HEADER SIGNALING PROTEIN 02-MAR-16 5IJR
TITLE X-RAY STRUCTURE OF NEUROPILIN-1 B1 DOMAIN COMPLEXED WITH ARG-1 LIGAND.
COMPND MOL_ID: 1;
COMPND 2 MOLECULE: NEUROPILIN-1;
COMPND 3 CHAIN: A, B;
COMPND 4 FRAGMENT: B1 DOMAIN, UNP RESIDUES 273-427;
COMPND 5 SYNONYM: VASCULAR ENDOTHELIAL CELL GROWTH FACTOR 165 RECEPTOR;
COMPND 6 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: NRP1, NRP, VEGF165R;
SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21;
SOURCE 7 EXPRESSION_SYSTEM_TAXID: 511693;
SOURCE 8 EXPRESSION_SYSTEM_VARIANT: ROSETTA-GAMI2(DE3)PLYSS;
SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PET15B-TEV;
SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PET15B-TEV-NRP1B1
KEYWDS SIGNALING PROTEIN, NEUROPILIN-1, ANGIOGENESIS
EXPDTA X-RAY DIFFRACTION
AUTHOR C.FOTINOU,R.RANA,S.DJORDJEVIC,T.YELLAND
REVDAT 3 11-JUL-18 5IJR 1 JRNL
REVDAT 2 28-FEB-18 5IJR 1 JRNL
REVDAT 1 29-MAR-17 5IJR 0
JRNL AUTH F.MOTA,C.FOTINOU,R.R.RANA,A.W.E.CHAN,T.YELLAND,M.T.AROOZ,
JRNL AUTH 2 A.P.O'LEARY,J.HUTTON,P.FRANKEL,I.ZACHARY,D.SELWOOD,
JRNL AUTH 3 S.DJORDJEVIC
JRNL TITL ARCHITECTURE AND HYDRATION OF THE ARGININE-BINDING SITE OF
JRNL TITL 2 NEUROPILIN-1.
JRNL REF FEBS J. V. 285 1290 2018
JRNL REFN ISSN 1742-4658
JRNL PMID 29430837
JRNL DOI 10.1111/FEBS.14405
REMARK 2
REMARK 2 RESOLUTION. 1.52 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) : 1.52
REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 40.68
REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL
REMARK 3 COMPLETENESS FOR RANGE (%) : 95.3
REMARK 3 NUMBER OF REFLECTIONS : 39714
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) : 0.183
REMARK 3 R VALUE (WORKING SET) : 0.181
REMARK 3 FREE R VALUE : 0.213
REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000
REMARK 3 FREE R VALUE TEST SET COUNT : 2093
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) : 1.52
REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.56
REMARK 3 REFLECTION IN BIN (WORKING SET) : 2114
REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 69.41
REMARK 3 BIN R VALUE (WORKING SET) : 0.3010
REMARK 3 BIN FREE R VALUE SET COUNT : 126
REMARK 3 BIN FREE R VALUE : 0.2780
REMARK 3
REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT.
REMARK 3 PROTEIN ATOMS : 2475
REMARK 3 NUCLEIC ACID ATOMS : 0
REMARK 3 HETEROGEN ATOMS : 17
REMARK 3 SOLVENT ATOMS : 280
REMARK 3
REMARK 3 B VALUES.
REMARK 3 FROM WILSON PLOT (A**2) : NULL
REMARK 3 MEAN B VALUE (OVERALL, A**2) : 20.08
REMARK 3 OVERALL ANISOTROPIC B VALUE.
REMARK 3 B11 (A**2) : 0.46000
REMARK 3 B22 (A**2) : -1.57000
REMARK 3 B33 (A**2) : 1.33000
REMARK 3 B12 (A**2) : 0.00000
REMARK 3 B13 (A**2) : -1.08000
REMARK 3 B23 (A**2) : 0.00000
REMARK 3
REMARK 3 ESTIMATED OVERALL COORDINATE ERROR.
REMARK 3 ESU BASED ON R VALUE (A): 0.089
REMARK 3 ESU BASED ON FREE R VALUE (A): 0.089
REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.069
REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 3.862
REMARK 3
REMARK 3 CORRELATION COEFFICIENTS.
REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.964
REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.950
REMARK 3
REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT
REMARK 3 BOND LENGTHS REFINED ATOMS (A): 2565 ; 0.018 ; 0.020
REMARK 3 BOND LENGTHS OTHERS (A): 2408 ; 0.009 ; 0.020
REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 3481 ; 1.883 ; 1.947
REMARK 3 BOND ANGLES OTHERS (DEGREES): 5561 ; 1.543 ; 2.992
REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 314 ; 7.391 ; 5.000
REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 112 ;35.801 ;24.196
REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 445 ;12.594 ;15.000
REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 14 ;20.695 ;15.000
REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 379 ; 0.116 ; 0.200
REMARK 3 GENERAL PLANES REFINED ATOMS (A): 2875 ; 0.012 ; 0.021
REMARK 3 GENERAL PLANES OTHERS (A): 583 ; 0.008 ; 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): 1245 ; 0.983 ; 1.141
REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): 1245 ; 0.983 ; 1.141
REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 1554 ; 1.651 ; 1.704
REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): 1555 ; 1.651 ; 1.705
REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 1320 ; 1.626 ; 1.376
REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): 1321 ; 1.625 ; 1.380
REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL
REMARK 3 SIDE-CHAIN ANGLE OTHER ATOMS (A**2): 1925 ; 2.541 ; 1.979
REMARK 3 LONG RANGE B REFINED ATOMS (A**2): 2988 ; 5.172 ;10.592
REMARK 3 LONG RANGE B OTHER ATOMS (A**2): 2989 ; 5.171 ;10.611
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 NCS TYPE: LOCAL
REMARK 3 NUMBER OF DIFFERENT NCS PAIRS : 1
REMARK 3 GROUP CHAIN1 RANGE CHAIN2 RANGE COUNT RMS WEIGHT
REMARK 3 1 A 274 426 B 274 426 18270 0.10 0.05
REMARK 3
REMARK 3 TLS DETAILS
REMARK 3 NUMBER OF TLS GROUPS : 2
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 274 A 427
REMARK 3 ORIGIN FOR THE GROUP (A): 36.1900 -21.4972 42.6309
REMARK 3 T TENSOR
REMARK 3 T11: 0.0617 T22: 0.0478
REMARK 3 T33: 0.0139 T12: -0.0095
REMARK 3 T13: 0.0219 T23: 0.0046
REMARK 3 L TENSOR
REMARK 3 L11: 0.3668 L22: 0.7454
REMARK 3 L33: 0.3810 L12: -0.4944
REMARK 3 L13: 0.2156 L23: -0.2403
REMARK 3 S TENSOR
REMARK 3 S11: 0.0362 S12: -0.0069 S13: -0.0205
REMARK 3 S21: -0.0916 S22: -0.0270 S23: 0.0018
REMARK 3 S31: 0.0088 S32: -0.0131 S33: -0.0092
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 : B 272 B 427
REMARK 3 ORIGIN FOR THE GROUP (A): 55.7931 1.1985 56.8921
REMARK 3 T TENSOR
REMARK 3 T11: 0.0666 T22: 0.0819
REMARK 3 T33: 0.1212 T12: 0.0302
REMARK 3 T13: -0.0710 T23: -0.0034
REMARK 3 L TENSOR
REMARK 3 L11: 0.2036 L22: 1.6177
REMARK 3 L33: 0.0739 L12: 0.0460
REMARK 3 L13: -0.0982 L23: 0.1736
REMARK 3 S TENSOR
REMARK 3 S11: -0.0939 S12: -0.1112 S13: 0.0475
REMARK 3 S21: -0.2189 S22: 0.0719 S23: 0.4294
REMARK 3 S31: 0.0164 S32: 0.0722 S33: 0.0220
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 5IJR COMPLIES WITH FORMAT V. 3.30, 13-JUL-11
REMARK 100
REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 02-MAR-16.
REMARK 100 THE DEPOSITION ID IS D_1000218763.
REMARK 200
REMARK 200 EXPERIMENTAL DETAILS
REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION
REMARK 200 DATE OF DATA COLLECTION : 23-FEB-15
REMARK 200 TEMPERATURE (KELVIN) : 100
REMARK 200 PH : 7.9
REMARK 200 NUMBER OF CRYSTALS USED : 1
REMARK 200
REMARK 200 SYNCHROTRON (Y/N) : Y
REMARK 200 RADIATION SOURCE : DIAMOND
REMARK 200 BEAMLINE : I04
REMARK 200 X-RAY GENERATOR MODEL : NULL
REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M
REMARK 200 WAVELENGTH OR RANGE (A) : 0.979
REMARK 200 MONOCHROMATOR : NULL
REMARK 200 OPTICS : NULL
REMARK 200
REMARK 200 DETECTOR TYPE : PIXEL
REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS 6M-F
REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XIA2
REMARK 200 DATA SCALING SOFTWARE : AIMLESS
REMARK 200
REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 41807
REMARK 200 RESOLUTION RANGE HIGH (A) : 1.520
REMARK 200 RESOLUTION RANGE LOW (A) : 40.680
REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL
REMARK 200
REMARK 200 OVERALL.
REMARK 200 COMPLETENESS FOR RANGE (%) : 95.4
REMARK 200 DATA REDUNDANCY : 6.600
REMARK 200 R MERGE (I) : 0.04800
REMARK 200 R SYM (I) : NULL
REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 22.8000
REMARK 200
REMARK 200 IN THE HIGHEST RESOLUTION SHELL.
REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.52
REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.55
REMARK 200 COMPLETENESS FOR SHELL (%) : 67.8
REMARK 200 DATA REDUNDANCY IN SHELL : 5.10
REMARK 200 R MERGE FOR SHELL (I) : 0.51000
REMARK 200 R SYM FOR SHELL (I) : NULL
REMARK 200 <I/SIGMA(I)> FOR SHELL : 2.800
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 (%): 39.96
REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.05
REMARK 280
REMARK 280 CRYSTALLIZATION CONDITIONS: 28% W/V PEG3350, 0.2 M AMCL, PH 7.9,
REMARK 280 VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 293K
REMARK 290
REMARK 290 CRYSTALLOGRAPHIC SYMMETRY
REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 1 21 1
REMARK 290
REMARK 290 SYMOP SYMMETRY
REMARK 290 NNNMMM OPERATOR
REMARK 290 1555 X,Y,Z
REMARK 290 2555 -X,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 44.46800
REMARK 290 SMTRY3 2 0.000000 0.000000 -1.000000 0.00000
REMARK 290
REMARK 290 REMARK: NULL
REMARK 300
REMARK 300 BIOMOLECULE: 1, 2
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 AUTHOR DETERMINED BIOLOGICAL UNIT: MONOMERIC
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 350
REMARK 350 BIOMOLECULE: 2
REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: MONOMERIC
REMARK 350 APPLY THE FOLLOWING TO CHAINS: B
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 MET A 272
REMARK 465 PHE A 273
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 ASP B 289 CB - CG - OD1 ANGL. DEV. = 7.1 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 CYS A 275 57.48 -154.11
REMARK 500 ASN A 313 -144.55 61.91
REMARK 500 THR A 413 -48.12 76.94
REMARK 500 CYS B 275 65.64 -155.18
REMARK 500 ASN B 313 -143.52 62.07
REMARK 500 THR B 413 -49.67 74.86
REMARK 500
REMARK 500 REMARK: NULL
REMARK 525
REMARK 525 SOLVENT
REMARK 525
REMARK 525 THE SOLVENT MOLECULES HAVE CHAIN IDENTIFIERS THAT
REMARK 525 INDICATE THE POLYMER CHAIN WITH WHICH THEY ARE MOST
REMARK 525 CLOSELY ASSOCIATED. THE REMARK LISTS ALL THE SOLVENT
REMARK 525 MOLECULES WHICH ARE MORE THAN 5A AWAY FROM THE
REMARK 525 NEAREST POLYMER CHAIN (M = MODEL NUMBER;
REMARK 525 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE
REMARK 525 NUMBER; I=INSERTION CODE):
REMARK 525
REMARK 525 M RES CSSEQI
REMARK 525 HOH A 763 DISTANCE = 5.90 ANGSTROMS
REMARK 800
REMARK 800 SITE
REMARK 800 SITE_IDENTIFIER: AC1
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: binding site for residue HRG A 501
REMARK 800
REMARK 800 SITE_IDENTIFIER: AC2
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: binding site for residue DMS B 501
DBREF 5IJR A 273 427 UNP O14786 NRP1_HUMAN 273 427
DBREF 5IJR B 273 427 UNP O14786 NRP1_HUMAN 273 427
SEQADV 5IJR MET A 272 UNP O14786 CLONING ARTIFACT
SEQADV 5IJR MET B 272 UNP O14786 CLONING ARTIFACT
SEQRES 1 A 156 MET PHE LYS CYS MET GLU ALA LEU GLY MET GLU SER GLY
SEQRES 2 A 156 GLU ILE HIS SER ASP GLN ILE THR ALA SER SER GLN TYR
SEQRES 3 A 156 SER THR ASN TRP SER ALA GLU ARG SER ARG LEU ASN TYR
SEQRES 4 A 156 PRO GLU ASN GLY TRP THR PRO GLY GLU ASP SER TYR ARG
SEQRES 5 A 156 GLU TRP ILE GLN VAL ASP LEU GLY LEU LEU ARG PHE VAL
SEQRES 6 A 156 THR ALA VAL GLY THR GLN GLY ALA ILE SER LYS GLU THR
SEQRES 7 A 156 LYS LYS LYS TYR TYR VAL LYS THR TYR LYS ILE ASP VAL
SEQRES 8 A 156 SER SER ASN GLY GLU ASP TRP ILE THR ILE LYS GLU GLY
SEQRES 9 A 156 ASN LYS PRO VAL LEU PHE GLN GLY ASN THR ASN PRO THR
SEQRES 10 A 156 ASP VAL VAL VAL ALA VAL PHE PRO LYS PRO LEU ILE THR
SEQRES 11 A 156 ARG PHE VAL ARG ILE LYS PRO ALA THR TRP GLU THR GLY
SEQRES 12 A 156 ILE SER MET ARG PHE GLU VAL TYR GLY CYS LYS ILE THR
SEQRES 1 B 156 MET PHE LYS CYS MET GLU ALA LEU GLY MET GLU SER GLY
SEQRES 2 B 156 GLU ILE HIS SER ASP GLN ILE THR ALA SER SER GLN TYR
SEQRES 3 B 156 SER THR ASN TRP SER ALA GLU ARG SER ARG LEU ASN TYR
SEQRES 4 B 156 PRO GLU ASN GLY TRP THR PRO GLY GLU ASP SER TYR ARG
SEQRES 5 B 156 GLU TRP ILE GLN VAL ASP LEU GLY LEU LEU ARG PHE VAL
SEQRES 6 B 156 THR ALA VAL GLY THR GLN GLY ALA ILE SER LYS GLU THR
SEQRES 7 B 156 LYS LYS LYS TYR TYR VAL LYS THR TYR LYS ILE ASP VAL
SEQRES 8 B 156 SER SER ASN GLY GLU ASP TRP ILE THR ILE LYS GLU GLY
SEQRES 9 B 156 ASN LYS PRO VAL LEU PHE GLN GLY ASN THR ASN PRO THR
SEQRES 10 B 156 ASP VAL VAL VAL ALA VAL PHE PRO LYS PRO LEU ILE THR
SEQRES 11 B 156 ARG PHE VAL ARG ILE LYS PRO ALA THR TRP GLU THR GLY
SEQRES 12 B 156 ILE SER MET ARG PHE GLU VAL TYR GLY CYS LYS ILE THR
HET HRG A 501 13
HET DMS B 501 4
HETNAM HRG L-HOMOARGININE
HETNAM DMS DIMETHYL SULFOXIDE
FORMUL 3 HRG C7 H16 N4 O2
FORMUL 4 DMS C2 H6 O S
FORMUL 5 HOH *280(H2 O)
HELIX 1 AA1 HIS A 287 ASP A 289 5 3
HELIX 2 AA2 SER A 298 ARG A 307 5 10
HELIX 3 AA3 HIS B 287 ASP B 289 5 3
HELIX 4 AA4 SER B 298 ARG B 307 5 10
SHEET 1 A 4 ILE A 291 ALA A 293 0
SHEET 2 A 4 ILE A 326 ASP A 329 -1
SHEET 3 A 4 PHE A 403 PRO A 408 -1
SHEET 4 A 4 TYR A 358 SER A 363 -1
SHEET 1 B 3 LEU A 399 THR A 401 0
SHEET 2 B 3 ARG A 334 GLN A 342 -1
SHEET 3 B 3 ARG A 418 CYS A 424 -1
SHEET 1 C 2 ALA A 338 THR A 341 0
SHEET 2 C 2 VAL A 391 VAL A 394 -1
SHEET 1 D 2 TYR A 354 THR A 357 0
SHEET 2 D 2 THR A 410 GLU A 412 -1
SHEET 1 E 4 ILE B 291 ALA B 293 0
SHEET 2 E 4 ILE B 326 ASP B 329 -1
SHEET 3 E 4 PHE B 403 PRO B 408 -1
SHEET 4 E 4 TYR B 358 SER B 363 -1
SHEET 1 F 3 LEU B 399 THR B 401 0
SHEET 2 F 3 ARG B 334 GLN B 342 -1
SHEET 3 F 3 ARG B 418 CYS B 424 -1
SHEET 1 G 2 ALA B 338 THR B 341 0
SHEET 2 G 2 VAL B 391 VAL B 394 -1
SHEET 1 H 2 TYR B 354 THR B 357 0
SHEET 2 H 2 THR B 410 GLU B 412 -1
SSBOND 1 CYS A 275 CYS A 424 1555 1555 2.08
SSBOND 2 CYS B 275 CYS B 424 1555 1555 2.13
SITE 1 AC1 12 TYR A 297 TRP A 301 THR A 316 ASP A 320
SITE 2 AC1 12 SER A 346 GLU A 348 TYR A 353 GLY A 414
SITE 3 AC1 12 ILE A 415 HOH A 637 HOH A 643 HOH A 660
SITE 1 AC2 4 TYR B 297 TRP B 301 TYR B 353 HOH B 683
CRYST1 40.139 88.936 40.962 90.00 96.73 90.00 P 1 21 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 0.024913 0.000000 0.002939 0.00000
SCALE2 0.000000 0.011244 0.000000 0.00000
SCALE3 0.000000 0.000000 0.024582 0.00000
(ATOM LINES ARE NOT SHOWN.)
END
