHAINS: L, H, D, E
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 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 THR L -4
REMARK 465 PHE L -3
REMARK 465 GLY L -2
REMARK 465 SER L -1
REMARK 465 GLY L 0
REMARK 465 ASP L 15
REMARK 465 GLY L 16
REMARK 465 ARG L 17
REMARK 465 TRP H 147A
REMARK 465 THR H 147B
REMARK 465 ALA H 147C
REMARK 465 ASN H 147D
REMARK 465 VAL H 147E
REMARK 465 GLY H 147F
REMARK 465 LYS H 147G
REMARK 465 GLU H 247
REMARK 465 DG D 1
REMARK 465 DC D 27
REMARK 500
REMARK 500 GEOMETRY AND STEREOCHEMISTRY
REMARK 500 SUBTOPIC: CLOSE CONTACTS IN SAME ASYMMETRIC UNIT
REMARK 500
REMARK 500 THE FOLLOWING ATOMS ARE IN CLOSE CONTACT.
REMARK 500
REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI DISTANCE
REMARK 500 O LEU L 14F OG SER L 14I 2.00
REMARK 500 ND2 ASN H 60G C1 NAG H 301 2.12
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 H 187 NE - CZ - NH2 ANGL. DEV. = 3.0 DEGREES
REMARK 500 DG D 25 O5' - P - OP1 ANGL. DEV. = -6.0 DEGREES
REMARK 500 DT E 7 C1' - O4' - C4' ANGL. DEV. = -7.5 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 PHE L 7 -72.60 -128.37
REMARK 500 GLN H 38 93.45 -68.28
REMARK 500 ASN H 60G 88.97 -157.09
REMARK 500 HIS H 71 -56.35 -132.98
REMARK 500 ASN H 78 17.75 57.19
REMARK 500 ILE H 79 -52.92 -124.40
REMARK 500 ASN H 98 18.62 -163.65
REMARK 500 SER H 115 -167.97 -168.81
REMARK 500 ASN H 204B 10.58 -144.98
REMARK 500 SER H 214 -64.06 -107.83
REMARK 500
REMARK 500 REMARK: NULL
REMARK 610
REMARK 610 MISSING HETEROATOM
REMARK 610 THE FOLLOWING RESIDUES HAVE MISSING ATOMS (M=MODEL NUMBER;
REMARK 610 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER;
REMARK 610 I=INSERTION CODE):
REMARK 610 M RES C SSEQI
REMARK 610 NAG H 301
REMARK 620
REMARK 620 METAL COORDINATION
REMARK 620 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER;
REMARK 620 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE):
REMARK 620
REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL
REMARK 620 NA D 101 NA
REMARK 620 N RES CSSEQI ATOM
REMARK 620 1 DG D 8 O6
REMARK 620 2 DG D 11 O6 83.8
REMARK 620 3 DG D 17 O6 172.8 95.3
REMARK 620 4 DG D 20 O6 85.9 169.7 95.0
REMARK 620 N 1 2 3
REMARK 620
REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL
REMARK 620 NA E 101 NA
REMARK 620 N RES CSSEQI ATOM
REMARK 620 1 DG E 1 O6
REMARK 620 2 DG E 2 O6 65.6
REMARK 620 3 DG E 5 O6 118.1 71.4
REMARK 620 4 DG E 6 O6 73.3 104.0 76.5
REMARK 620 5 DG E 10 O6 122.8 168.6 97.2 73.3
REMARK 620 6 DG E 11 O6 167.3 109.8 69.1 119.4 63.8
REMARK 620 7 DG E 14 O6 101.7 65.2 98.2 169.1 117.1 66.1
REMARK 620 8 DG E 15 O6 73.9 111.1 166.5 114.6 79.7 98.0 72.2
REMARK 620 N 1 2 3 4 5 6 7
REMARK 630
REMARK 630 MOLECULE TYPE: PEPTIDE-LIKE INHIBITOR
REMARK 630 MOLECULE NAME: D-PHENYLALANYL-N-[(2S,3S)-6-{[AMINO(IMINIO)METHYL]
REMARK 630 AMINO}-1-CHLORO-2-HYDROXYHEXAN-3-YL]-L-PROLINAMIDE
REMARK 630 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER;
REMARK 630 SSSEQ=SEQUENCE NUMBER; I=INSERTION CODE.)
REMARK 630
REMARK 630 M RES C SSSEQI
REMARK 630 0G6 H 302
REMARK 630 SOURCE: NULL
REMARK 630 TAXONOMY: NULL
REMARK 630 SUBCOMP: DPN PRO AR7 0QE
REMARK 630 DETAILS: NULL
DBREF 5EW2 L -4 17 UNP P00734 THRB_HUMAN 328 363
DBREF 5EW2 H 16 247 UNP P00734 THRB_HUMAN 364 622
DBREF 5EW2 D 1 27 PDB 5EW2 5EW2 1 27
DBREF 5EW2 E 1 15 PDB 5EW2 5EW2 1 15
SEQRES 1 L 36 THR PHE GLY SER GLY GLU ALA ASP CYS GLY LEU ARG PRO
SEQRES 2 L 36 LEU PHE GLU LYS LYS SER LEU GLU ASP LYS THR GLU ARG
SEQRES 3 L 36 GLU LEU LEU GLU SER TYR ILE ASP GLY ARG
SEQRES 1 H 259 ILE VAL GLU GLY SER ASP ALA GLU ILE GLY MET SER PRO
SEQRES 2 H 259 TRP GLN VAL MET LEU PHE ARG LYS SER PRO GLN GLU LEU
SEQRES 3 H 259 LEU CYS GLY ALA SER LEU ILE SER ASP ARG TRP VAL LEU
SEQRES 4 H 259 THR ALA ALA HIS CYS LEU LEU TYR PRO PRO TRP ASP LYS
SEQRES 5 H 259 ASN PHE THR GLU ASN ASP LEU LEU VAL ARG ILE GLY LYS
SEQRES 6 H 259 HIS SER ARG THR ARG TYR GLU ARG ASN ILE GLU LYS ILE
SEQRES 7 H 259 SER MET LEU GLU LYS ILE TYR ILE HIS PRO ARG TYR ASN
SEQRES 8 H 259 TRP ARG GLU ASN LEU ASP ARG ASP ILE ALA LEU MET LYS
SEQRES 9 H 259 LEU LYS LYS PRO VAL ALA PHE SER ASP TYR ILE HIS PRO
SEQRES 10 H 259 VAL CYS LEU PRO ASP ARG GLU THR ALA ALA SER LEU LEU
SEQRES 11 H 259 GLN ALA GLY TYR LYS GLY ARG VAL THR GLY TRP GLY ASN
SEQRES 12 H 259 LEU LYS GLU THR TRP THR ALA ASN VAL GLY LYS GLY GLN
SEQRES 13 H 259 PRO SER VAL LEU GLN VAL VAL ASN LEU PRO ILE VAL GLU
SEQRES 14 H 259 ARG PRO VAL CYS LYS ASP SER THR ARG ILE ARG ILE THR
SEQRES 15 H 259 ASP ASN MET PHE CYS ALA GLY TYR LYS PRO ASP GLU GLY
SEQRES 16 H 259 LYS ARG GLY ASP ALA CYS GLU GLY ASP SER GLY GLY PRO
SEQRES 17 H 259 PHE VAL MET LYS SER PRO PHE ASN ASN ARG TRP TYR GLN
SEQRES 18 H 259 MET GLY ILE VAL SER TRP GLY GLU GLY CYS ASP ARG ASP
SEQRES 19 H 259 GLY LYS TYR GLY PHE TYR THR HIS VAL PHE ARG LEU LYS
SEQRES 20 H 259 LYS TRP ILE GLN LYS VAL ILE ASP GLN PHE GLY GLU
SEQRES 1 D 27 DG DT DC DC DG DT DG DG DT DA DG DG DG
SEQRES 2 D 27 DC DA DG DG DT DT DG DG DG DG DT DG DA
SEQRES 3 D 27 DC
SEQRES 1 E 15 DG DG DT DT DG DG DT DG DT DG DG 3DR DT
SEQRES 2 E 15 DG DG
HET 3DR E 12 11
HET NAG H 301 14
HET 0G6 H 302 30
HET NA H 303 1
HET NA D 101 1
HET NA E 101 1
HETNAM 3DR 1',2'-DIDEOXYRIBOFURANOSE-5'-PHOSPHATE
HETNAM NAG 2-ACETAMIDO-2-DEOXY-BETA-D-GLUCOPYRANOSE
HETNAM 0G6 D-PHENYLALANYL-N-[(2S,3S)-6-{[AMINO(IMINIO)
HETNAM 2 0G6 METHYL]AMINO}-1-CHLORO-2-HYDROXYHEXAN-3-YL]-L-
HETNAM 3 0G6 PROLINAMIDE
HETNAM NA SODIUM ION
HETSYN 3DR ABASIC DIDEOXYRIBOSE
HETSYN 0G6 PPACK
FORMUL 4 3DR C5 H11 O6 P
FORMUL 5 NAG C8 H15 N O6
FORMUL 6 0G6 C21 H34 CL N6 O3 1+
FORMUL 7 NA 3(NA 1+)
FORMUL 10 HOH *7(H2 O)
HELIX 1 AA1 PHE L 7 SER L 11 5 5
HELIX 2 AA2 THR L 14B TYR L 14J 1 9
HELIX 3 AA3 ALA H 55 CYS H 58 5 4
HELIX 4 AA4 PRO H 60B ASP H 60E 5 4
HELIX 5 AA5 THR H 60I ASN H 62 5 3
HELIX 6 AA6 ASP H 125 LEU H 130 1 9
HELIX 7 AA7 GLU H 164 SER H 171 1 8
HELIX 8 AA8 LYS H 185 GLY H 186C 5 5
HELIX 9 AA9 LEU H 234 GLY H 246 1 13
SHEET 1 AA1 7 SER H 20 ASP H 21 0
SHEET 2 AA1 7 GLN H 156 PRO H 161 -1 O VAL H 157 N SER H 20
SHEET 3 AA1 7 LYS H 135 GLY H 140 -1 N VAL H 138 O VAL H 158
SHEET 4 AA1 7 PRO H 198 LYS H 202 -1 O VAL H 200 N ARG H 137
SHEET 5 AA1 7 TRP H 207 TRP H 215 -1 O TYR H 208 N MET H 201
SHEET 6 AA1 7 GLY H 226 HIS H 230 -1 O THR H 229 N ILE H 212
SHEET 7 AA1 7 MET H 180 ALA H 183 -1 N PHE H 181 O TYR H 228
SHEET 1 AA2 7 GLN H 30 ARG H 35 0
SHEET 2 AA2 7 GLU H 39 LEU H 46 -1 O CYS H 42 N LEU H 33
SHEET 3 AA2 7 TRP H 51 THR H 54 -1 O LEU H 53 N SER H 45
SHEET 4 AA2 7 ALA H 104 LEU H 108 -1 O ALA H 104 N THR H 54
SHEET 5 AA2 7 LYS H 81 ILE H 90 -1 N GLU H 86 O LYS H 107
SHEET 6 AA2 7 LEU H 64 ILE H 68 -1 N ILE H 68 O LYS H 81
SHEET 7 AA2 7 GLN H 30 ARG H 35 -1 N PHE H 34 O LEU H 65
SHEET 1 AA3 2 LEU H 60 TYR H 60A 0
SHEET 2 AA3 2 LYS H 60F ASN H 60G-1 O LYS H 60F N TYR H 60A
SSBOND 1 CYS L 1 CYS H 122 1555 1555 2.00
SSBOND 2 CYS H 42 CYS H 58 1555 1555 2.03
SSBOND 3 CYS H 168 CYS H 182 1555 1555 2.03
SSBOND 4 CYS H 191 CYS H 220 1555 1555 2.04
LINK NE2 HIS H 57 C3 0G6 H 302 1555 1555 1.48
LINK OG SER H 195 C2 0G6 H 302 1555 1555 1.43
LINK O3' DG E 11 P 3DR E 12 1555 1555 1.57
LINK O3' 3DR E 12 P DT E 13 1555 1555 1.62
LINK O LYS H 224 NA NA H 303 1555 1555 2.64
LINK O6 DG D 8 NA NA D 101 1555 1555 2.29
LINK O6 DG D 11 NA NA D 101 1555 1555 2.03
LINK O6 DG D 17 NA NA D 101 1555 1555 2.06
LINK O6 DG D 20 NA NA D 101 1555 1555 2.05
LINK O6 DG E 1 NA NA E 101 1555 1555 2.43
LINK O6 DG E 2 NA NA E 101 1555 1555 2.93
LINK O6 DG E 5 NA NA E 101 1555 1555 2.51
LINK O6 DG E 6 NA NA E 101 1555 1555 2.65
LINK O6 DG E 10 NA NA E 101 1555 1555 2.47
LINK O6 DG E 11 NA NA E 101 1555 1555 2.86
LINK O6 DG E 14 NA NA E 101 1555 1555 2.59
LINK O6 DG E 15 NA NA E 101 1555 1555 2.89
CISPEP 1 SER H 36A PRO H 37 0 -3.56
CRYST1 117.089 41.296 104.923 90.00 102.90 90.00 C 1 2 1 4
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 0.008541 0.000000 0.001956 0.00000
SCALE2 0.000000 0.024215 0.000000 0.00000
SCALE3 0.000000 0.000000 0.009777 0.00000
(ATOM LINES ARE NOT SHOWN.)
END
