HEADER SIGNALING PROTEIN 20-APR-16 5JGI TITLE X-RAY STRUCTURE OF NEUROPILIN-1 B1 DOMAIN COMPLEXED WITH M45 COMPOUND 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: PLYSS ROSETTA-GAMI2; 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 4 10-JAN-24 5JGI 1 REMARK REVDAT 3 25-APR-18 5JGI 1 JRNL REVDAT 2 28-FEB-18 5JGI 1 JRNL REVDAT 1 10-MAY-17 5JGI 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. 1.38 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 : NULL REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.38 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 41.16 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 95.6 REMARK 3 NUMBER OF REFLECTIONS : 54794 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) : 0.152 REMARK 3 R VALUE (WORKING SET) : 0.151 REMARK 3 FREE R VALUE : 0.169 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.700 REMARK 3 FREE R VALUE TEST SET COUNT : 2717 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) : 1.38 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.42 REMARK 3 REFLECTION IN BIN (WORKING SET) : 3033 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 72.11 REMARK 3 BIN R VALUE (WORKING SET) : 0.1630 REMARK 3 BIN FREE R VALUE SET COUNT : 149 REMARK 3 BIN FREE R VALUE : 0.1960 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 : 15 REMARK 3 SOLVENT ATOMS : 339 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 13.71 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.79000 REMARK 3 B22 (A**2) : -0.72000 REMARK 3 B33 (A**2) : 0.26000 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : -1.12000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): 0.055 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.055 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.032 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 1.527 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.970 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.968 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 2606 ; 0.020 ; 0.020 REMARK 3 BOND LENGTHS OTHERS (A): 2459 ; 0.007 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 3547 ; 1.978 ; 1.950 REMARK 3 BOND ANGLES OTHERS (DEGREES): 5687 ; 1.424 ; 3.000 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 326 ; 7.496 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 115 ;36.951 ;24.174 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 459 ;11.643 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 15 ;19.533 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 387 ; 0.129 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 2939 ; 0.013 ; 0.021 REMARK 3 GENERAL PLANES OTHERS (A): 602 ; 0.006 ; 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): 1256 ; 1.184 ; 0.937 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): 1257 ; 1.183 ; 0.938 REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 1572 ; 1.800 ; 1.409 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): 1572 ; 1.799 ; 1.408 REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 1350 ; 2.287 ; 1.208 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): 1351 ; 2.286 ; 1.208 REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE OTHER ATOMS (A**2): 1967 ; 3.485 ; 1.704 REMARK 3 LONG RANGE B REFINED ATOMS (A**2): 3129 ; 5.128 ; 9.070 REMARK 3 LONG RANGE B OTHER ATOMS (A**2): 2963 ; 4.893 ; 8.371 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 18340 0.13 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 272 A 427 REMARK 3 ORIGIN FOR THE GROUP (A): 81.2917 -21.7938 16.1359 REMARK 3 T TENSOR REMARK 3 T11: 0.0111 T22: 0.0141 REMARK 3 T33: 0.0062 T12: 0.0005 REMARK 3 T13: -0.0021 T23: -0.0001 REMARK 3 L TENSOR REMARK 3 L11: 0.2151 L22: 0.3089 REMARK 3 L33: 0.3416 L12: -0.0649 REMARK 3 L13: 0.0519 L23: 0.1095 REMARK 3 S TENSOR REMARK 3 S11: -0.0400 S12: 0.0116 S13: -0.0105 REMARK 3 S21: 0.0055 S22: 0.0026 S23: 0.0052 REMARK 3 S31: -0.0422 S32: -0.0026 S33: 0.0374 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 274 B 427 REMARK 3 ORIGIN FOR THE GROUP (A): 61.7052 -44.4969 1.9426 REMARK 3 T TENSOR REMARK 3 T11: 0.0123 T22: 0.0099 REMARK 3 T33: 0.0125 T12: -0.0038 REMARK 3 T13: -0.0046 T23: 0.0061 REMARK 3 L TENSOR REMARK 3 L11: 0.2476 L22: 0.2747 REMARK 3 L33: 0.4220 L12: -0.1566 REMARK 3 L13: 0.2442 L23: 0.0025 REMARK 3 S TENSOR REMARK 3 S11: 0.0419 S12: -0.0012 S13: -0.0193 REMARK 3 S21: -0.0186 S22: 0.0133 S23: -0.0074 REMARK 3 S31: 0.0494 S32: -0.0062 S33: -0.0553 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : NULL 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 5JGI COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 20-APR-16. REMARK 100 THE DEPOSITION ID IS D_1000220510. 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 : 57512 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.380 REMARK 200 RESOLUTION RANGE LOW (A) : 41.160 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 95.7 REMARK 200 DATA REDUNDANCY : 6.600 REMARK 200 R MERGE (I) : 0.03400 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 28.4000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.38 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.40 REMARK 200 COMPLETENESS FOR SHELL (%) : 70.0 REMARK 200 DATA REDUNDANCY IN SHELL : 5.20 REMARK 200 R MERGE FOR SHELL (I) : 0.13600 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 8.600 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: NEEDLES REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 41.59 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.11 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 20% PEG3350+0.2 M NH4CL, PH 7.9, VAPOR REMARK 280 DIFFUSION, HANGING DROP, TEMPERATURE 289K 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 44.60150 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 MET B 272 REMARK 465 PHE B 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 O HOH A 571 O HOH A 652 2.18 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 ARG B 305 CZ ARG B 305 NH1 -0.079 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 A 289 CB - CG - OD1 ANGL. DEV. = 7.7 DEGREES REMARK 500 ASP B 289 CB - CG - OD1 ANGL. DEV. = 5.5 DEGREES REMARK 500 ARG B 305 NE - CZ - NH2 ANGL. DEV. = -3.8 DEGREES REMARK 500 ARG B 307 NE - CZ - NH1 ANGL. DEV. = 3.5 DEGREES REMARK 500 GLU B 324 OE1 - CD - OE2 ANGL. DEV. = -8.3 DEGREES REMARK 500 ARG B 402 NE - CZ - NH2 ANGL. DEV. = -3.7 DEGREES REMARK 500 ARG B 405 NE - CZ - NH1 ANGL. DEV. = -3.4 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 MET A 276 30.61 -142.81 REMARK 500 ASN A 313 -141.23 55.10 REMARK 500 THR A 413 -45.36 75.17 REMARK 500 ASN B 313 -142.35 56.45 REMARK 500 THR B 413 -47.10 78.53 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 AAG B 501 DBREF 5JGI A 273 427 UNP O14786 NRP1_HUMAN 273 427 DBREF 5JGI B 273 427 UNP O14786 NRP1_HUMAN 273 427 SEQADV 5JGI MET A 272 UNP O14786 INITIATING METHIONINE SEQADV 5JGI MET B 272 UNP O14786 INITIATING METHIONINE 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 AAG B 501 15 HETNAM AAG N-ALPHA-L-ACETYL-ARGININE FORMUL 3 AAG C8 H16 N4 O3 FORMUL 4 HOH *339(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 2.09 SITE 1 AC1 14 MET A 276 VAL A 394 TYR B 297 THR B 316 SITE 2 AC1 14 ASP B 320 SER B 346 THR B 349 TYR B 353 SITE 3 AC1 14 GLY B 414 ILE B 415 HOH B 613 HOH B 627 SITE 4 AC1 14 HOH B 649 HOH B 689 CRYST1 40.650 89.203 41.645 90.00 98.71 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 0.024600 0.000000 0.003770 0.00000 SCALE2 0.000000 0.011210 0.000000 0.00000 SCALE3 0.000000 0.000000 0.024293 0.00000