PDB Short entry for 4QDQ HEADER CELL ADHESION 14-MAY-14 4QDQ TITLE PHYSICAL BASIS FOR NRP2 LIGAND BINDING COMPND MOL_ID: 1; COMPND 2 MOLECULE: NEUROPILIN-2; COMPND 3 CHAIN: A, B; COMPND 4 FRAGMENT: NEUROPILIN-2 B1B2 DOMAIN, VEGF-C C-TERMINUS; COMPND 5 SYNONYM: VASCULAR ENDOTHELIAL CELL GROWTH FACTOR 165 RECEPTOR 2; 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: NRP2, VEGF165R2; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: ROSETTA-GAMI 2(DE3); SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PET28B KEYWDS COAGULATION FACTOR DOMAIN, DISCOIDIN DOMAIN, RECEPTOR, VEGF-C, KEYWDS 2 MEMBRANE, CELL ADHESION EXPDTA X-RAY DIFFRACTION AUTHOR M.W.PARKER,C.W.VANDER KOOI REVDAT 4 20-SEP-23 4QDQ 1 REMARK SEQADV SSBOND REVDAT 3 13-MAY-15 4QDQ 1 REMARK REVDAT 2 06-MAY-15 4QDQ 1 JRNL REVDAT 1 15-APR-15 4QDQ 0 JRNL AUTH M.W.PARKER,A.D.LINKUGEL,H.L.GOEL,T.WU,A.M.MERCURIO, JRNL AUTH 2 C.W.VANDER KOOI JRNL TITL STRUCTURAL BASIS FOR VEGF-C BINDING TO NEUROPILIN-2 AND JRNL TITL 2 SEQUESTRATION BY A SOLUBLE SPLICE FORM. JRNL REF STRUCTURE V. 23 677 2015 JRNL REFN ISSN 0969-2126 JRNL PMID 25752543 JRNL DOI 10.1016/J.STR.2015.01.018 REMARK 2 REMARK 2 RESOLUTION. 1.95 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.6.0117 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) : 1.95 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 19.75 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 90.6 REMARK 3 NUMBER OF REFLECTIONS : 41511 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) : 0.211 REMARK 3 R VALUE (WORKING SET) : 0.210 REMARK 3 FREE R VALUE : 0.241 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.900 REMARK 3 FREE R VALUE TEST SET COUNT : 2140 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) : 1.95 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.00 REMARK 3 REFLECTION IN BIN (WORKING SET) : 2745 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 82.43 REMARK 3 BIN R VALUE (WORKING SET) : 0.2970 REMARK 3 BIN FREE R VALUE SET COUNT : 108 REMARK 3 BIN FREE R VALUE : 0.3340 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 5060 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 34 REMARK 3 SOLVENT ATOMS : 327 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 33.32 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -0.23000 REMARK 3 B22 (A**2) : 0.00000 REMARK 3 B33 (A**2) : 0.29000 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : 0.13000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): 0.226 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.179 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.142 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 9.908 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.947 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.929 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 5244 ; 0.006 ; 0.019 REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 7119 ; 1.113 ; 1.946 REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 634 ; 6.494 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 253 ;36.190 ;23.043 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 869 ;13.044 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 51 ;13.671 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 755 ; 0.072 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 4045 ; 0.005 ; 0.021 REMARK 3 GENERAL PLANES OTHERS (A): NULL ; NULL ; NULL 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): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL 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 : 2 REMARK 3 REMARK 3 TLS GROUP : 1 REMARK 3 NUMBER OF COMPONENTS GROUP : 3 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : A 276 A 600 REMARK 3 RESIDUE RANGE : A 701 A 704 REMARK 3 RESIDUE RANGE : A 801 A 969 REMARK 3 ORIGIN FOR THE GROUP (A): 11.597 0.096 23.735 REMARK 3 T TENSOR REMARK 3 T11: 0.1468 T22: 0.0842 REMARK 3 T33: 0.0614 T12: 0.0101 REMARK 3 T13: 0.0098 T23: -0.0046 REMARK 3 L TENSOR REMARK 3 L11: 0.2953 L22: 0.4651 REMARK 3 L33: 2.8732 L12: -0.0145 REMARK 3 L13: -0.4320 L23: -0.1245 REMARK 3 S TENSOR REMARK 3 S11: 0.0025 S12: -0.0057 S13: 0.0051 REMARK 3 S21: 0.0646 S22: -0.0105 S23: 0.0355 REMARK 3 S31: -0.1193 S32: -0.1360 S33: 0.0080 REMARK 3 REMARK 3 TLS GROUP : 2 REMARK 3 NUMBER OF COMPONENTS GROUP : 3 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : B 276 B 600 REMARK 3 RESIDUE RANGE : B 701 B 702 REMARK 3 RESIDUE RANGE : B 801 B 958 REMARK 3 ORIGIN FOR THE GROUP (A): 21.056 -28.333 11.651 REMARK 3 T TENSOR REMARK 3 T11: 0.1859 T22: 0.0797 REMARK 3 T33: 0.0633 T12: 0.0193 REMARK 3 T13: -0.0453 T23: -0.0051 REMARK 3 L TENSOR REMARK 3 L11: 0.3253 L22: 0.9781 REMARK 3 L33: 2.0563 L12: 0.0476 REMARK 3 L13: 0.3038 L23: 0.8362 REMARK 3 S TENSOR REMARK 3 S11: 0.0369 S12: 0.0030 S13: -0.0084 REMARK 3 S21: 0.1348 S22: 0.0126 S23: -0.0846 REMARK 3 S31: 0.2070 S32: 0.0221 S33: -0.0495 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 USED IF PRESENT IN REMARK 3 THE INPUT REMARK 4 REMARK 4 4QDQ COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 15-MAY-14. REMARK 100 THE DEPOSITION ID IS D_1000085925. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 10-OCT-11 REMARK 200 TEMPERATURE (KELVIN) : 110 REMARK 200 PH : 6.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : APS REMARK 200 BEAMLINE : 22-ID REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.0000 REMARK 200 MONOCHROMATOR : SI(111) REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : MARMOSAIC 300 MM CCD REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 44081 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.950 REMARK 200 RESOLUTION RANGE LOW (A) : 20.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : -3.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 90.6 REMARK 200 DATA REDUNDANCY : NULL REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : NULL REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.95 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.02 REMARK 200 COMPLETENESS FOR SHELL (%) : 82.0 REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> 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: MOLREP REMARK 200 STARTING MODEL: 2QQJ REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 45.74 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.27 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1 M HEPES, 0.5 M AMMONIUM SULFATE, REMARK 280 PH 6.5, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 298K 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 60.40400 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: DIMERIC 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 BIOMT1 2 1.000000 0.000000 0.000000 -24.99288 REMARK 350 BIOMT2 2 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 2 0.000000 0.000000 1.000000 -67.96670 REMARK 350 REMARK 350 BIOMOLECULE: 2 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: DIMERIC 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 350 BIOMT1 2 1.000000 0.000000 0.000000 16.05412 REMARK 350 BIOMT2 2 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 2 0.000000 0.000000 1.000000 -67.96670 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 272 REMARK 465 SER A 273 REMARK 465 HIS A 274 REMARK 465 MET A 275 REMARK 465 GLY A 508 REMARK 465 GLY A 509 REMARK 465 ASP A 510 REMARK 465 SER A 511 REMARK 465 ILE A 512 REMARK 465 THR A 513 REMARK 465 ALA A 514 REMARK 465 VAL A 515 REMARK 465 GLU A 516 REMARK 465 GLY B 272 REMARK 465 SER B 273 REMARK 465 HIS B 274 REMARK 465 MET B 275 REMARK 465 GLY B 508 REMARK 465 GLY B 509 REMARK 465 ASP B 510 REMARK 465 SER B 511 REMARK 465 ILE B 512 REMARK 465 THR B 513 REMARK 465 ALA B 514 REMARK 465 VAL B 515 REMARK 465 GLU B 516 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 316 -134.61 51.30 REMARK 500 ARG A 334 -53.61 77.29 REMARK 500 ALA A 386 -148.34 -118.58 REMARK 500 SER A 416 -41.02 65.57 REMARK 500 SER A 416 -39.94 65.27 REMARK 500 VAL A 468 -56.01 69.77 REMARK 500 SER A 472 -108.86 -136.15 REMARK 500 ASN B 316 -133.84 48.31 REMARK 500 ARG B 334 -38.08 76.61 REMARK 500 ALA B 386 -146.00 -119.63 REMARK 500 SER B 416 -33.19 69.50 REMARK 500 SER B 416 -46.53 69.71 REMARK 500 VAL B 468 -56.05 67.39 REMARK 500 SER B 472 -105.80 -140.09 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 GOL A 701 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL A 702 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL A 703 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 A 704 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL B 701 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 B 702 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 4QDR RELATED DB: PDB REMARK 900 RELATED ID: 4QDS RELATED DB: PDB DBREF 4QDQ A 276 595 UNP O60462 NRP2_HUMAN 276 595 DBREF 4QDQ B 276 595 UNP O60462 NRP2_HUMAN 276 595 SEQADV 4QDQ GLY A 272 UNP O60462 EXPRESSION TAG SEQADV 4QDQ SER A 273 UNP O60462 EXPRESSION TAG SEQADV 4QDQ HIS A 274 UNP O60462 EXPRESSION TAG SEQADV 4QDQ MET A 275 UNP O60462 EXPRESSION TAG SEQADV 4QDQ SER A 596 UNP O60462 EXPRESSION TAG SEQADV 4QDQ ILE A 597 UNP O60462 EXPRESSION TAG SEQADV 4QDQ ILE A 598 UNP O60462 EXPRESSION TAG SEQADV 4QDQ ARG A 599 UNP O60462 EXPRESSION TAG SEQADV 4QDQ ARG A 600 UNP O60462 EXPRESSION TAG SEQADV 4QDQ GLY B 272 UNP O60462 EXPRESSION TAG SEQADV 4QDQ SER B 273 UNP O60462 EXPRESSION TAG SEQADV 4QDQ HIS B 274 UNP O60462 EXPRESSION TAG SEQADV 4QDQ MET B 275 UNP O60462 EXPRESSION TAG SEQADV 4QDQ SER B 596 UNP O60462 EXPRESSION TAG SEQADV 4QDQ ILE B 597 UNP O60462 EXPRESSION TAG SEQADV 4QDQ ILE B 598 UNP O60462 EXPRESSION TAG SEQADV 4QDQ ARG B 599 UNP O60462 EXPRESSION TAG SEQADV 4QDQ ARG B 600 UNP O60462 EXPRESSION TAG SEQRES 1 A 329 GLY SER HIS MET GLN CYS ASN VAL PRO LEU GLY MET GLU SEQRES 2 A 329 SER GLY ARG ILE ALA ASN GLU GLN ILE SER ALA SER SER SEQRES 3 A 329 THR TYR SER ASP GLY ARG TRP THR PRO GLN GLN SER ARG SEQRES 4 A 329 LEU HIS GLY ASP ASP ASN GLY TRP THR PRO ASN LEU ASP SEQRES 5 A 329 SER ASN LYS GLU TYR LEU GLN VAL ASP LEU ARG PHE LEU SEQRES 6 A 329 THR MET LEU THR ALA ILE ALA THR GLN GLY ALA ILE SER SEQRES 7 A 329 ARG GLU THR GLN ASN GLY TYR TYR VAL LYS SER TYR LYS SEQRES 8 A 329 LEU GLU VAL SER THR ASN GLY GLU ASP TRP MET VAL TYR SEQRES 9 A 329 ARG HIS GLY LYS ASN HIS LYS VAL PHE GLN ALA ASN ASN SEQRES 10 A 329 ASP ALA THR GLU VAL VAL LEU ASN LYS LEU HIS ALA PRO SEQRES 11 A 329 LEU LEU THR ARG PHE VAL ARG ILE ARG PRO GLN THR TRP SEQRES 12 A 329 HIS SER GLY ILE ALA LEU ARG LEU GLU LEU PHE GLY CYS SEQRES 13 A 329 ARG VAL THR ASP ALA PRO CYS SER ASN MET LEU GLY MET SEQRES 14 A 329 LEU SER GLY LEU ILE ALA ASP SER GLN ILE SER ALA SER SEQRES 15 A 329 SER THR GLN GLU TYR LEU TRP SER PRO SER ALA ALA ARG SEQRES 16 A 329 LEU VAL SER SER ARG SER GLY TRP PHE PRO ARG ILE PRO SEQRES 17 A 329 GLN ALA GLN PRO GLY GLU GLU TRP LEU GLN VAL ASP LEU SEQRES 18 A 329 GLY THR PRO LYS THR VAL LYS GLY VAL ILE ILE GLN GLY SEQRES 19 A 329 ALA ARG GLY GLY ASP SER ILE THR ALA VAL GLU ALA ARG SEQRES 20 A 329 ALA PHE VAL ARG LYS PHE LYS VAL SER TYR SER LEU ASN SEQRES 21 A 329 GLY LYS ASP TRP GLU TYR ILE GLN ASP PRO ARG THR GLN SEQRES 22 A 329 GLN PRO LYS LEU PHE GLU GLY ASN MET HIS TYR ASP THR SEQRES 23 A 329 PRO ASP ILE ARG ARG PHE ASP PRO ILE PRO ALA GLN TYR SEQRES 24 A 329 VAL ARG VAL TYR PRO GLU ARG TRP SER PRO ALA GLY ILE SEQRES 25 A 329 GLY MET ARG LEU GLU VAL LEU GLY CYS ASP TRP THR SER SEQRES 26 A 329 ILE ILE ARG ARG SEQRES 1 B 329 GLY SER HIS MET GLN CYS ASN VAL PRO LEU GLY MET GLU SEQRES 2 B 329 SER GLY ARG ILE ALA ASN GLU GLN ILE SER ALA SER SER SEQRES 3 B 329 THR TYR SER ASP GLY ARG TRP THR PRO GLN GLN SER ARG SEQRES 4 B 329 LEU HIS GLY ASP ASP ASN GLY TRP THR PRO ASN LEU ASP SEQRES 5 B 329 SER ASN LYS GLU TYR LEU GLN VAL ASP LEU ARG PHE LEU SEQRES 6 B 329 THR MET LEU THR ALA ILE ALA THR GLN GLY ALA ILE SER SEQRES 7 B 329 ARG GLU THR GLN ASN GLY TYR TYR VAL LYS SER TYR LYS SEQRES 8 B 329 LEU GLU VAL SER THR ASN GLY GLU ASP TRP MET VAL TYR SEQRES 9 B 329 ARG HIS GLY LYS ASN HIS LYS VAL PHE GLN ALA ASN ASN SEQRES 10 B 329 ASP ALA THR GLU VAL VAL LEU ASN LYS LEU HIS ALA PRO SEQRES 11 B 329 LEU LEU THR ARG PHE VAL ARG ILE ARG PRO GLN THR TRP SEQRES 12 B 329 HIS SER GLY ILE ALA LEU ARG LEU GLU LEU PHE GLY CYS SEQRES 13 B 329 ARG VAL THR ASP ALA PRO CYS SER ASN MET LEU GLY MET SEQRES 14 B 329 LEU SER GLY LEU ILE ALA ASP SER GLN ILE SER ALA SER SEQRES 15 B 329 SER THR GLN GLU TYR LEU TRP SER PRO SER ALA ALA ARG SEQRES 16 B 329 LEU VAL SER SER ARG SER GLY TRP PHE PRO ARG ILE PRO SEQRES 17 B 329 GLN ALA GLN PRO GLY GLU GLU TRP LEU GLN VAL ASP LEU SEQRES 18 B 329 GLY THR PRO LYS THR VAL LYS GLY VAL ILE ILE GLN GLY SEQRES 19 B 329 ALA ARG GLY GLY ASP SER ILE THR ALA VAL GLU ALA ARG SEQRES 20 B 329 ALA PHE VAL ARG LYS PHE LYS VAL SER TYR SER LEU ASN SEQRES 21 B 329 GLY LYS ASP TRP GLU TYR ILE GLN ASP PRO ARG THR GLN SEQRES 22 B 329 GLN PRO LYS LEU PHE GLU GLY ASN MET HIS TYR ASP THR SEQRES 23 B 329 PRO ASP ILE ARG ARG PHE ASP PRO ILE PRO ALA GLN TYR SEQRES 24 B 329 VAL ARG VAL TYR PRO GLU ARG TRP SER PRO ALA GLY ILE SEQRES 25 B 329 GLY MET ARG LEU GLU VAL LEU GLY CYS ASP TRP THR SER SEQRES 26 B 329 ILE ILE ARG ARG HET GOL A 701 6 HET GOL A 702 6 HET GOL A 703 6 HET SO4 A 704 5 HET GOL B 701 6 HET SO4 B 702 5 HETNAM GOL GLYCEROL HETNAM SO4 SULFATE ION HETSYN GOL GLYCERIN; PROPANE-1,2,3-TRIOL FORMUL 3 GOL 4(C3 H8 O3) FORMUL 6 SO4 2(O4 S 2-) FORMUL 9 HOH *327(H2 O) HELIX 1 1 ALA A 289 GLU A 291 5 3 HELIX 2 2 THR A 305 SER A 309 5 5 HELIX 3 3 ARG A 428 ALA A 432 5 5 HELIX 4 4 ALA A 446 SER A 448 5 3 HELIX 5 5 SER A 461 ARG A 466 5 6 HELIX 6 6 ALA B 289 GLU B 291 5 3 HELIX 7 7 THR B 305 SER B 309 5 5 HELIX 8 8 THR B 430 ALA B 432 5 3 HELIX 9 9 ALA B 446 SER B 448 5 3 HELIX 10 10 SER B 461 ARG B 466 5 6 SHEET 1 A 6 VAL A 279 PRO A 280 0 SHEET 2 A 6 ARG A 421 CYS A 427 -1 O GLY A 426 N VAL A 279 SHEET 3 A 6 LEU A 329 GLN A 345 -1 N MET A 338 O CYS A 427 SHEET 4 A 6 VAL A 394 HIS A 415 -1 O ASN A 396 N ILE A 342 SHEET 5 A 6 GLY A 355 SER A 366 -1 N SER A 360 O GLN A 412 SHEET 6 A 6 PHE A 384 GLN A 385 -1 O PHE A 384 N TYR A 361 SHEET 1 B 3 ILE A 293 ALA A 295 0 SHEET 2 B 3 LEU A 329 GLN A 345 -1 O GLN A 330 N SER A 294 SHEET 3 B 3 VAL A 394 HIS A 415 -1 O ASN A 396 N ILE A 342 SHEET 1 C 3 ALA A 347 ILE A 348 0 SHEET 2 C 3 GLY A 355 SER A 366 -1 O TYR A 356 N ALA A 347 SHEET 3 C 3 MET A 373 VAL A 374 -1 O MET A 373 N VAL A 365 SHEET 1 D 2 ARG A 376 HIS A 377 0 SHEET 2 D 2 ASN A 380 HIS A 381 -1 O ASN A 380 N HIS A 377 SHEET 1 E 5 ILE A 450 ALA A 452 0 SHEET 2 E 5 LEU A 488 GLN A 504 -1 O GLN A 489 N SER A 451 SHEET 3 E 5 ASP A 559 TRP A 578 -1 O GLN A 569 N LEU A 492 SHEET 4 E 5 VAL A 521 SER A 529 -1 N LYS A 523 O GLU A 576 SHEET 5 E 5 PHE A 549 GLU A 550 -1 O PHE A 549 N PHE A 524 SHEET 1 F 5 GLU A 536 TYR A 537 0 SHEET 2 F 5 VAL A 521 SER A 529 -1 N TYR A 528 O GLU A 536 SHEET 3 F 5 ASP A 559 TRP A 578 -1 O GLU A 576 N LYS A 523 SHEET 4 F 5 LEU A 488 GLN A 504 -1 N LEU A 492 O GLN A 569 SHEET 5 F 5 ARG A 586 ASP A 593 -1 O LEU A 590 N GLY A 500 SHEET 1 G 6 VAL B 279 PRO B 280 0 SHEET 2 G 6 ARG B 421 ARG B 428 -1 O GLY B 426 N VAL B 279 SHEET 3 G 6 LEU B 329 GLN B 345 -1 N MET B 338 O CYS B 427 SHEET 4 G 6 VAL B 394 HIS B 415 -1 O LEU B 402 N LEU B 339 SHEET 5 G 6 GLY B 355 SER B 366 -1 N TYR B 357 O HIS B 415 SHEET 6 G 6 PHE B 384 GLN B 385 -1 O PHE B 384 N TYR B 361 SHEET 1 H 3 ILE B 293 ALA B 295 0 SHEET 2 H 3 LEU B 329 GLN B 345 -1 O GLN B 330 N SER B 294 SHEET 3 H 3 VAL B 394 HIS B 415 -1 O LEU B 402 N LEU B 339 SHEET 1 I 3 ALA B 347 ILE B 348 0 SHEET 2 I 3 GLY B 355 SER B 366 -1 O TYR B 356 N ALA B 347 SHEET 3 I 3 MET B 373 VAL B 374 -1 O MET B 373 N VAL B 365 SHEET 1 J 2 ARG B 376 HIS B 377 0 SHEET 2 J 2 ASN B 380 HIS B 381 -1 O ASN B 380 N HIS B 377 SHEET 1 K 6 ASN B 436 MET B 437 0 SHEET 2 K 6 ARG B 586 CYS B 592 -1 O GLY B 591 N ASN B 436 SHEET 3 K 6 LEU B 488 GLN B 504 -1 N GLY B 500 O LEU B 590 SHEET 4 K 6 ASP B 559 TRP B 578 -1 O GLN B 569 N LEU B 492 SHEET 5 K 6 VAL B 521 SER B 529 -1 N LYS B 523 O GLU B 576 SHEET 6 K 6 GLU B 536 TYR B 537 -1 O GLU B 536 N TYR B 528 SHEET 1 L 5 ILE B 450 ALA B 452 0 SHEET 2 L 5 LEU B 488 GLN B 504 -1 O GLN B 489 N SER B 451 SHEET 3 L 5 ASP B 559 TRP B 578 -1 O GLN B 569 N LEU B 492 SHEET 4 L 5 VAL B 521 SER B 529 -1 N LYS B 523 O GLU B 576 SHEET 5 L 5 PHE B 549 GLU B 550 -1 O PHE B 549 N PHE B 524 SSBOND 1 CYS A 277 CYS A 427 1555 1555 2.04 SSBOND 2 CYS A 434 CYS A 592 1555 1555 2.04 SSBOND 3 CYS B 277 CYS B 427 1555 1555 2.05 SSBOND 4 CYS B 434 CYS B 592 1555 1555 2.05 SITE 1 AC1 7 LYS A 547 PHE A 549 GLU A 550 ARG A 562 SITE 2 AC1 7 HOH A 856 HOH A 868 HOH A 903 SITE 1 AC2 5 ASN A 354 GLY A 355 HIS A 415 ARG A 572 SITE 2 AC2 5 HOH A 942 SITE 1 AC3 8 TRP A 372 MET A 373 VAL A 374 ARG A 376 SITE 2 AC3 8 HIS A 381 HIS A 554 HOH A 833 HOH A 939 SITE 1 AC4 4 HIS A 312 GLN A 345 ARG A 421 LYS A 533 SITE 1 AC5 3 GLY B 355 HIS B 415 SER B 416 SITE 1 AC6 6 TRP B 372 MET B 373 VAL B 374 ARG B 376 SITE 2 AC6 6 HIS B 554 HOH B 829 CRYST1 41.047 120.808 69.837 90.00 103.29 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 0.024362 0.000000 0.005753 0.00000 SCALE2 0.000000 0.008278 0.000000 0.00000 SCALE3 0.000000 0.000000 0.014713 0.00000