HEADER SIGNALING PROTEIN 21-APR-16 5JHK TITLE X-RAY STRUCTURE OF NEUROPILIN-1 B1 DOMAIN COMPLEXED WITH ARG-6 LIGAND. COMPND MOL_ID: 1; COMPND 2 MOLECULE: NEUROPILIN-1; COMPND 3 CHAIN: A, B; 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 BL21(DE3); SOURCE 7 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 8 EXPRESSION_SYSTEM_VARIANT: ROSETTA-GAMI2-PLYSS; SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 10 EXPRESSION_SYSTEM_VECTOR: PET15B-TEV; SOURCE 11 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 4 10-JAN-24 5JHK 1 REMARK REVDAT 3 25-APR-18 5JHK 1 JRNL REVDAT 2 28-FEB-18 5JHK 1 JRNL REVDAT 1 24-MAY-17 5JHK 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. 1.80 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) : 1.80 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 45.39 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 3 NUMBER OF REFLECTIONS : 25765 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) : 0.170 REMARK 3 R VALUE (WORKING SET) : 0.167 REMARK 3 FREE R VALUE : 0.215 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.800 REMARK 3 FREE R VALUE TEST SET COUNT : 1303 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) : 1.80 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.85 REMARK 3 REFLECTION IN BIN (WORKING SET) : 1898 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 99.80 REMARK 3 BIN R VALUE (WORKING SET) : 0.2690 REMARK 3 BIN FREE R VALUE SET COUNT : 118 REMARK 3 BIN FREE R VALUE : 0.3240 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 2489 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 24 REMARK 3 SOLVENT ATOMS : 206 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 24.72 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -0.08000 REMARK 3 B22 (A**2) : -0.16000 REMARK 3 B33 (A**2) : 0.45000 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : -0.78000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): 0.131 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.128 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.090 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 5.915 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.964 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.944 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 2580 ; 0.016 ; 0.020 REMARK 3 BOND LENGTHS OTHERS (A): 2414 ; 0.001 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 3499 ; 1.731 ; 1.941 REMARK 3 BOND ANGLES OTHERS (DEGREES): 5573 ; 0.884 ; 2.988 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 312 ; 7.274 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 112 ;36.260 ;24.107 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 444 ;13.262 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 14 ;20.801 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 378 ; 0.118 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 2909 ; 0.009 ; 0.021 REMARK 3 GENERAL PLANES OTHERS (A): 594 ; 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): 1249 ; 1.328 ; 1.626 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): 1247 ; 1.329 ; 1.625 REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 1557 ; 2.091 ; 2.427 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): 1558 ; 2.090 ; 2.427 REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 1331 ; 1.819 ; 1.907 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): 1332 ; 1.818 ; 1.909 REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE OTHER ATOMS (A**2): 1942 ; 2.963 ; 2.760 REMARK 3 LONG RANGE B REFINED ATOMS (A**2): 2959 ; 5.236 ;14.243 REMARK 3 LONG RANGE B OTHER ATOMS (A**2): 2901 ; 5.083 ;13.930 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 : 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): 34.8066 -21.6850 42.8396 REMARK 3 T TENSOR REMARK 3 T11: 0.0614 T22: 0.0563 REMARK 3 T33: 0.0547 T12: -0.0103 REMARK 3 T13: 0.0052 T23: 0.0033 REMARK 3 L TENSOR REMARK 3 L11: 0.6099 L22: 1.2641 REMARK 3 L33: 0.3457 L12: -0.8612 REMARK 3 L13: 0.1639 L23: -0.3222 REMARK 3 S TENSOR REMARK 3 S11: 0.1009 S12: 0.0173 S13: -0.0211 REMARK 3 S21: -0.1735 S22: -0.0497 S23: 0.0216 REMARK 3 S31: 0.0659 S32: -0.0290 S33: -0.0512 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 270 B 427 REMARK 3 ORIGIN FOR THE GROUP (A): 54.6002 0.9342 56.9944 REMARK 3 T TENSOR REMARK 3 T11: 0.0162 T22: 0.0512 REMARK 3 T33: 0.0883 T12: 0.0003 REMARK 3 T13: -0.0252 T23: -0.0093 REMARK 3 L TENSOR REMARK 3 L11: 0.7924 L22: 1.0062 REMARK 3 L33: 0.5408 L12: 0.0997 REMARK 3 L13: -0.2357 L23: 0.4852 REMARK 3 S TENSOR REMARK 3 S11: -0.0866 S12: 0.0018 S13: 0.0437 REMARK 3 S21: -0.0817 S22: 0.0287 S23: 0.1467 REMARK 3 S31: -0.0054 S32: 0.0092 S33: 0.0579 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 5JHK COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 21-APR-16. REMARK 100 THE DEPOSITION ID IS D_1000220341. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 18-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 : 36381 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.630 REMARK 200 RESOLUTION RANGE LOW (A) : 40.540 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.8 REMARK 200 DATA REDUNDANCY : 6.700 REMARK 200 R MERGE (I) : 0.06400 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 18.9000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.63 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.67 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.7 REMARK 200 DATA REDUNDANCY IN SHELL : 6.80 REMARK 200 R MERGE FOR SHELL (I) : 1.39300 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 1.200 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 (%): 40.69 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.07 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 30%PEG3350+0,2M NH4CL, PH 7.9, VAPOR REMARK 280 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 45.39050 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 GLY A 270 REMARK 465 HIS A 271 REMARK 465 MET A 272 REMARK 465 PHE A 273 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 OE2 GLU B 277 O HOH B 501 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 ASP B 289 CB - CG - OD1 ANGL. DEV. = 5.5 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 CYS A 275 68.89 -151.29 REMARK 500 MET A 276 42.43 -144.32 REMARK 500 ASN A 313 -136.86 64.56 REMARK 500 THR A 413 -55.89 78.77 REMARK 500 CYS B 275 71.99 -150.68 REMARK 500 MET B 276 37.30 -140.03 REMARK 500 ASN B 313 -140.49 62.81 REMARK 500 GLU B 367 -55.05 -126.23 REMARK 500 ASP B 368 94.92 -61.21 REMARK 500 THR B 413 -44.58 79.43 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 6K8 A 501 DBREF 5JHK A 273 427 UNP O14786 NRP1_HUMAN 273 427 DBREF 5JHK B 273 427 UNP O14786 NRP1_HUMAN 273 427 SEQADV 5JHK GLY A 270 UNP O14786 EXPRESSION TAG SEQADV 5JHK HIS A 271 UNP O14786 EXPRESSION TAG SEQADV 5JHK MET A 272 UNP O14786 EXPRESSION TAG SEQADV 5JHK GLY B 270 UNP O14786 EXPRESSION TAG SEQADV 5JHK HIS B 271 UNP O14786 EXPRESSION TAG SEQADV 5JHK MET B 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 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 6K8 A 501 24 HETNAM 6K8 N-(BENZENECARBONYL)GLYCYL-L-ARGININE FORMUL 3 6K8 C15 H21 N5 O4 FORMUL 4 HOH *206(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 2.03 SSBOND 2 CYS B 275 CYS B 424 1555 1555 2.08 SITE 1 AC1 14 TYR A 297 TRP A 301 THR A 316 ASP A 320 SITE 2 AC1 14 SER A 346 THR A 349 TYR A 353 GLY A 414 SITE 3 AC1 14 ILE A 415 HOH A 606 HOH A 632 HOH A 677 SITE 4 AC1 14 MET B 276 TYR B 422 CRYST1 40.376 90.781 40.965 90.00 98.27 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 0.024767 0.000000 0.003599 0.00000 SCALE2 0.000000 0.011016 0.000000 0.00000 SCALE3 0.000000 0.000000 0.024668 0.00000