HEADER SIGNALING PROTEIN 30-JAN-18 6FMC TITLE NEUROPILIN1-B1 DOMAIN IN COMPLEX WITH EG01377, 0.9 ANGSTROM STRUCTURE COMPND MOL_ID: 1; COMPND 2 MOLECULE: NEUROPILIN-1; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: VASCULAR ENDOTHELIAL CELL GROWTH FACTOR 165 RECEPTOR; COMPND 5 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; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS VEGF-RECEPTOR, SEMAPHORIN-RECEPTOR, SMALL MOLECULE INHIBITOR, KEYWDS 2 ANGIOGENESIS, DISCOIDIN DOMAIN, SIGNALING PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR T.YELLAND,S.DJORDJEVIC,K.FOTINOU,D.SELWOOD,I.ZACHARY,P.FRANKEL REVDAT 2 17-JAN-24 6FMC 1 REMARK REVDAT 1 17-OCT-18 6FMC 0 JRNL AUTH J.POWELL,F.MOTA,D.STEADMAN,C.SOUDY,J.T.MIYAUCHI,S.CROSBY, JRNL AUTH 2 A.JARVIS,T.REISINGER,N.WINFIELD,G.EVANS,A.FINNIEAR, JRNL AUTH 3 T.YELLAND,Y.T.CHOU,A.W.E.CHAN,A.O'LEARY,L.CHENG,D.LIU, JRNL AUTH 4 C.FOTINOU,C.MILAGRE,J.F.MARTIN,H.JIA,P.FRANKEL,S.DJORDJEVIC, JRNL AUTH 5 S.E.TSIRKA,I.C.ZACHARY,D.L.SELWOOD JRNL TITL SMALL MOLECULE NEUROPILIN-1 ANTAGONISTS COMBINE JRNL TITL 2 ANTIANGIOGENIC AND ANTITUMOR ACTIVITY WITH IMMUNE MODULATION JRNL TITL 3 THROUGH REDUCTION OF TRANSFORMING GROWTH FACTOR BETA (TGF JRNL TITL 4 BETA ) PRODUCTION IN REGULATORY T-CELLS. JRNL REF J. MED. CHEM. V. 61 4135 2018 JRNL REFN ISSN 1520-4804 JRNL PMID 29648813 JRNL DOI 10.1021/ACS.JMEDCHEM.8B00210 REMARK 2 REMARK 2 RESOLUTION. 0.90 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.8.0123 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) : 0.90 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 43.44 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 94.7 REMARK 3 NUMBER OF REFLECTIONS : 111866 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) : 0.110 REMARK 3 R VALUE (WORKING SET) : 0.109 REMARK 3 FREE R VALUE : 0.132 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.100 REMARK 3 FREE R VALUE TEST SET COUNT : 6027 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) : 0.90 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 0.92 REMARK 3 REFLECTION IN BIN (WORKING SET) : 5268 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 60.98 REMARK 3 BIN R VALUE (WORKING SET) : 0.2970 REMARK 3 BIN FREE R VALUE SET COUNT : 318 REMARK 3 BIN FREE R VALUE : 0.2930 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 1261 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 40 REMARK 3 SOLVENT ATOMS : 472 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 16.79 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.00000 REMARK 3 B22 (A**2) : 0.00000 REMARK 3 B33 (A**2) : 0.01000 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): 0.014 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.016 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.012 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 0.496 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.989 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.982 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 1505 ; 0.020 ; 0.020 REMARK 3 BOND LENGTHS OTHERS (A): 1441 ; 0.001 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 2072 ; 2.647 ; 1.986 REMARK 3 BOND ANGLES OTHERS (DEGREES): 3363 ; 3.282 ; 3.009 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 203 ; 7.652 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 64 ;36.593 ;24.375 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 282 ;14.861 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 8 ;18.625 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 221 ; 0.104 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 1713 ; 0.012 ; 0.021 REMARK 3 GENERAL PLANES OTHERS (A): 344 ; 0.015 ; 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): 693 ; 1.200 ; 1.049 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): 691 ; 1.197 ; 1.049 REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 875 ; 1.576 ; 1.590 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): 876 ; 1.575 ; 1.590 REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 812 ; 3.011 ; 1.423 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): 813 ; 3.009 ; 1.423 REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE OTHER ATOMS (A**2): 1176 ; 3.405 ; 2.003 REMARK 3 LONG RANGE B REFINED ATOMS (A**2): 2251 ; 6.334 ;15.266 REMARK 3 LONG RANGE B OTHER ATOMS (A**2): 1877 ; 4.551 ;11.366 REMARK 3 REMARK 3 ANISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 RIGID-BOND RESTRAINTS (A**2): 2946 ; 9.893 ; 3.000 REMARK 3 SPHERICITY; FREE ATOMS (A**2): 78 ;34.773 ; 5.000 REMARK 3 SPHERICITY; BONDED ATOMS (A**2): 3281 ;13.469 ; 5.000 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 : NULL 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 6FMC COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 31-JAN-18. REMARK 100 THE DEPOSITION ID IS D_1200008593. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 07-DEC-14 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : NULL REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SOLEIL REMARK 200 BEAMLINE : PROXIMA 1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.813010 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS3 6M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : XSCALE REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 117690 REMARK 200 RESOLUTION RANGE HIGH (A) : 0.900 REMARK 200 RESOLUTION RANGE LOW (A) : 43.440 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 94.5 REMARK 200 DATA REDUNDANCY : 3.300 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 10.5500 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 0.90 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 0.95 REMARK 200 COMPLETENESS FOR SHELL (%) : 70.7 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 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: 1KEX REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 48.79 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.40 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 16 % W/V PEG3350 AND 200 MM AMMONIUM REMARK 280 CHLORIDE, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 277.15K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 41 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+1/4 REMARK 290 4555 Y,-X,Z+3/4 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 45.61500 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 22.80750 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 68.42250 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 AUTHOR DETERMINED BIOLOGICAL UNIT: MONOMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 0 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 8510 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: 0.0 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 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 HOH A 985 O HOH A 1040 2.17 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS REMARK 500 REMARK 500 THE FOLLOWING ATOMS THAT ARE RELATED BY CRYSTALLOGRAPHIC REMARK 500 SYMMETRY ARE IN CLOSE CONTACT. AN ATOM LOCATED WITHIN 0.15 REMARK 500 ANGSTROMS OF A SYMMETRY RELATED ATOM IS ASSUMED TO BE ON A REMARK 500 SPECIAL POSITION AND IS, THEREFORE, LISTED IN REMARK 375 REMARK 500 INSTEAD OF REMARK 500. ATOMS WITH NON-BLANK ALTERNATE REMARK 500 LOCATION INDICATORS ARE NOT INCLUDED IN THE CALCULATIONS. REMARK 500 REMARK 500 DISTANCE CUTOFF: REMARK 500 2.2 ANGSTROMS FOR CONTACTS NOT INVOLVING HYDROGEN ATOMS REMARK 500 1.6 ANGSTROMS FOR CONTACTS INVOLVING HYDROGEN ATOMS REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI SSYMOP DISTANCE REMARK 500 O HOH A 935 O HOH A 1096 4554 2.17 REMARK 500 REMARK 500 REMARK: NULL 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 SER A 321 CB SER A 321 OG -0.095 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 305 NE - CZ - NH2 ANGL. DEV. = -4.2 DEGREES REMARK 500 ARG A 334 NE - CZ - NH1 ANGL. DEV. = 6.5 DEGREES REMARK 500 ARG A 334 NE - CZ - NH2 ANGL. DEV. = 6.1 DEGREES REMARK 500 ARG A 334 NE - CZ - NH2 ANGL. DEV. = -12.2 DEGREES REMARK 500 LYS A 373 CB - CA - C ANGL. DEV. = -12.8 DEGREES REMARK 500 LYS A 373 CG - CD - CE ANGL. DEV. = 25.3 DEGREES REMARK 500 LYS A 373 CA - C - N ANGL. DEV. = -14.1 DEGREES REMARK 500 LYS A 407 CG - CD - CE ANGL. DEV. = 20.2 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 70.76 -156.04 REMARK 500 MET A 276 39.15 -142.17 REMARK 500 ASN A 313 -146.83 60.20 REMARK 500 THR A 413 -48.76 73.24 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: NON-CIS, NON-TRANS REMARK 500 REMARK 500 THE FOLLOWING PEPTIDE BONDS DEVIATE SIGNIFICANTLY FROM BOTH REMARK 500 CIS AND TRANS CONFORMATION. CIS BONDS, IF ANY, ARE LISTED REMARK 500 ON CISPEP RECORDS. TRANS IS DEFINED AS 180 +/- 30 AND REMARK 500 CIS IS DEFINED AS 0 +/- 30 DEGREES. REMARK 500 MODEL OMEGA REMARK 500 ARG A 334 PHE A 335 148.36 REMARK 500 LYS A 373 GLU A 374 149.86 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: MAIN CHAIN PLANARITY REMARK 500 REMARK 500 THE FOLLOWING RESIDUES HAVE A PSEUDO PLANARITY REMARK 500 TORSION ANGLE, C(I) - CA(I) - N(I+1) - O(I), GREATER REMARK 500 10.0 DEGREES. (M=MODEL NUMBER; RES=RESIDUE NAME; REMARK 500 C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 500 I=INSERTION CODE). REMARK 500 REMARK 500 M RES CSSEQI ANGLE REMARK 500 LYS A 373 -10.01 REMARK 500 LYS A 373 12.78 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 A1252 DISTANCE = 5.81 ANGSTROMS REMARK 525 HOH A1253 DISTANCE = 5.96 ANGSTROMS REMARK 525 HOH A1254 DISTANCE = 5.97 ANGSTROMS REMARK 525 HOH A1255 DISTANCE = 6.05 ANGSTROMS REMARK 525 HOH A1256 DISTANCE = 6.06 ANGSTROMS REMARK 525 HOH A1257 DISTANCE = 6.22 ANGSTROMS REMARK 525 HOH A1258 DISTANCE = 6.24 ANGSTROMS REMARK 525 HOH A1259 DISTANCE = 6.24 ANGSTROMS REMARK 525 HOH A1260 DISTANCE = 6.30 ANGSTROMS REMARK 525 HOH A1261 DISTANCE = 6.38 ANGSTROMS REMARK 525 HOH A1262 DISTANCE = 6.48 ANGSTROMS REMARK 525 HOH A1263 DISTANCE = 6.53 ANGSTROMS REMARK 525 HOH A1264 DISTANCE = 6.57 ANGSTROMS REMARK 525 HOH A1265 DISTANCE = 6.57 ANGSTROMS REMARK 525 HOH A1266 DISTANCE = 6.78 ANGSTROMS REMARK 525 HOH A1267 DISTANCE = 6.80 ANGSTROMS REMARK 525 HOH A1268 DISTANCE = 6.86 ANGSTROMS REMARK 525 HOH A1269 DISTANCE = 6.94 ANGSTROMS REMARK 525 HOH A1270 DISTANCE = 6.98 ANGSTROMS REMARK 525 HOH A1271 DISTANCE = 7.25 ANGSTROMS REMARK 525 HOH A1272 DISTANCE = 7.36 ANGSTROMS REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue DUE A 501 DBREF 6FMC A 273 427 UNP O14786 NRP1_HUMAN 273 427 SEQADV 6FMC GLY A 270 UNP O14786 EXPRESSION TAG SEQADV 6FMC HIS A 271 UNP O14786 EXPRESSION TAG SEQADV 6FMC MET A 272 UNP O14786 EXPRESSION TAG SEQRES 1 A 158 GLY HIS MET PHE LYS CYS MET GLU ALA LEU GLY MET GLU SEQRES 2 A 158 SER GLY GLU ILE HIS SER ASP GLN ILE THR ALA SER SER SEQRES 3 A 158 GLN TYR SER THR ASN TRP SER ALA GLU ARG SER ARG LEU SEQRES 4 A 158 ASN TYR PRO GLU ASN GLY TRP THR PRO GLY GLU ASP SER SEQRES 5 A 158 TYR ARG GLU TRP ILE GLN VAL ASP LEU GLY LEU LEU ARG SEQRES 6 A 158 PHE VAL THR ALA VAL GLY THR GLN GLY ALA ILE SER LYS SEQRES 7 A 158 GLU THR LYS LYS LYS TYR TYR VAL LYS THR TYR LYS ILE SEQRES 8 A 158 ASP VAL SER SER ASN GLY GLU ASP TRP ILE THR ILE LYS SEQRES 9 A 158 GLU GLY ASN LYS PRO VAL LEU PHE GLN GLY ASN THR ASN SEQRES 10 A 158 PRO THR ASP VAL VAL VAL ALA VAL PHE PRO LYS PRO LEU SEQRES 11 A 158 ILE THR ARG PHE VAL ARG ILE LYS PRO ALA THR TRP GLU SEQRES 12 A 158 THR GLY ILE SER MET ARG PHE GLU VAL TYR GLY CYS LYS SEQRES 13 A 158 ILE THR HET DUE A 501 40 HETNAM DUE (2~{S})-2-[[3-[[5-[4-(AMINOMETHYL)PHENYL]-1-BENZOFURAN- HETNAM 2 DUE 7-YL]SULFONYLAMINO]THIOPHEN-2-YL]CARBONYLAMINO]-5- HETNAM 3 DUE CARBAMIMIDAMIDO-PENTANOIC ACID FORMUL 2 DUE C26 H28 N6 O6 S2 FORMUL 3 HOH *472(H2 O) HELIX 1 AA1 HIS A 287 ASP A 289 5 3 HELIX 2 AA2 SER A 298 ARG A 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 SSBOND 1 CYS A 275 CYS A 424 1555 1555 2.06 SITE 1 AC1 22 GLY A 270 MET A 272 MET A 276 TYR A 297 SITE 2 AC1 22 THR A 316 ASP A 320 SER A 346 GLU A 348 SITE 3 AC1 22 THR A 349 LYS A 351 TYR A 353 VAL A 392 SITE 4 AC1 22 GLY A 414 ILE A 415 HOH A 911 HOH A 918 SITE 5 AC1 22 HOH A 944 HOH A 950 HOH A 963 HOH A 972 SITE 6 AC1 22 HOH A 988 HOH A1009 CRYST1 43.440 43.440 91.230 90.00 90.00 90.00 P 41 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 0.023020 0.000000 0.000000 0.00000 SCALE2 0.000000 0.023020 0.000000 0.00000 SCALE3 0.000000 0.000000 0.010961 0.00000