PDB Short entry for 4DEQ HEADER PROTEIN BINDING/CYTOKINE 21-JAN-12 4DEQ TITLE STRUCTURE OF THE NEUROPILIN-1/VEGF-A COMPLEX COMPND MOL_ID: 1; COMPND 2 MOLECULE: NEUROPILIN-1, VASCULAR ENDOTHELIAL GROWTH FACTOR A; COMPND 3 CHAIN: A, B; COMPND 4 FRAGMENT: NEUROPILIN B1 DOMAIN/VEGF-A HEPARIN BINDING DOMAIN; COMPND 5 SYNONYM: VASCULAR ENDOTHELIAL CELL GROWTH FACTOR 165 RECEPTOR, VEGF- COMPND 6 A, VASCULAR PERMEABILITY FACTOR, VPF; COMPND 7 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, VEGF, VEGFA; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS COAGULATION FACTOR DOMAIN, HEPARIN BINDING DOMAIN, ANGIOGENESIS, KEYWDS 2 PROTEIN BINDING-CYTOKINE COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR C.W.VANDER KOOI REVDAT 5 13-SEP-23 4DEQ 1 REMARK SEQADV REVDAT 4 02-AUG-17 4DEQ 1 SOURCE REMARK REVDAT 3 18-JUL-12 4DEQ 1 JRNL REVDAT 2 29-FEB-12 4DEQ 1 JRNL REVDAT 1 08-FEB-12 4DEQ 0 JRNL AUTH M.W.PARKER,P.XU,X.LI,C.W.VANDER KOOI JRNL TITL STRUCTURAL BASIS FOR SELECTIVE VASCULAR ENDOTHELIAL GROWTH JRNL TITL 2 FACTOR-A (VEGF-A) BINDING TO NEUROPILIN-1. JRNL REF J.BIOL.CHEM. V. 287 11082 2012 JRNL REFN ISSN 0021-9258 JRNL PMID 22318724 JRNL DOI 10.1074/JBC.M111.331140 REMARK 2 REMARK 2 RESOLUTION. 2.65 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.6.0117 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) : 2.65 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 19.90 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 91.2 REMARK 3 NUMBER OF REFLECTIONS : 17074 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) : 0.209 REMARK 3 FREE R VALUE : 0.267 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.100 REMARK 3 FREE R VALUE TEST SET COUNT : 916 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) : 2.65 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.72 REMARK 3 REFLECTION IN BIN (WORKING SET) : 667 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 51.41 REMARK 3 BIN R VALUE (WORKING SET) : 0.4360 REMARK 3 BIN FREE R VALUE SET COUNT : 43 REMARK 3 BIN FREE R VALUE : 0.4980 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 3424 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 5 REMARK 3 SOLVENT ATOMS : 16 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 78.23 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.11000 REMARK 3 B22 (A**2) : 0.11000 REMARK 3 B33 (A**2) : -0.22000 REMARK 3 B12 (A**2) : 0.00000 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): 0.594 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.333 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.251 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 26.465 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.946 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.916 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 3510 ; 0.005 ; 0.020 REMARK 3 BOND LENGTHS OTHERS (A): 2501 ; 0.001 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 4747 ; 1.011 ; 1.953 REMARK 3 BOND ANGLES OTHERS (DEGREES): 6043 ; 0.724 ; 3.006 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 430 ; 5.906 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 159 ;33.431 ;23.522 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 628 ;13.144 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 30 ;12.111 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 504 ; 0.057 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 3876 ; 0.003 ; 0.021 REMARK 3 GENERAL PLANES OTHERS (A): 722 ; 0.001 ; 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): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 LONG RANGE B REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 LONG RANGE B OTHER ATOMS (A**2): NULL ; NULL ; NULL 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 : A 0 A 155 REMARK 3 ORIGIN FOR THE GROUP (A): 6.8535 21.4271 -7.9612 REMARK 3 T TENSOR REMARK 3 T11: 0.1784 T22: 0.1604 REMARK 3 T33: 0.0657 T12: -0.0433 REMARK 3 T13: -0.0143 T23: 0.0141 REMARK 3 L TENSOR REMARK 3 L11: 4.5847 L22: 4.5733 REMARK 3 L33: 2.0082 L12: -1.4475 REMARK 3 L13: 1.1556 L23: 0.5975 REMARK 3 S TENSOR REMARK 3 S11: -0.0885 S12: 0.1638 S13: 0.5113 REMARK 3 S21: -0.1230 S22: -0.1152 S23: -0.2578 REMARK 3 S31: -0.1718 S32: -0.0163 S33: 0.2037 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 0 B 155 REMARK 3 ORIGIN FOR THE GROUP (A): 29.3310 44.2408 6.9105 REMARK 3 T TENSOR REMARK 3 T11: 0.1120 T22: 0.0578 REMARK 3 T33: 0.0752 T12: 0.0602 REMARK 3 T13: -0.0458 T23: -0.0278 REMARK 3 L TENSOR REMARK 3 L11: 6.3675 L22: 4.2949 REMARK 3 L33: 2.7831 L12: -1.7281 REMARK 3 L13: 0.1628 L23: 0.7806 REMARK 3 S TENSOR REMARK 3 S11: -0.1463 S12: -0.1269 S13: 0.0811 REMARK 3 S21: 0.1656 S22: 0.1371 S23: -0.4794 REMARK 3 S31: 0.0008 S32: 0.2226 S33: 0.0091 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 : A 156 A 214 REMARK 3 ORIGIN FOR THE GROUP (A): 39.2458 20.4311 -5.9145 REMARK 3 T TENSOR REMARK 3 T11: 0.3776 T22: 0.4395 REMARK 3 T33: 0.4158 T12: 0.0722 REMARK 3 T13: 0.1692 T23: -0.0554 REMARK 3 L TENSOR REMARK 3 L11: 15.3780 L22: 3.9871 REMARK 3 L33: 2.4969 L12: 7.7211 REMARK 3 L13: 4.4914 L23: 2.4055 REMARK 3 S TENSOR REMARK 3 S11: -0.3602 S12: 0.8682 S13: -0.6862 REMARK 3 S21: -0.3328 S22: 0.4676 S23: -0.4582 REMARK 3 S31: -0.0487 S32: 0.1717 S33: -0.1075 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 : B 156 B 214 REMARK 3 ORIGIN FOR THE GROUP (A): 5.2881 62.5084 -11.9045 REMARK 3 T TENSOR REMARK 3 T11: 0.3241 T22: 0.2875 REMARK 3 T33: 0.3406 T12: 0.0593 REMARK 3 T13: 0.0231 T23: 0.0612 REMARK 3 L TENSOR REMARK 3 L11: 2.5280 L22: 4.3236 REMARK 3 L33: 7.4026 L12: -3.1591 REMARK 3 L13: 4.2588 L23: -5.1787 REMARK 3 S TENSOR REMARK 3 S11: -0.0728 S12: 0.0040 S13: 0.2370 REMARK 3 S21: 0.2239 S22: -0.0937 S23: -0.3527 REMARK 3 S31: -0.1410 S32: 0.0064 S33: 0.1665 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 4DEQ COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 26-JAN-12. REMARK 100 THE DEPOSITION ID IS D_1000070236. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 21-MAR-11 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 6.5 REMARK 200 NUMBER OF CRYSTALS USED : NULL REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : APS REMARK 200 BEAMLINE : 22-ID REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.0000 REMARK 200 MONOCHROMATOR : SI (111) REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : MARMOSAIC 300 MM CCD REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 18014 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.649 REMARK 200 RESOLUTION RANGE LOW (A) : 20.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : -3.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 91.5 REMARK 200 DATA REDUNDANCY : NULL REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : NULL REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : NULL REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : NULL REMARK 200 COMPLETENESS FOR SHELL (%) : NULL REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : NULL 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 REMARK 200 STARTING MODEL: PDB ENTRY 2QQI REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 63.97 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.41 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 1.5M NA/K PHOSPHATE, PH 6.5, VAPOR REMARK 280 DIFFUSION, HANGING DROP, TEMPERATURE 298K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 43 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,-Y,Z+1/2 REMARK 290 3555 -Y,X,Z+3/4 REMARK 290 4555 Y,-X,Z+1/4 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 25.47300 REMARK 290 SMTRY1 3 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 38.20950 REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY2 4 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 12.73650 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1, 2, 3 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: DIMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, 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 350 REMARK 350 BIOMOLECULE: 2 REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PISA 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: 3 REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PISA 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 GLY A -3 REMARK 465 GLY B -3 REMARK 465 SER B -2 REMARK 465 HIS B -1 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 SER A 25 -172.77 -170.54 REMARK 500 ASN A 40 -164.55 59.31 REMARK 500 ASN A 103 40.88 -140.80 REMARK 500 THR A 140 -58.60 67.20 REMARK 500 ASP A 158 -157.37 71.99 REMARK 500 LYS A 174 -71.12 60.78 REMARK 500 ASN B 40 -158.01 60.64 REMARK 500 THR B 140 -46.52 63.03 REMARK 500 ASP B 158 -141.92 75.30 REMARK 500 ARG B 173 104.15 -160.68 REMARK 500 CYS B 184 16.92 58.41 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 PO4 B 301 DBREF 4DEQ A 1 156 UNP O14786 NRP1_HUMAN 274 429 DBREF 4DEQ A 165 214 UNP P15692 VEGFA_HUMAN 183 232 DBREF 4DEQ B 1 156 UNP O14786 NRP1_HUMAN 274 429 DBREF 4DEQ B 165 214 UNP P15692 VEGFA_HUMAN 183 232 SEQADV 4DEQ GLY A -3 UNP O14786 EXPRESSION TAG SEQADV 4DEQ SER A -2 UNP O14786 EXPRESSION TAG SEQADV 4DEQ HIS A -1 UNP O14786 EXPRESSION TAG SEQADV 4DEQ MET A 0 UNP O14786 EXPRESSION TAG SEQADV 4DEQ VAL A 157 UNP O14786 LINKER SEQADV 4DEQ ASP A 158 UNP O14786 LINKER SEQADV 4DEQ GLY A 159 UNP O14786 LINKER SEQADV 4DEQ SER A 160 UNP O14786 LINKER SEQADV 4DEQ GLY A 161 UNP O14786 LINKER SEQADV 4DEQ SER A 162 UNP O14786 LINKER SEQADV 4DEQ GLY A 163 UNP O14786 LINKER SEQADV 4DEQ SER A 164 UNP O14786 LINKER SEQADV 4DEQ GLY B -3 UNP O14786 EXPRESSION TAG SEQADV 4DEQ SER B -2 UNP O14786 EXPRESSION TAG SEQADV 4DEQ HIS B -1 UNP O14786 EXPRESSION TAG SEQADV 4DEQ MET B 0 UNP O14786 EXPRESSION TAG SEQADV 4DEQ VAL B 157 UNP O14786 LINKER SEQADV 4DEQ ASP B 158 UNP O14786 LINKER SEQADV 4DEQ GLY B 159 UNP O14786 LINKER SEQADV 4DEQ SER B 160 UNP O14786 LINKER SEQADV 4DEQ GLY B 161 UNP O14786 LINKER SEQADV 4DEQ SER B 162 UNP O14786 LINKER SEQADV 4DEQ GLY B 163 UNP O14786 LINKER SEQADV 4DEQ SER B 164 UNP O14786 LINKER SEQRES 1 A 218 GLY SER HIS MET LYS CYS MET GLU ALA LEU GLY MET GLU SEQRES 2 A 218 SER GLY GLU ILE HIS SER ASP GLN ILE THR ALA SER SER SEQRES 3 A 218 GLN TYR SER THR ASN TRP SER ALA GLU ARG SER ARG LEU SEQRES 4 A 218 ASN TYR PRO GLU ASN GLY TRP THR PRO GLY GLU ASP SER SEQRES 5 A 218 TYR ARG GLU TRP ILE GLN VAL ASP LEU GLY LEU LEU ARG SEQRES 6 A 218 PHE VAL THR ALA VAL GLY THR GLN GLY ALA ILE SER LYS SEQRES 7 A 218 GLU THR LYS LYS LYS TYR TYR VAL LYS THR TYR LYS ILE SEQRES 8 A 218 ASP VAL SER SER ASN GLY GLU ASP TRP ILE THR ILE LYS SEQRES 9 A 218 GLU GLY ASN LYS PRO VAL LEU PHE GLN GLY ASN THR ASN SEQRES 10 A 218 PRO THR ASP VAL VAL VAL ALA VAL PHE PRO LYS PRO LEU SEQRES 11 A 218 ILE THR ARG PHE VAL ARG ILE LYS PRO ALA THR TRP GLU SEQRES 12 A 218 THR GLY ILE SER MET ARG PHE GLU VAL TYR GLY CYS LYS SEQRES 13 A 218 ILE THR ASP TYR VAL ASP GLY SER GLY SER GLY SER PRO SEQRES 14 A 218 CYS GLY PRO CYS SER GLU ARG ARG LYS HIS LEU PHE VAL SEQRES 15 A 218 GLN ASP PRO GLN THR CYS LYS CYS SER CYS LYS ASN THR SEQRES 16 A 218 ASP SER ARG CYS LYS ALA ARG GLN LEU GLU LEU ASN GLU SEQRES 17 A 218 ARG THR CYS ARG CYS ASP LYS PRO ARG ARG SEQRES 1 B 218 GLY SER HIS MET LYS CYS MET GLU ALA LEU GLY MET GLU SEQRES 2 B 218 SER GLY GLU ILE HIS SER ASP GLN ILE THR ALA SER SER SEQRES 3 B 218 GLN TYR SER THR ASN TRP SER ALA GLU ARG SER ARG LEU SEQRES 4 B 218 ASN TYR PRO GLU ASN GLY TRP THR PRO GLY GLU ASP SER SEQRES 5 B 218 TYR ARG GLU TRP ILE GLN VAL ASP LEU GLY LEU LEU ARG SEQRES 6 B 218 PHE VAL THR ALA VAL GLY THR GLN GLY ALA ILE SER LYS SEQRES 7 B 218 GLU THR LYS LYS LYS TYR TYR VAL LYS THR TYR LYS ILE SEQRES 8 B 218 ASP VAL SER SER ASN GLY GLU ASP TRP ILE THR ILE LYS SEQRES 9 B 218 GLU GLY ASN LYS PRO VAL LEU PHE GLN GLY ASN THR ASN SEQRES 10 B 218 PRO THR ASP VAL VAL VAL ALA VAL PHE PRO LYS PRO LEU SEQRES 11 B 218 ILE THR ARG PHE VAL ARG ILE LYS PRO ALA THR TRP GLU SEQRES 12 B 218 THR GLY ILE SER MET ARG PHE GLU VAL TYR GLY CYS LYS SEQRES 13 B 218 ILE THR ASP TYR VAL ASP GLY SER GLY SER GLY SER PRO SEQRES 14 B 218 CYS GLY PRO CYS SER GLU ARG ARG LYS HIS LEU PHE VAL SEQRES 15 B 218 GLN ASP PRO GLN THR CYS LYS CYS SER CYS LYS ASN THR SEQRES 16 B 218 ASP SER ARG CYS LYS ALA ARG GLN LEU GLU LEU ASN GLU SEQRES 17 B 218 ARG THR CYS ARG CYS ASP LYS PRO ARG ARG HET PO4 B 301 5 HETNAM PO4 PHOSPHATE ION FORMUL 3 PO4 O4 P 3- FORMUL 4 HOH *16(H2 O) HELIX 1 1 HIS A 14 ASP A 16 5 3 HELIX 2 2 SER A 25 SER A 33 5 9 HELIX 3 3 THR A 191 ALA A 197 1 7 HELIX 4 4 HIS B 14 ASP B 16 5 3 HELIX 5 5 SER B 25 ARG B 34 5 10 HELIX 6 6 ARG B 173 HIS B 175 5 3 HELIX 7 7 THR B 191 ARG B 198 1 8 SHEET 1 A 3 ALA A 71 ILE A 72 0 SHEET 2 A 3 LYS A 79 SER A 90 -1 O TYR A 80 N ALA A 71 SHEET 3 A 3 PHE A 108 GLN A 109 -1 O PHE A 108 N TYR A 85 SHEET 1 B 6 GLU A 4 ALA A 5 0 SHEET 2 B 6 ARG A 145 CYS A 151 -1 O GLY A 150 N GLU A 4 SHEET 3 B 6 ILE A 53 GLN A 69 -1 N ALA A 65 O TYR A 149 SHEET 4 B 6 VAL A 118 GLU A 139 -1 O ALA A 120 N VAL A 66 SHEET 5 B 6 LYS A 79 SER A 90 -1 N SER A 90 O PHE A 130 SHEET 6 B 6 ILE A 97 THR A 98 -1 O ILE A 97 N VAL A 89 SHEET 1 C 5 ILE A 18 ALA A 20 0 SHEET 2 C 5 ILE A 53 GLN A 69 -1 O GLN A 54 N THR A 19 SHEET 3 C 5 VAL A 118 GLU A 139 -1 O ALA A 120 N VAL A 66 SHEET 4 C 5 LYS A 79 SER A 90 -1 N SER A 90 O PHE A 130 SHEET 5 C 5 PHE A 108 GLN A 109 -1 O PHE A 108 N TYR A 85 SHEET 1 D 2 LYS A 100 GLU A 101 0 SHEET 2 D 2 LYS A 104 PRO A 105 -1 O LYS A 104 N GLU A 101 SHEET 1 E 2 PHE A 177 GLN A 179 0 SHEET 2 E 2 CYS A 186 CYS A 188 -1 O SER A 187 N VAL A 178 SHEET 1 F 2 LEU A 200 GLU A 201 0 SHEET 2 F 2 LYS A 211 PRO A 212 -1 O LYS A 211 N GLU A 201 SHEET 1 G 3 ALA B 71 ILE B 72 0 SHEET 2 G 3 LYS B 79 SER B 90 -1 O TYR B 80 N ALA B 71 SHEET 3 G 3 PHE B 108 GLN B 109 -1 O PHE B 108 N TYR B 85 SHEET 1 H 6 GLU B 4 ALA B 5 0 SHEET 2 H 6 ARG B 145 CYS B 151 -1 O GLY B 150 N GLU B 4 SHEET 3 H 6 ILE B 53 GLN B 69 -1 N ALA B 65 O TYR B 149 SHEET 4 H 6 VAL B 118 GLU B 139 -1 O PHE B 122 N THR B 64 SHEET 5 H 6 LYS B 79 SER B 90 -1 N SER B 90 O PHE B 130 SHEET 6 H 6 ILE B 97 THR B 98 -1 O ILE B 97 N VAL B 89 SHEET 1 I 5 ILE B 18 ALA B 20 0 SHEET 2 I 5 ILE B 53 GLN B 69 -1 O GLN B 54 N THR B 19 SHEET 3 I 5 VAL B 118 GLU B 139 -1 O PHE B 122 N THR B 64 SHEET 4 I 5 LYS B 79 SER B 90 -1 N SER B 90 O PHE B 130 SHEET 5 I 5 PHE B 108 GLN B 109 -1 O PHE B 108 N TYR B 85 SHEET 1 J 2 LYS B 100 GLU B 101 0 SHEET 2 J 2 LYS B 104 PRO B 105 -1 O LYS B 104 N GLU B 101 SHEET 1 K 2 PHE B 177 GLN B 179 0 SHEET 2 K 2 CYS B 186 CYS B 188 -1 O SER B 187 N VAL B 178 SHEET 1 L 2 GLU B 201 ASN B 203 0 SHEET 2 L 2 ARG B 208 ASP B 210 -1 O ASP B 210 N GLU B 201 SSBOND 1 CYS A 2 CYS A 151 1555 1555 2.05 SSBOND 2 CYS A 166 CYS A 184 1555 1555 2.03 SSBOND 3 CYS A 169 CYS A 186 1555 1555 2.04 SSBOND 4 CYS A 195 CYS A 209 1555 1555 2.04 SSBOND 5 CYS B 2 CYS B 151 1555 1555 2.04 SSBOND 6 CYS B 166 CYS B 184 1555 1555 2.04 SSBOND 7 CYS B 169 CYS B 186 1555 1555 2.04 SSBOND 8 CYS B 188 CYS B 207 1555 1555 2.04 SSBOND 9 CYS B 195 CYS B 209 1555 1555 2.03 SITE 1 AC1 5 ASN B 190 ARG B 198 ARG B 208 CYS B 209 SITE 2 AC1 5 HOH B 401 CRYST1 114.978 114.978 50.946 90.00 90.00 90.00 P 43 8 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 0.008697 0.000000 0.000000 0.00000 SCALE2 0.000000 0.008697 0.000000 0.00000 SCALE3 0.000000 0.000000 0.019629 0.00000