HEADER SIGNALING PROTEIN 10-JUL-09 3I97 TITLE B1 DOMAIN OF HUMAN NEUROPILIN-1 BOUND WITH SMALL MOLECULE EG00229 COMPND MOL_ID: 1; COMPND 2 MOLECULE: NEUROPILIN-1; COMPND 3 CHAIN: A, B; COMPND 4 FRAGMENT: DOMAIN B1, F5/8 TYPE C 1; 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: NP1-B1, NRP, NRP1, VEGF165R; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: ROSETTA KEYWDS NEUROPILIN-1, DRUG, VEGF, ANGIOGENESIS, NEUROPILIN, ALTERNATIVE KEYWDS 2 SPLICING, CELL MEMBRANE, DEVELOPMENTAL PROTEIN, DIFFERENTIATION, KEYWDS 3 DISULFIDE BOND, GLYCOPROTEIN, HEPARAN SULFATE, MEMBRANE, KEYWDS 4 NEUROGENESIS, PHOSPHOPROTEIN, POLYMORPHISM, PROTEOGLYCAN, RECEPTOR, KEYWDS 5 SECRETED, TRANSMEMBRANE, MEMBRANE PROTEIN, SIGNALING PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR C.K.ALLERSTON,S.DJORDJEVIC REVDAT 4 20-NOV-24 3I97 1 REMARK REVDAT 3 06-SEP-23 3I97 1 REMARK REVDAT 2 28-APR-10 3I97 1 JRNL REVDAT 1 02-MAR-10 3I97 0 JRNL AUTH A.JARVIS,C.K.ALLERSTON,H.JIA,B.HERZOG,A.GARZA-GARCIA, JRNL AUTH 2 N.WINFIELD,K.ELLARD,R.AQIL,R.LYNCH,C.CHAPMAN,B.HARTZOULAKIS, JRNL AUTH 3 J.NALLY,M.STEWART,L.CHENG,M.MENON,M.TICKNER,S.DJORDJEVIC, JRNL AUTH 4 P.C.DRISCOLL,I.ZACHARY,D.L.SELWOOD JRNL TITL SMALL MOLECULE INHIBITORS OF THE NEUROPILIN-1 VASCULAR JRNL TITL 2 ENDOTHELIAL GROWTH FACTOR A (VEGF-A) INTERACTION. JRNL REF J.MED.CHEM. V. 53 2215 2010 JRNL REFN ISSN 0022-2623 JRNL PMID 20151671 JRNL DOI 10.1021/JM901755G REMARK 2 REMARK 2 RESOLUTION. 2.90 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.2.0019 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) : 2.90 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 30.33 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 87.8 REMARK 3 NUMBER OF REFLECTIONS : 5573 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) : 0.219 REMARK 3 R VALUE (WORKING SET) : 0.216 REMARK 3 FREE R VALUE : 0.282 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.800 REMARK 3 FREE R VALUE TEST SET COUNT : 278 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) : 2.90 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.97 REMARK 3 REFLECTION IN BIN (WORKING SET) : 396 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 83.20 REMARK 3 BIN R VALUE (WORKING SET) : 0.2970 REMARK 3 BIN FREE R VALUE SET COUNT : 15 REMARK 3 BIN FREE R VALUE : 0.3410 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 2455 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 70 REMARK 3 SOLVENT ATOMS : 8 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 16.96 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.43000 REMARK 3 B22 (A**2) : -0.82000 REMARK 3 B33 (A**2) : 0.35000 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : -0.14000 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): 0.585 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.280 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 30.153 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.924 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.829 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 2588 ; 0.012 ; 0.022 REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 3513 ; 1.416 ; 1.970 REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 306 ; 4.432 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 110 ;30.513 ;24.182 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 438 ;14.543 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 14 ;17.784 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 376 ; 0.082 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 1954 ; 0.003 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): 1156 ; 0.247 ; 0.300 REMARK 3 NON-BONDED CONTACTS OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): 1784 ; 0.332 ; 0.500 REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): 148 ; 0.179 ; 0.500 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): 40 ; 0.320 ; 0.300 REMARK 3 SYMMETRY VDW OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): 2 ; 0.201 ; 0.500 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): 1569 ; 0.405 ; 2.000 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 2510 ; 0.660 ; 3.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 1195 ; 0.355 ; 2.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 1003 ; 0.561 ; 3.000 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 : 3 REMARK 3 REMARK 3 NCS GROUP NUMBER : 1 REMARK 3 CHAIN NAMES : A B REMARK 3 NUMBER OF COMPONENTS NCS GROUP : 1 REMARK 3 COMPONENT C SSSEQI TO C SSSEQI CODE REMARK 3 1 A 5 A 44 1 REMARK 3 1 B 5 B 44 1 REMARK 3 GROUP CHAIN COUNT RMS WEIGHT REMARK 3 TIGHT POSITIONAL 1 A (A): 316 ; 0.04 ; 0.05 REMARK 3 TIGHT THERMAL 1 A (A**2): 316 ; 0.07 ; 0.50 REMARK 3 REMARK 3 NCS GROUP NUMBER : 2 REMARK 3 CHAIN NAMES : A B REMARK 3 NUMBER OF COMPONENTS NCS GROUP : 1 REMARK 3 COMPONENT C SSSEQI TO C SSSEQI CODE REMARK 3 1 A 54 A 91 1 REMARK 3 1 B 54 B 91 1 REMARK 3 GROUP CHAIN COUNT RMS WEIGHT REMARK 3 TIGHT POSITIONAL 2 A (A): 300 ; 0.06 ; 0.05 REMARK 3 TIGHT THERMAL 2 A (A**2): 300 ; 0.19 ; 0.50 REMARK 3 REMARK 3 NCS GROUP NUMBER : 3 REMARK 3 CHAIN NAMES : A B REMARK 3 NUMBER OF COMPONENTS NCS GROUP : 1 REMARK 3 COMPONENT C SSSEQI TO C SSSEQI CODE REMARK 3 1 A 111 A 150 1 REMARK 3 1 B 111 B 150 1 REMARK 3 GROUP CHAIN COUNT RMS WEIGHT REMARK 3 TIGHT POSITIONAL 3 A (A): 321 ; 0.04 ; 0.05 REMARK 3 TIGHT THERMAL 3 A (A**2): 321 ; 0.16 ; 0.50 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : NULL REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : BABINET MODEL WITH 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 3I97 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 15-JUL-09. REMARK 100 THE DEPOSITION ID IS D_1000054122. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 01-MAY-08 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 6 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 REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.54 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : OSMIC MIRRORS REMARK 200 REMARK 200 DETECTOR TYPE : IMAGE PLATE REMARK 200 DETECTOR MANUFACTURER : RIGAKU RAXIS IV REMARK 200 INTENSITY-INTEGRATION SOFTWARE : D*TREK REMARK 200 DATA SCALING SOFTWARE : D*TREK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 5852 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.900 REMARK 200 RESOLUTION RANGE LOW (A) : 30.330 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 88.0 REMARK 200 DATA REDUNDANCY : 2.400 REMARK 200 R MERGE (I) : 0.07900 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 8.5000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.90 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 3.00 REMARK 200 COMPLETENESS FOR SHELL (%) : 85.4 REMARK 200 DATA REDUNDANCY IN SHELL : 2.30 REMARK 200 R MERGE FOR SHELL (I) : 0.19100 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 4.000 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 1KEX REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 42.85 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.15 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 100 MM MES (PH 6.0), 10% PEG 8K AND REMARK 280 200 MM ZN(ACO, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 293.15K 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 44.80000 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 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: 2 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: MONOMERIC 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 -2 REMARK 465 HIS A -1 REMARK 465 MET A 0 REMARK 465 PHE A 1 REMARK 465 GLY B -2 REMARK 465 HIS B -1 REMARK 465 MET B 0 REMARK 465 PHE B 1 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 PRO A 106 C - N - CA ANGL. DEV. = 9.3 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 3 77.95 -151.50 REMARK 500 MET A 4 47.64 -150.70 REMARK 500 SER A 23 -176.82 -170.08 REMARK 500 SER A 26 168.18 179.96 REMARK 500 TRP A 29 42.27 -141.56 REMARK 500 ASN A 41 -149.91 59.59 REMARK 500 ARG A 51 8.37 -66.99 REMARK 500 LEU A 60 167.05 179.69 REMARK 500 GLU A 95 -53.46 -120.23 REMARK 500 PRO A 106 118.39 -30.45 REMARK 500 ARG A 130 -36.17 -143.47 REMARK 500 THR A 141 -56.43 71.05 REMARK 500 SER B 23 -177.82 -171.15 REMARK 500 SER B 26 170.57 178.28 REMARK 500 TRP B 29 40.64 -143.81 REMARK 500 ASN B 41 -151.70 58.13 REMARK 500 LYS B 78 -0.75 76.88 REMARK 500 ASN B 93 21.74 -146.15 REMARK 500 ARG B 130 -38.57 -137.12 REMARK 500 THR B 141 -56.65 72.22 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 8DR A 156 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL A 157 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE 8DR B 156 DBREF 3I97 A 1 155 UNP O14786 NRP1_HUMAN 273 427 DBREF 3I97 B 1 155 UNP O14786 NRP1_HUMAN 273 427 SEQADV 3I97 GLY A -2 UNP O14786 EXPRESSION TAG SEQADV 3I97 HIS A -1 UNP O14786 EXPRESSION TAG SEQADV 3I97 MET A 0 UNP O14786 EXPRESSION TAG SEQADV 3I97 GLY B -2 UNP O14786 EXPRESSION TAG SEQADV 3I97 HIS B -1 UNP O14786 EXPRESSION TAG SEQADV 3I97 MET B 0 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 SEQRES 1 B 158 GLY HIS MET PHE LYS CYS MET GLU ALA LEU GLY MET GLU SEQRES 2 B 158 SER GLY GLU ILE HIS SER ASP GLN ILE THR ALA SER SER SEQRES 3 B 158 GLN TYR SER THR ASN TRP SER ALA GLU ARG SER ARG LEU SEQRES 4 B 158 ASN TYR PRO GLU ASN GLY TRP THR PRO GLY GLU ASP SER SEQRES 5 B 158 TYR ARG GLU TRP ILE GLN VAL ASP LEU GLY LEU LEU ARG SEQRES 6 B 158 PHE VAL THR ALA VAL GLY THR GLN GLY ALA ILE SER LYS SEQRES 7 B 158 GLU THR LYS LYS LYS TYR TYR VAL LYS THR TYR LYS ILE SEQRES 8 B 158 ASP VAL SER SER ASN GLY GLU ASP TRP ILE THR ILE LYS SEQRES 9 B 158 GLU GLY ASN LYS PRO VAL LEU PHE GLN GLY ASN THR ASN SEQRES 10 B 158 PRO THR ASP VAL VAL VAL ALA VAL PHE PRO LYS PRO LEU SEQRES 11 B 158 ILE THR ARG PHE VAL ARG ILE LYS PRO ALA THR TRP GLU SEQRES 12 B 158 THR GLY ILE SER MET ARG PHE GLU VAL TYR GLY CYS LYS SEQRES 13 B 158 ILE THR HET 8DR A 156 32 HET GOL A 157 6 HET 8DR B 156 32 HETNAM 8DR (S)-2-(3-(BENZO[C][1,2,5]THIADIAZOLE-4-SULFONAMIDO) HETNAM 2 8DR THIOPHENE-2-CARBOXAMIDO)-5-GUANIDINOPENTANOIC ACID HETNAM GOL GLYCEROL HETSYN 8DR (2S)-2-[[3-(2,1,3-BENZOTHIADIAZOL-4-YLSULFONYLAMINO) HETSYN 2 8DR THIOPHEN-2-YL]CARBONYLAMINO]-5-CARBAMIMIDAMIDO- HETSYN 3 8DR PENTANOIC ACID HETSYN GOL GLYCERIN; PROPANE-1,2,3-TRIOL FORMUL 3 8DR 2(C17 H19 N7 O5 S3) FORMUL 4 GOL C3 H8 O3 FORMUL 6 HOH *8(H2 O) HELIX 1 1 HIS A 15 ASP A 17 5 3 HELIX 2 2 SER A 26 SER A 34 5 9 HELIX 3 3 HIS B 15 ASP B 17 5 3 HELIX 4 4 SER B 26 SER B 34 5 9 SSBOND 1 CYS A 3 CYS A 152 1555 1555 2.02 SSBOND 2 CYS B 3 CYS B 152 1555 1555 2.04 SITE 1 AC1 12 TYR A 25 SER A 26 THR A 44 ASP A 48 SITE 2 AC1 12 SER A 74 GLU A 76 THR A 77 TYR A 81 SITE 3 AC1 12 GLY A 142 ILE A 143 MET B 4 VAL B 120 SITE 1 AC2 3 SER A 26 THR A 27 ASN A 28 SITE 1 AC3 12 TYR B 25 SER B 26 ASN B 28 TRP B 29 SITE 2 AC3 12 THR B 44 ASP B 48 SER B 74 GLU B 76 SITE 3 AC3 12 THR B 77 TYR B 81 GLY B 142 ILE B 143 CRYST1 41.000 89.600 41.600 90.00 97.70 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 0.024390 0.000000 0.003298 0.00000 SCALE2 0.000000 0.011161 0.000000 0.00000 SCALE3 0.000000 0.000000 0.024257 0.00000