HEADER SIGNALING PROTEIN 26-JUL-07 2QQN TITLE NEUROPILIN-1 B1 DOMAIN IN COMPLEX WITH A VEGF-BLOCKING FAB COMPND MOL_ID: 1; COMPND 2 MOLECULE: NEUROPILIN-1; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: F5/8 TYPE C 1 DOMAIN; COMPND 5 SYNONYM: VASCULAR ENDOTHELIAL CELL GROWTH FACTOR 165 RECEPTOR, CD304 COMPND 6 ANTIGEN; COMPND 7 ENGINEERED: YES; COMPND 8 MOL_ID: 2; COMPND 9 MOLECULE: ANTIBODY HEAVY CHAIN; COMPND 10 CHAIN: H; COMPND 11 ENGINEERED: YES; COMPND 12 MOL_ID: 3; COMPND 13 MOLECULE: ANTIBODY LIGHT CHAIN; COMPND 14 CHAIN: L; COMPND 15 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; SOURCE 8 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 9 MOL_ID: 2; SOURCE 10 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 11 ORGANISM_COMMON: HUMAN; SOURCE 12 ORGANISM_TAXID: 9606; SOURCE 13 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 14 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 15 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 16 MOL_ID: 3; SOURCE 17 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 18 ORGANISM_COMMON: HUMAN; SOURCE 19 ORGANISM_TAXID: 9606; SOURCE 20 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 21 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 22 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID KEYWDS VEGF RECEPTOR, SEMAPHORIN RECEPTOR, PHAGE-DERIVED ANTIBODY, KEYWDS 2 ANGIOGENESIS, DEVELOPMENTAL PROTEIN, DIFFERENTIATION, GLYCOPROTEIN, KEYWDS 3 HEPARAN SULFATE, MEMBRANE, NEUROGENESIS, PROTEOGLYCAN, SECRETED, KEYWDS 4 TRANSMEMBRANE, HORMONE, SIGNALING PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR B.A.APPLETON,C.WIESMANN REVDAT 6 30-AUG-23 2QQN 1 REMARK SEQADV REVDAT 5 25-OCT-17 2QQN 1 REMARK REVDAT 4 13-JUL-11 2QQN 1 VERSN REVDAT 3 24-FEB-09 2QQN 1 VERSN REVDAT 2 15-JAN-08 2QQN 1 JRNL REVDAT 1 20-NOV-07 2QQN 0 JRNL AUTH B.A.APPLETON,P.WU,J.MALONEY,J.YIN,W.C.LIANG,S.STAWICKI, JRNL AUTH 2 K.MORTARA,K.K.BOWMAN,J.M.ELLIOTT,W.DESMARAIS,J.F.BAZAN, JRNL AUTH 3 A.BAGRI,M.TESSIER-LAVIGNE,A.W.KOCH,Y.WU,R.J.WATTS,C.WIESMANN JRNL TITL STRUCTURAL STUDIES OF NEUROPILIN/ANTIBODY COMPLEXES PROVIDE JRNL TITL 2 INSIGHTS INTO SEMAPHORIN AND VEGF BINDING JRNL REF EMBO J. V. 26 4902 2007 JRNL REFN ISSN 0261-4189 JRNL PMID 17989695 JRNL DOI 10.1038/SJ.EMBOJ.7601906 REMARK 2 REMARK 2 RESOLUTION. 2.20 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 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) : 2.20 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 20.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.1 REMARK 3 NUMBER OF REFLECTIONS : 37085 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) : 0.162 REMARK 3 R VALUE (WORKING SET) : 0.159 REMARK 3 FREE R VALUE : 0.207 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.100 REMARK 3 FREE R VALUE TEST SET COUNT : 1976 REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : 25 REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 2.20 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.25 REMARK 3 REFLECTION IN BIN (WORKING SET) : 2202 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 98.21 REMARK 3 BIN R VALUE (WORKING SET) : 0.1980 REMARK 3 BIN FREE R VALUE SET COUNT : 96 REMARK 3 BIN FREE R VALUE : 0.2600 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 4540 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 12 REMARK 3 SOLVENT ATOMS : 249 REMARK 3 REMARK 3 B VALUES. REMARK 3 B VALUE TYPE : LIKELY RESIDUAL REMARK 3 FROM WILSON PLOT (A**2) : 41.10 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 33.24 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.16000 REMARK 3 B22 (A**2) : 0.16000 REMARK 3 B33 (A**2) : -0.23000 REMARK 3 B12 (A**2) : 0.08000 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): 0.185 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.167 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.115 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 8.831 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.969 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.949 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 4660 ; 0.013 ; 0.022 REMARK 3 BOND LENGTHS OTHERS (A): 3149 ; 0.001 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 6330 ; 1.427 ; 1.955 REMARK 3 BOND ANGLES OTHERS (DEGREES): 7684 ; 0.886 ; 3.003 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 590 ; 6.906 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 183 ;35.918 ;24.208 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 754 ;13.805 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 20 ;21.285 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 703 ; 0.090 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 5180 ; 0.005 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): 921 ; 0.001 ; 0.020 REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): 652 ; 0.178 ; 0.200 REMARK 3 NON-BONDED CONTACTS OTHERS (A): 3001 ; 0.196 ; 0.200 REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): 2163 ; 0.176 ; 0.200 REMARK 3 NON-BONDED TORSION OTHERS (A): 2484 ; 0.084 ; 0.200 REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): 202 ; 0.135 ; 0.200 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): 11 ; 0.159 ; 0.200 REMARK 3 SYMMETRY VDW OTHERS (A): 54 ; 0.197 ; 0.200 REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): 16 ; 0.160 ; 0.200 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): 3758 ; 3.523 ; 2.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): 1201 ; 0.713 ; 2.500 REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 4777 ; 4.335 ; 5.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 2064 ; 3.610 ; 2.500 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 1553 ; 5.051 ; 5.000 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 : NULL REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 5 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): -53.6429 62.4083 -11.6637 REMARK 3 T TENSOR REMARK 3 T11: -0.1527 T22: -0.1501 REMARK 3 T33: -0.1672 T12: 0.0181 REMARK 3 T13: -0.0076 T23: -0.0071 REMARK 3 L TENSOR REMARK 3 L11: 1.7157 L22: 2.1146 REMARK 3 L33: 1.7441 L12: -0.0839 REMARK 3 L13: -0.2484 L23: -0.0226 REMARK 3 S TENSOR REMARK 3 S11: -0.0061 S12: 0.1052 S13: 0.0355 REMARK 3 S21: -0.0085 S22: 0.0133 S23: 0.2172 REMARK 3 S31: -0.0175 S32: -0.1307 S33: -0.0072 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 : H 1 H 113 REMARK 3 ORIGIN FOR THE GROUP (A): -43.6770 26.5672 -14.4336 REMARK 3 T TENSOR REMARK 3 T11: -0.0212 T22: -0.1244 REMARK 3 T33: -0.0713 T12: -0.0551 REMARK 3 T13: 0.0157 T23: -0.0104 REMARK 3 L TENSOR REMARK 3 L11: 2.3012 L22: 2.3639 REMARK 3 L33: 1.3631 L12: -1.2923 REMARK 3 L13: -0.5067 L23: -0.2701 REMARK 3 S TENSOR REMARK 3 S11: -0.0703 S12: 0.0800 S13: -0.1456 REMARK 3 S21: -0.0074 S22: -0.0209 S23: 0.0038 REMARK 3 S31: 0.1077 S32: 0.0049 S33: 0.0912 REMARK 3 REMARK 3 TLS GROUP : 3 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : H 114 H 220 REMARK 3 ORIGIN FOR THE GROUP (A): -43.3867 -4.1755 6.0656 REMARK 3 T TENSOR REMARK 3 T11: 0.2635 T22: 0.0168 REMARK 3 T33: 0.0713 T12: 0.0071 REMARK 3 T13: 0.0375 T23: -0.1133 REMARK 3 L TENSOR REMARK 3 L11: 3.2880 L22: 2.0779 REMARK 3 L33: 0.9984 L12: -0.0824 REMARK 3 L13: 1.3642 L23: -0.9816 REMARK 3 S TENSOR REMARK 3 S11: 0.0633 S12: 0.5723 S13: -0.4991 REMARK 3 S21: -0.2188 S22: -0.0139 S23: -0.1718 REMARK 3 S31: 0.1915 S32: 0.0765 S33: -0.0494 REMARK 3 REMARK 3 TLS GROUP : 4 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : L 1 L 109 REMARK 3 ORIGIN FOR THE GROUP (A): -58.0713 30.2129 1.4371 REMARK 3 T TENSOR REMARK 3 T11: -0.0122 T22: -0.1134 REMARK 3 T33: -0.0781 T12: -0.0396 REMARK 3 T13: 0.0476 T23: 0.0053 REMARK 3 L TENSOR REMARK 3 L11: 1.2381 L22: 2.1344 REMARK 3 L33: 1.8455 L12: 0.7790 REMARK 3 L13: -0.8071 L23: -1.2300 REMARK 3 S TENSOR REMARK 3 S11: -0.1057 S12: -0.0943 S13: -0.0865 REMARK 3 S21: 0.1840 S22: 0.0837 S23: 0.1095 REMARK 3 S31: 0.0943 S32: -0.1197 S33: 0.0220 REMARK 3 REMARK 3 TLS GROUP : 5 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : L 110 L 214 REMARK 3 ORIGIN FOR THE GROUP (A): -42.1173 3.8797 19.7137 REMARK 3 T TENSOR REMARK 3 T11: 0.1515 T22: -0.1511 REMARK 3 T33: -0.0042 T12: -0.0292 REMARK 3 T13: 0.0416 T23: 0.0169 REMARK 3 L TENSOR REMARK 3 L11: 4.5361 L22: 1.2953 REMARK 3 L33: 2.0292 L12: -0.8091 REMARK 3 L13: 0.2555 L23: 0.1642 REMARK 3 S TENSOR REMARK 3 S11: 0.0378 S12: 0.0511 S13: -0.2023 REMARK 3 S21: 0.0118 S22: -0.0222 S23: -0.1225 REMARK 3 S31: 0.2136 S32: 0.2593 S33: -0.0156 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : MASK REMARK 3 PARAMETERS FOR MASK CALCULATION REMARK 3 VDW PROBE RADIUS : 1.40 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 2QQN COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 10-AUG-07. REMARK 100 THE DEPOSITION ID IS D_1000043933. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 06-DEC-06 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 : SSRL REMARK 200 BEAMLINE : BL11-1 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 : CCD REMARK 200 DETECTOR MANUFACTURER : MARMOSAIC 325 MM CCD REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO, HKL-2000 REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 39195 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.200 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.0 REMARK 200 DATA REDUNDANCY : 4.400 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : 0.09600 REMARK 200 FOR THE DATA SET : 14.3000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.20 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.28 REMARK 200 COMPLETENESS FOR SHELL (%) : 98.0 REMARK 200 DATA REDUNDANCY IN SHELL : 3.60 REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : 0.48500 REMARK 200 FOR SHELL : 2.200 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 (B1 DOMAIN), 2FJH (FAB) REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 59.77 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.06 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 25% PEG 1500, 4% TERT-BUTANOL, VAPOR REMARK 280 DIFFUSION, SITTING DROP, TEMPERATURE 297K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: H 3 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -Y,X-Y,Z REMARK 290 3555 -X+Y,-X,Z REMARK 290 4555 X+2/3,Y+1/3,Z+1/3 REMARK 290 5555 -Y+2/3,X-Y+1/3,Z+1/3 REMARK 290 6555 -X+Y+2/3,-X+1/3,Z+1/3 REMARK 290 7555 X+1/3,Y+2/3,Z+2/3 REMARK 290 8555 -Y+1/3,X-Y+2/3,Z+2/3 REMARK 290 9555 -X+Y+1/3,-X+2/3,Z+2/3 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 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 2 0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 3 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 3 -0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 107.05750 REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 61.80968 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 15.15500 REMARK 290 SMTRY1 5 -0.500000 -0.866025 0.000000 107.05750 REMARK 290 SMTRY2 5 0.866025 -0.500000 0.000000 61.80968 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 15.15500 REMARK 290 SMTRY1 6 -0.500000 0.866025 0.000000 107.05750 REMARK 290 SMTRY2 6 -0.866025 -0.500000 0.000000 61.80968 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 15.15500 REMARK 290 SMTRY1 7 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 7 0.000000 1.000000 0.000000 123.61935 REMARK 290 SMTRY3 7 0.000000 0.000000 1.000000 30.31000 REMARK 290 SMTRY1 8 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 8 0.866025 -0.500000 0.000000 123.61935 REMARK 290 SMTRY3 8 0.000000 0.000000 1.000000 30.31000 REMARK 290 SMTRY1 9 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 9 -0.866025 -0.500000 0.000000 123.61935 REMARK 290 SMTRY3 9 0.000000 0.000000 1.000000 30.31000 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: TRIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: TRIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 5040 ANGSTROM**2 REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, H, L 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 269 REMARK 465 SER A 270 REMARK 465 HIS A 271 REMARK 465 MET A 272 REMARK 465 PHE A 273 REMARK 465 LYS H 129 REMARK 465 SER H 130 REMARK 465 THR H 131 REMARK 465 SER H 132 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 LYS H 218 CG CD CE NZ 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 ASN A 313 -144.83 63.97 REMARK 500 THR A 413 -45.38 74.10 REMARK 500 PRO H 98 49.39 -77.27 REMARK 500 MET H 100F 64.36 35.61 REMARK 500 PHE L 29 28.97 -146.41 REMARK 500 ALA L 51 -32.80 61.72 REMARK 500 ALA L 84 -179.28 -170.93 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 EDO L 215 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE EDO H 221 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE EDO A 3 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 2QQI RELATED DB: PDB REMARK 900 RELATED ID: 2QQJ RELATED DB: PDB REMARK 900 RELATED ID: 2QQK RELATED DB: PDB REMARK 900 RELATED ID: 2QQL RELATED DB: PDB REMARK 900 RELATED ID: 2QQM RELATED DB: PDB REMARK 900 RELATED ID: 2QQO RELATED DB: PDB DBREF 2QQN A 273 427 UNP O14786 NRP1_HUMAN 273 427 DBREF 2QQN H 1 220 PDB 2QQN 2QQN 1 220 DBREF 2QQN L 1 214 PDB 2QQN 2QQN 1 214 SEQADV 2QQN GLY A 269 UNP O14786 EXPRESSION TAG SEQADV 2QQN SER A 270 UNP O14786 EXPRESSION TAG SEQADV 2QQN HIS A 271 UNP O14786 EXPRESSION TAG SEQADV 2QQN MET A 272 UNP O14786 EXPRESSION TAG SEQRES 1 A 159 GLY SER HIS MET PHE LYS CYS MET GLU ALA LEU GLY MET SEQRES 2 A 159 GLU SER GLY GLU ILE HIS SER ASP GLN ILE THR ALA SER SEQRES 3 A 159 SER GLN TYR SER THR ASN TRP SER ALA GLU ARG SER ARG SEQRES 4 A 159 LEU ASN TYR PRO GLU ASN GLY TRP THR PRO GLY GLU ASP SEQRES 5 A 159 SER TYR ARG GLU TRP ILE GLN VAL ASP LEU GLY LEU LEU SEQRES 6 A 159 ARG PHE VAL THR ALA VAL GLY THR GLN GLY ALA ILE SER SEQRES 7 A 159 LYS GLU THR LYS LYS LYS TYR TYR VAL LYS THR TYR LYS SEQRES 8 A 159 ILE ASP VAL SER SER ASN GLY GLU ASP TRP ILE THR ILE SEQRES 9 A 159 LYS GLU GLY ASN LYS PRO VAL LEU PHE GLN GLY ASN THR SEQRES 10 A 159 ASN PRO THR ASP VAL VAL VAL ALA VAL PHE PRO LYS PRO SEQRES 11 A 159 LEU ILE THR ARG PHE VAL ARG ILE LYS PRO ALA THR TRP SEQRES 12 A 159 GLU THR GLY ILE SER MET ARG PHE GLU VAL TYR GLY CYS SEQRES 13 A 159 LYS ILE THR SEQRES 1 H 230 GLU VAL GLN LEU VAL GLU SER GLY GLY GLY LEU VAL GLN SEQRES 2 H 230 PRO GLY GLY SER LEU ARG LEU SER CYS ALA ALA SER GLY SEQRES 3 H 230 PHE THR PHE SER SER TYR ALA MET SER TRP VAL ARG GLN SEQRES 4 H 230 ALA PRO GLY LYS GLY LEU GLU TRP VAL SER GLN ILE SER SEQRES 5 H 230 PRO ALA GLY GLY TYR THR ASN TYR ALA ASP SER VAL LYS SEQRES 6 H 230 GLY ARG PHE THR ILE SER ALA ASP THR SER LYS ASN THR SEQRES 7 H 230 ALA TYR LEU GLN MET ASN SER LEU ARG ALA GLU ASP THR SEQRES 8 H 230 ALA VAL TYR TYR CYS ALA ARG GLY GLU LEU PRO TYR TYR SEQRES 9 H 230 ARG MET SER LYS VAL MET ASP VAL TRP GLY GLN GLY THR SEQRES 10 H 230 LEU VAL THR VAL SER SER ALA SER THR LYS GLY PRO SER SEQRES 11 H 230 VAL PHE PRO LEU ALA PRO SER SER LYS SER THR SER GLY SEQRES 12 H 230 GLY THR ALA ALA LEU GLY CYS LEU VAL LYS ASP TYR PHE SEQRES 13 H 230 PRO GLU PRO VAL THR VAL SER TRP ASN SER GLY ALA LEU SEQRES 14 H 230 THR SER GLY VAL HIS THR PHE PRO ALA VAL LEU GLN SER SEQRES 15 H 230 SER GLY LEU TYR SER LEU SER SER VAL VAL THR VAL PRO SEQRES 16 H 230 SER SER SER LEU GLY THR GLN THR TYR ILE CYS ASN VAL SEQRES 17 H 230 ASN HIS LYS PRO SER ASN THR LYS VAL ASP LYS LYS VAL SEQRES 18 H 230 GLU PRO LYS SER CYS ASP LYS THR HIS SEQRES 1 L 214 ASP ILE GLN MET THR GLN SER PRO SER SER LEU SER ALA SEQRES 2 L 214 SER VAL GLY ASP ARG VAL THR ILE THR CYS ARG ALA SER SEQRES 3 L 214 GLN TYR PHE SER SER TYR LEU ALA TRP TYR GLN GLN LYS SEQRES 4 L 214 PRO GLY LYS ALA PRO LYS LEU LEU ILE TYR GLY ALA SER SEQRES 5 L 214 SER ARG ALA SER GLY VAL PRO SER ARG PHE SER GLY SER SEQRES 6 L 214 GLY SER GLY THR ASP PHE THR LEU THR ILE SER SER LEU SEQRES 7 L 214 GLN PRO GLU ASP PHE ALA THR TYR TYR CYS GLN GLN TYR SEQRES 8 L 214 LEU GLY SER PRO PRO THR PHE GLY GLN GLY THR LYS VAL SEQRES 9 L 214 GLU ILE LYS ARG THR VAL ALA ALA PRO SER VAL PHE ILE SEQRES 10 L 214 PHE PRO PRO SER ASP GLU GLN LEU LYS SER GLY THR ALA SEQRES 11 L 214 SER VAL VAL CYS LEU LEU ASN ASN PHE TYR PRO ARG GLU SEQRES 12 L 214 ALA LYS VAL GLN TRP LYS VAL ASP ASN ALA LEU GLN SER SEQRES 13 L 214 GLY ASN SER GLN GLU SER VAL THR GLU GLN ASP SER LYS SEQRES 14 L 214 ASP SER THR TYR SER LEU SER SER THR LEU THR LEU SER SEQRES 15 L 214 LYS ALA ASP TYR GLU LYS HIS LYS VAL TYR ALA CYS GLU SEQRES 16 L 214 VAL THR HIS GLN GLY LEU SER SER PRO VAL THR LYS SER SEQRES 17 L 214 PHE ASN ARG GLY GLU CYS HET EDO A 3 4 HET EDO H 221 4 HET EDO L 215 4 HETNAM EDO 1,2-ETHANEDIOL HETSYN EDO ETHYLENE GLYCOL FORMUL 4 EDO 3(C2 H6 O2) FORMUL 7 HOH *249(H2 O) HELIX 1 1 HIS A 287 ASP A 289 5 3 HELIX 2 2 SER A 298 ARG A 307 5 10 HELIX 3 3 THR H 28 TYR H 32 5 5 HELIX 4 4 ARG H 83 THR H 87 5 5 HELIX 5 5 SER H 156 ALA H 158 5 3 HELIX 6 6 SER H 187 LEU H 189 5 3 HELIX 7 7 LYS H 201 ASN H 204 5 4 HELIX 8 8 GLN L 79 PHE L 83 5 5 HELIX 9 9 SER L 121 SER L 127 1 7 HELIX 10 10 LYS L 183 GLU L 187 1 5 SHEET 1 A 9 ILE A 291 ALA A 293 0 SHEET 2 A 9 ILE A 326 GLN A 342 -1 O GLN A 327 N THR A 292 SHEET 3 A 9 VAL A 391 GLU A 412 -1 O ALA A 393 N VAL A 339 SHEET 4 A 9 LYS A 352 SER A 363 -1 N TYR A 354 O GLU A 412 SHEET 5 A 9 ALA A 344 ILE A 345 -1 N ALA A 344 O TYR A 353 SHEET 6 A 9 LYS A 352 SER A 363 -1 O TYR A 353 N ALA A 344 SHEET 7 A 9 TRP A 369 THR A 371 -1 O ILE A 370 N VAL A 362 SHEET 8 A 9 LYS A 352 SER A 363 -1 N VAL A 362 O ILE A 370 SHEET 9 A 9 PHE A 381 GLN A 382 -1 O PHE A 381 N TYR A 358 SHEET 1 B 3 ILE A 326 GLN A 342 0 SHEET 2 B 3 ARG A 418 LYS A 425 -1 O TYR A 422 N ALA A 338 SHEET 3 B 3 GLU A 277 ALA A 278 -1 N GLU A 277 O GLY A 423 SHEET 1 C 2 LYS A 373 GLU A 374 0 SHEET 2 C 2 LYS A 377 PRO A 378 -1 O LYS A 377 N GLU A 374 SHEET 1 D 4 GLN H 3 SER H 7 0 SHEET 2 D 4 LEU H 18 SER H 25 -1 O ALA H 23 N VAL H 5 SHEET 3 D 4 THR H 77 MET H 82 -1 O MET H 82 N LEU H 18 SHEET 4 D 4 PHE H 67 ASP H 72 -1 N ASP H 72 O THR H 77 SHEET 1 E 6 LEU H 11 VAL H 12 0 SHEET 2 E 6 THR H 107 VAL H 111 1 O THR H 110 N VAL H 12 SHEET 3 E 6 ALA H 88 GLY H 95 -1 N ALA H 88 O VAL H 109 SHEET 4 E 6 ALA H 33 GLN H 39 -1 N VAL H 37 O TYR H 91 SHEET 5 E 6 LEU H 45 ILE H 51 -1 O GLU H 46 N ARG H 38 SHEET 6 E 6 THR H 57 TYR H 59 -1 O ASN H 58 N GLN H 50 SHEET 1 F 4 LEU H 11 VAL H 12 0 SHEET 2 F 4 THR H 107 VAL H 111 1 O THR H 110 N VAL H 12 SHEET 3 F 4 ALA H 88 GLY H 95 -1 N ALA H 88 O VAL H 109 SHEET 4 F 4 VAL H 102 TRP H 103 -1 O VAL H 102 N ARG H 94 SHEET 1 G 4 SER H 120 LEU H 124 0 SHEET 2 G 4 THR H 135 TYR H 145 -1 O GLY H 139 N LEU H 124 SHEET 3 G 4 TYR H 176 PRO H 185 -1 O LEU H 178 N VAL H 142 SHEET 4 G 4 VAL H 163 THR H 165 -1 N HIS H 164 O VAL H 181 SHEET 1 H 4 SER H 120 LEU H 124 0 SHEET 2 H 4 THR H 135 TYR H 145 -1 O GLY H 139 N LEU H 124 SHEET 3 H 4 TYR H 176 PRO H 185 -1 O LEU H 178 N VAL H 142 SHEET 4 H 4 VAL H 169 LEU H 170 -1 N VAL H 169 O SER H 177 SHEET 1 I 3 THR H 151 TRP H 154 0 SHEET 2 I 3 ILE H 195 HIS H 200 -1 O ASN H 197 N SER H 153 SHEET 3 I 3 THR H 205 LYS H 210 -1 O VAL H 207 N VAL H 198 SHEET 1 J 4 MET L 4 SER L 7 0 SHEET 2 J 4 VAL L 19 ALA L 25 -1 O ARG L 24 N THR L 5 SHEET 3 J 4 ASP L 70 ILE L 75 -1 O PHE L 71 N CYS L 23 SHEET 4 J 4 PHE L 62 SER L 67 -1 N SER L 65 O THR L 72 SHEET 1 K 6 SER L 10 ALA L 13 0 SHEET 2 K 6 THR L 102 ILE L 106 1 O GLU L 105 N LEU L 11 SHEET 3 K 6 THR L 85 GLN L 90 -1 N TYR L 86 O THR L 102 SHEET 4 K 6 LEU L 33 GLN L 38 -1 N GLN L 38 O THR L 85 SHEET 5 K 6 LYS L 45 TYR L 49 -1 O LEU L 47 N TRP L 35 SHEET 6 K 6 SER L 53 ARG L 54 -1 O SER L 53 N TYR L 49 SHEET 1 L 4 SER L 10 ALA L 13 0 SHEET 2 L 4 THR L 102 ILE L 106 1 O GLU L 105 N LEU L 11 SHEET 3 L 4 THR L 85 GLN L 90 -1 N TYR L 86 O THR L 102 SHEET 4 L 4 THR L 97 PHE L 98 -1 O THR L 97 N GLN L 90 SHEET 1 M 4 SER L 114 PHE L 118 0 SHEET 2 M 4 THR L 129 PHE L 139 -1 O LEU L 135 N PHE L 116 SHEET 3 M 4 TYR L 173 SER L 182 -1 O LEU L 175 N LEU L 136 SHEET 4 M 4 SER L 159 VAL L 163 -1 N GLN L 160 O THR L 178 SHEET 1 N 4 ALA L 153 LEU L 154 0 SHEET 2 N 4 ALA L 144 VAL L 150 -1 N VAL L 150 O ALA L 153 SHEET 3 N 4 VAL L 191 HIS L 198 -1 O GLU L 195 N GLN L 147 SHEET 4 N 4 VAL L 205 ASN L 210 -1 O VAL L 205 N VAL L 196 SSBOND 1 CYS A 275 CYS A 424 1555 1555 2.13 SSBOND 2 CYS H 22 CYS H 92 1555 1555 2.10 SSBOND 3 CYS H 140 CYS H 196 1555 1555 2.04 SSBOND 4 CYS H 216 CYS L 214 1555 1555 2.04 SSBOND 5 CYS L 23 CYS L 88 1555 1555 2.18 SSBOND 6 CYS L 134 CYS L 194 1555 1555 2.07 CISPEP 1 PHE H 146 PRO H 147 0 -12.69 CISPEP 2 GLU H 148 PRO H 149 0 -6.26 CISPEP 3 SER L 7 PRO L 8 0 -14.66 CISPEP 4 SER L 94 PRO L 95 0 0.85 CISPEP 5 TYR L 140 PRO L 141 0 -1.47 SITE 1 AC1 3 GLY L 200 LEU L 201 SER L 202 SITE 1 AC2 9 PHE H 29 SER H 30 TYR H 32 MET H 34 SITE 2 AC2 9 SER H 52 PRO H 52A ALA H 53 GLY H 54 SITE 3 AC2 9 ALA H 71 SITE 1 AC3 6 ALA A 293 SER A 295 GLN A 296 TYR H 99 SITE 2 AC3 6 HOH H 265 TYR L 32 CRYST1 214.115 214.115 45.465 90.00 90.00 120.00 H 3 9 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 0.004670 0.002696 0.000000 0.00000 SCALE2 0.000000 0.005393 0.000000 0.00000 SCALE3 0.000000 0.000000 0.021995 0.00000