HEADER SIGNALING PROTEIN 01-JUN-16 5L73 TITLE MAM DOMAIN OF HUMAN NEUROPILIN-1 COMPND MOL_ID: 1; COMPND 2 MOLECULE: NEUROPILIN-1; COMPND 3 CHAIN: A, B; COMPND 4 FRAGMENT: UNP RESIDUES 628-813; 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: NRP1, NRP, VEGF165R; SOURCE 6 EXPRESSION_SYSTEM: HOMO SAPIENS; SOURCE 7 EXPRESSION_SYSTEM_COMMON: HUMAN; SOURCE 8 EXPRESSION_SYSTEM_TAXID: 9606 KEYWDS MAM DOMAIN, DIMERISATION DOMAIN, NEUROPILIN, SIGNALING PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR T.YELLAND,S.DJORDJEVIC REVDAT 3 10-JAN-24 5L73 1 LINK REVDAT 2 09-NOV-16 5L73 1 JRNL REVDAT 1 26-OCT-16 5L73 0 JRNL AUTH T.YELLAND,S.DJORDJEVIC JRNL TITL CRYSTAL STRUCTURE OF THE NEUROPILIN-1 MAM DOMAIN: COMPLETING JRNL TITL 2 THE NEUROPILIN-1 ECTODOMAIN PICTURE. JRNL REF STRUCTURE V. 24 2008 2016 JRNL REFN ISSN 0969-2126 JRNL PMID 27720589 JRNL DOI 10.1016/J.STR.2016.08.017 REMARK 2 REMARK 2 RESOLUTION. 2.24 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) : 2.24 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 68.33 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 98.0 REMARK 3 NUMBER OF REFLECTIONS : 17492 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) : 0.175 REMARK 3 R VALUE (WORKING SET) : 0.172 REMARK 3 FREE R VALUE : 0.228 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.200 REMARK 3 FREE R VALUE TEST SET COUNT : 964 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) : 2.24 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.30 REMARK 3 REFLECTION IN BIN (WORKING SET) : 1256 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 95.37 REMARK 3 BIN R VALUE (WORKING SET) : 0.2130 REMARK 3 BIN FREE R VALUE SET COUNT : 63 REMARK 3 BIN FREE R VALUE : 0.2470 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 2798 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 37 REMARK 3 SOLVENT ATOMS : 123 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 25.33 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -0.37000 REMARK 3 B22 (A**2) : 0.09000 REMARK 3 B33 (A**2) : 0.28000 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): 0.289 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.216 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.143 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 5.734 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.950 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.913 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 2946 ; 0.011 ; 0.019 REMARK 3 BOND LENGTHS OTHERS (A): 2664 ; 0.003 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 3992 ; 1.553 ; 1.907 REMARK 3 BOND ANGLES OTHERS (DEGREES): 6145 ; 0.951 ; 3.000 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 356 ;10.989 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 151 ;34.801 ;24.570 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 475 ;15.215 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 8 ;18.404 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 400 ; 0.101 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 3383 ; 0.010 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): 749 ; 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): 1401 ; 2.071 ; 2.376 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): 1399 ; 2.034 ; 2.373 REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 1749 ; 3.558 ; 3.542 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): 1750 ; 3.561 ; 3.546 REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 1545 ; 2.234 ; 2.646 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): 1545 ; 2.232 ; 2.646 REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE OTHER ATOMS (A**2): 2239 ; 3.894 ; 3.858 REMARK 3 LONG RANGE B REFINED ATOMS (A**2): 3246 ; 6.141 ;18.330 REMARK 3 LONG RANGE B OTHER ATOMS (A**2): 3247 ; 6.140 ;18.334 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 : 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 5L73 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 01-JUN-16. REMARK 100 THE DEPOSITION ID IS D_1200000230. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 06-MAR-16 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 : 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) : 0.9895 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 : XIA2 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 18498 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.240 REMARK 200 RESOLUTION RANGE LOW (A) : 46.170 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 98.3 REMARK 200 DATA REDUNDANCY : 6.200 REMARK 200 R MERGE (I) : 0.11000 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 16.0000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.24 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) : 0.41000 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: 2C9A REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 42.53 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.14 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.06 M MGCL2 0.06 M CACL2 0.1 M TRIS REMARK 280 (BASE), 0.1 M BICINE PH 8.0 12.5 % MPD 12.5 % PEG 1000 12.5 % W/ REMARK 280 V PEG 3350., VAPOR DIFFUSION, TEMPERATURE 289K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 21 21 21 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X+1/2,-Y,Z+1/2 REMARK 290 3555 -X,Y+1/2,-Z+1/2 REMARK 290 4555 X+1/2,-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 23.08600 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 68.32700 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 29.77900 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 68.32700 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 23.08600 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 29.77900 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 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: DIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 2830 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 17350 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -60.0 KCAL/MOL 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 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 ALA A 628 REMARK 465 ASP A 629 REMARK 465 GLU A 630 REMARK 465 LYS A 631 REMARK 465 PRO A 632 REMARK 465 ASP A 633 REMARK 465 VAL A 634 REMARK 465 ILE A 635 REMARK 465 ASP A 636 REMARK 465 ASP A 637 REMARK 465 ASP A 638 REMARK 465 ILE A 639 REMARK 465 HIS A 814 REMARK 465 HIS A 815 REMARK 465 HIS A 816 REMARK 465 HIS A 817 REMARK 465 HIS A 818 REMARK 465 HIS A 819 REMARK 465 ALA B 628 REMARK 465 ASP B 629 REMARK 465 GLU B 630 REMARK 465 LYS B 631 REMARK 465 PRO B 632 REMARK 465 ASP B 633 REMARK 465 VAL B 634 REMARK 465 ILE B 635 REMARK 465 ASP B 636 REMARK 465 ASP B 637 REMARK 465 ASP B 638 REMARK 465 ILE B 639 REMARK 465 GLN B 640 REMARK 465 ASP B 641 REMARK 465 HIS B 816 REMARK 465 HIS B 817 REMARK 465 HIS B 818 REMARK 465 HIS B 819 REMARK 470 REMARK 470 MISSING ATOM REMARK 470 THE FOLLOWING RESIDUES HAVE MISSING ATOMS (M=MODEL NUMBER; REMARK 470 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 470 I=INSERTION CODE): REMARK 470 M RES CSSEQI ATOMS REMARK 470 GLN A 640 CG CD OE1 NE2 REMARK 470 HIS B 814 CG ND1 CD2 CE1 NE2 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 B 1002 O HOH B 1046 2.07 REMARK 500 O VAL A 713 O HOH A 1001 2.15 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 PRO A 812 C - N - CD ANGL. DEV. = -14.5 DEGREES REMARK 500 ARG B 767 NE - CZ - NH1 ANGL. DEV. = 3.6 DEGREES REMARK 500 ARG B 767 NE - CZ - NH2 ANGL. DEV. = -3.7 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 661 -128.61 60.91 REMARK 500 LYS A 679 -63.41 -123.06 REMARK 500 ASP A 698 112.65 -164.91 REMARK 500 LYS A 702 125.04 -35.97 REMARK 500 LYS A 744 172.29 -46.59 REMARK 500 PRO A 745 161.19 -39.08 REMARK 500 ASP A 761 48.48 -88.36 REMARK 500 PRO A 812 81.68 29.55 REMARK 500 HIS B 657 100.36 -164.23 REMARK 500 CYS B 661 -128.59 54.80 REMARK 500 ASP B 698 115.16 -166.05 REMARK 500 LYS B 702 129.10 -37.78 REMARK 500 PRO B 745 -62.28 -102.68 REMARK 500 HIS B 814 71.35 -69.52 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 LYS A 744 PRO A 745 -57.37 REMARK 500 LYS A 811 PRO A 812 -129.69 REMARK 500 LYS B 744 PRO B 745 114.18 REMARK 500 REMARK 500 REMARK: NULL REMARK 620 REMARK 620 METAL COORDINATION REMARK 620 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 620 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 CA A 901 CA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 GLU A 651 O REMARK 620 2 GLU A 651 OE2 86.1 REMARK 620 3 ASP A 685 OD2 155.6 94.6 REMARK 620 4 ASN A 691 O 86.3 167.0 96.6 REMARK 620 5 ASP A 796 OD1 77.3 84.7 127.1 83.4 REMARK 620 6 ASP A 796 OD2 130.6 92.2 73.8 84.7 53.5 REMARK 620 7 HOH A1033 O 74.6 93.4 81.0 94.8 151.9 154.5 REMARK 620 N 1 2 3 4 5 6 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 CA A 902 CA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 685 OD1 REMARK 620 2 BCN A 903 O22 81.5 REMARK 620 3 BCN A 903 O4 168.6 99.4 REMARK 620 4 BCN A 903 O6 79.3 103.8 111.3 REMARK 620 5 HOH A1035 O 93.7 175.0 85.6 73.9 REMARK 620 6 HOH A1065 O 87.5 91.2 81.1 158.2 89.9 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 CA B 901 CA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 GLU B 651 O REMARK 620 2 GLU B 651 OE2 90.6 REMARK 620 3 ASP B 685 OD2 148.8 92.1 REMARK 620 4 ASN B 691 O 85.3 172.9 94.5 REMARK 620 5 ASP B 796 OD1 77.8 90.8 133.2 82.7 REMARK 620 6 ASP B 796 OD2 129.3 97.0 81.1 81.3 52.2 REMARK 620 7 HOH B1014 O 75.2 91.6 73.6 92.9 152.9 153.6 REMARK 620 N 1 2 3 4 5 6 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 CA B 902 CA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP B 685 OD1 REMARK 620 2 THR B 687 OG1 90.1 REMARK 620 3 BCN B 903 O21 87.2 87.3 REMARK 620 4 BCN B 903 O4 163.8 77.1 101.9 REMARK 620 5 BCN B 903 O6 84.4 165.2 106.1 105.5 REMARK 620 6 HOH B1019 O 88.9 76.3 163.2 78.4 89.8 REMARK 620 N 1 2 3 4 5 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue CA A 901 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue CA A 902 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue BCN A 903 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue TAM A 904 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue CA B 901 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue CA B 902 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue BCN B 903 DBREF 5L73 A 628 813 UNP O14786 NRP1_HUMAN 628 813 DBREF 5L73 B 628 813 UNP O14786 NRP1_HUMAN 628 813 SEQADV 5L73 ASP A 629 UNP O14786 THR 629 CONFLICT SEQADV 5L73 ASP A 633 UNP O14786 THR 633 CONFLICT SEQADV 5L73 ASP A 637 UNP O14786 SER 637 CONFLICT SEQADV 5L73 ASP A 638 UNP O14786 THR 638 CONFLICT SEQADV 5L73 ASP A 641 UNP O14786 SER 641 CONFLICT SEQADV 5L73 ASP A 645 UNP O14786 THR 645 CONFLICT SEQADV 5L73 HIS A 814 UNP O14786 EXPRESSION TAG SEQADV 5L73 HIS A 815 UNP O14786 EXPRESSION TAG SEQADV 5L73 HIS A 816 UNP O14786 EXPRESSION TAG SEQADV 5L73 HIS A 817 UNP O14786 EXPRESSION TAG SEQADV 5L73 HIS A 818 UNP O14786 EXPRESSION TAG SEQADV 5L73 HIS A 819 UNP O14786 EXPRESSION TAG SEQADV 5L73 ASP B 629 UNP O14786 THR 629 CONFLICT SEQADV 5L73 ASP B 633 UNP O14786 THR 633 CONFLICT SEQADV 5L73 ASP B 637 UNP O14786 SER 637 CONFLICT SEQADV 5L73 ASP B 638 UNP O14786 THR 638 CONFLICT SEQADV 5L73 ASP B 641 UNP O14786 SER 641 CONFLICT SEQADV 5L73 ASP B 645 UNP O14786 THR 645 CONFLICT SEQADV 5L73 HIS B 814 UNP O14786 EXPRESSION TAG SEQADV 5L73 HIS B 815 UNP O14786 EXPRESSION TAG SEQADV 5L73 HIS B 816 UNP O14786 EXPRESSION TAG SEQADV 5L73 HIS B 817 UNP O14786 EXPRESSION TAG SEQADV 5L73 HIS B 818 UNP O14786 EXPRESSION TAG SEQADV 5L73 HIS B 819 UNP O14786 EXPRESSION TAG SEQRES 1 A 192 ALA ASP GLU LYS PRO ASP VAL ILE ASP ASP ASP ILE GLN SEQRES 2 A 192 ASP GLU PHE PRO ASP TYR GLY PHE ASN CYS GLU PHE GLY SEQRES 3 A 192 TRP GLY SER HIS LYS THR PHE CYS HIS TRP GLU HIS ASP SEQRES 4 A 192 ASN HIS VAL GLN LEU LYS TRP SER VAL LEU THR SER LYS SEQRES 5 A 192 THR GLY PRO ILE GLN ASP HIS THR GLY ASP GLY ASN PHE SEQRES 6 A 192 ILE TYR SER GLN ALA ASP GLU ASN GLN LYS GLY LYS VAL SEQRES 7 A 192 ALA ARG LEU VAL SER PRO VAL VAL TYR SER GLN ASN SER SEQRES 8 A 192 ALA HIS CYS MET THR PHE TRP TYR HIS MET SER GLY SER SEQRES 9 A 192 HIS VAL GLY THR LEU ARG VAL LYS LEU ARG TYR GLN LYS SEQRES 10 A 192 PRO GLU GLU TYR ASP GLN LEU VAL TRP MET ALA ILE GLY SEQRES 11 A 192 HIS GLN GLY ASP HIS TRP LYS GLU GLY ARG VAL LEU LEU SEQRES 12 A 192 HIS LYS SER LEU LYS LEU TYR GLN VAL ILE PHE GLU GLY SEQRES 13 A 192 GLU ILE GLY LYS GLY ASN LEU GLY GLY ILE ALA VAL ASP SEQRES 14 A 192 ASP ILE SER ILE ASN ASN HIS ILE SER GLN GLU ASP CYS SEQRES 15 A 192 ALA LYS PRO ALA HIS HIS HIS HIS HIS HIS SEQRES 1 B 192 ALA ASP GLU LYS PRO ASP VAL ILE ASP ASP ASP ILE GLN SEQRES 2 B 192 ASP GLU PHE PRO ASP TYR GLY PHE ASN CYS GLU PHE GLY SEQRES 3 B 192 TRP GLY SER HIS LYS THR PHE CYS HIS TRP GLU HIS ASP SEQRES 4 B 192 ASN HIS VAL GLN LEU LYS TRP SER VAL LEU THR SER LYS SEQRES 5 B 192 THR GLY PRO ILE GLN ASP HIS THR GLY ASP GLY ASN PHE SEQRES 6 B 192 ILE TYR SER GLN ALA ASP GLU ASN GLN LYS GLY LYS VAL SEQRES 7 B 192 ALA ARG LEU VAL SER PRO VAL VAL TYR SER GLN ASN SER SEQRES 8 B 192 ALA HIS CYS MET THR PHE TRP TYR HIS MET SER GLY SER SEQRES 9 B 192 HIS VAL GLY THR LEU ARG VAL LYS LEU ARG TYR GLN LYS SEQRES 10 B 192 PRO GLU GLU TYR ASP GLN LEU VAL TRP MET ALA ILE GLY SEQRES 11 B 192 HIS GLN GLY ASP HIS TRP LYS GLU GLY ARG VAL LEU LEU SEQRES 12 B 192 HIS LYS SER LEU LYS LEU TYR GLN VAL ILE PHE GLU GLY SEQRES 13 B 192 GLU ILE GLY LYS GLY ASN LEU GLY GLY ILE ALA VAL ASP SEQRES 14 B 192 ASP ILE SER ILE ASN ASN HIS ILE SER GLN GLU ASP CYS SEQRES 15 B 192 ALA LYS PRO ALA HIS HIS HIS HIS HIS HIS HET CA A 901 1 HET CA A 902 1 HET BCN A 903 11 HET TAM A 904 11 HET CA B 901 1 HET CA B 902 1 HET BCN B 903 11 HETNAM CA CALCIUM ION HETNAM BCN BICINE HETNAM TAM TRIS(HYDROXYETHYL)AMINOMETHANE FORMUL 3 CA 4(CA 2+) FORMUL 5 BCN 2(C6 H13 N O4) FORMUL 6 TAM C7 H17 N O3 FORMUL 10 HOH *123(H2 O) HELIX 1 AA1 GLU A 642 TYR A 646 5 5 HELIX 2 AA2 ASP A 698 LYS A 702 5 5 HELIX 3 AA3 ASP B 698 LYS B 702 5 5 HELIX 4 AA4 SER B 805 ALA B 810 1 6 SHEET 1 AA1 2 GLY A 653 TRP A 654 0 SHEET 2 AA1 2 HIS A 657 LYS A 658 -1 O HIS A 657 N TRP A 654 SHEET 1 AA2 5 GLU A 664 HIS A 665 0 SHEET 2 AA2 5 VAL A 705 VAL A 713 -1 O VAL A 709 N GLU A 664 SHEET 3 AA2 5 TYR A 777 ILE A 785 -1 O VAL A 779 N SER A 710 SHEET 4 AA2 5 GLY A 734 TYR A 742 -1 N ARG A 741 O GLN A 778 SHEET 5 AA2 5 ASP A 749 ILE A 756 -1 O ALA A 755 N LEU A 736 SHEET 1 AA3 5 SER A 674 THR A 677 0 SHEET 2 AA3 5 ASN A 691 GLN A 696 -1 O PHE A 692 N LEU A 676 SHEET 3 AA3 5 GLY A 792 ILE A 800 -1 O VAL A 795 N ILE A 693 SHEET 4 AA3 5 HIS A 720 MET A 728 -1 N THR A 723 O SER A 799 SHEET 5 AA3 5 LYS A 764 LEU A 770 -1 O LEU A 770 N HIS A 720 SHEET 1 AA4 2 GLY B 653 TRP B 654 0 SHEET 2 AA4 2 HIS B 657 LYS B 658 -1 O HIS B 657 N TRP B 654 SHEET 1 AA5 5 GLU B 664 HIS B 665 0 SHEET 2 AA5 5 VAL B 705 VAL B 709 -1 O VAL B 709 N GLU B 664 SHEET 3 AA5 5 TYR B 777 ILE B 785 -1 O PHE B 781 N LEU B 708 SHEET 4 AA5 5 GLY B 734 TYR B 742 -1 N THR B 735 O GLU B 784 SHEET 5 AA5 5 TYR B 748 ILE B 756 -1 O TRP B 753 N VAL B 738 SHEET 1 AA6 5 SER B 674 THR B 677 0 SHEET 2 AA6 5 ASN B 691 GLN B 696 -1 O PHE B 692 N LEU B 676 SHEET 3 AA6 5 GLY B 792 SER B 799 -1 O VAL B 795 N ILE B 693 SHEET 4 AA6 5 HIS B 720 MET B 728 -1 N THR B 723 O SER B 799 SHEET 5 AA6 5 LYS B 764 LEU B 770 -1 O LEU B 770 N HIS B 720 SSBOND 1 CYS A 650 CYS A 661 1555 1555 2.12 SSBOND 2 CYS A 721 CYS A 809 1555 1555 2.06 SSBOND 3 CYS B 650 CYS B 661 1555 1555 2.08 SSBOND 4 CYS B 721 CYS B 809 1555 1555 2.10 LINK O GLU A 651 CA CA A 901 1555 1555 2.46 LINK OE2 GLU A 651 CA CA A 901 1555 1555 2.23 LINK OD2 ASP A 685 CA CA A 901 1555 1555 2.36 LINK OD1 ASP A 685 CA CA A 902 1555 1555 2.36 LINK O ASN A 691 CA CA A 901 1555 1555 2.20 LINK OD1 ASP A 796 CA CA A 901 1555 1555 2.46 LINK OD2 ASP A 796 CA CA A 901 1555 1555 2.42 LINK CA CA A 901 O HOH A1033 1555 1555 2.32 LINK CA CA A 902 O22 BCN A 903 1555 1555 2.26 LINK CA CA A 902 O4 BCN A 903 1555 1555 2.40 LINK CA CA A 902 O6 BCN A 903 1555 1555 2.40 LINK CA CA A 902 O HOH A1035 1555 1555 2.27 LINK CA CA A 902 O HOH A1065 1555 1555 2.29 LINK O GLU B 651 CA CA B 901 1555 1555 2.50 LINK OE2 GLU B 651 CA CA B 901 1555 1555 2.22 LINK OD2 ASP B 685 CA CA B 901 1555 1555 2.45 LINK OD1 ASP B 685 CA CA B 902 1555 1555 2.25 LINK OG1 THR B 687 CA CA B 902 1555 1555 2.30 LINK O ASN B 691 CA CA B 901 1555 1555 2.27 LINK OD1 ASP B 796 CA CA B 901 1555 1555 2.46 LINK OD2 ASP B 796 CA CA B 901 1555 1555 2.51 LINK CA CA B 901 O HOH B1014 1555 1555 2.32 LINK CA CA B 902 O21 BCN B 903 1555 1555 2.39 LINK CA CA B 902 O4 BCN B 903 1555 1555 2.12 LINK CA CA B 902 O6 BCN B 903 1555 1555 2.42 LINK CA CA B 902 O HOH B1019 1555 1555 2.19 SITE 1 AC1 5 GLU A 651 ASP A 685 ASN A 691 ASP A 796 SITE 2 AC1 5 HOH A1033 SITE 1 AC2 4 ASP A 685 BCN A 903 HOH A1035 HOH A1065 SITE 1 AC3 12 ASP A 685 HIS A 686 THR A 687 TRP A 725 SITE 2 AC3 12 TRP A 763 ASP A 796 CA A 902 HOH A1027 SITE 3 AC3 12 HOH A1035 HOH A1065 GLU B 765 ARG B 767 SITE 1 AC4 12 PRO A 644 ASP A 645 GLY A 647 ASN A 649 SITE 2 AC4 12 THR A 659 CYS A 661 SER A 731 ILE A 756 SITE 3 AC4 12 HIS A 758 GLN A 759 HOH A1003 HOH A1005 SITE 1 AC5 5 GLU B 651 ASP B 685 ASN B 691 ASP B 796 SITE 2 AC5 5 HOH B1014 SITE 1 AC6 4 ASP B 685 THR B 687 BCN B 903 HOH B1019 SITE 1 AC7 9 ASP B 685 HIS B 686 THR B 687 TRP B 725 SITE 2 AC7 9 TRP B 763 ASP B 796 ASP B 797 CA B 902 SITE 3 AC7 9 HOH B1019 CRYST1 46.172 59.558 136.654 90.00 90.00 90.00 P 21 21 21 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 0.021658 0.000000 0.000000 0.00000 SCALE2 0.000000 0.016790 0.000000 0.00000 SCALE3 0.000000 0.000000 0.007318 0.00000