HEADER SIGNALING PROTEIN 26-JUL-07 2QQJ TITLE CRYSTAL STRUCTURE OF THE B1B2 DOMAINS FROM HUMAN NEUROPILIN-2 COMPND MOL_ID: 1; COMPND 2 MOLECULE: NEUROPILIN-2; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: F5/8 TYPE C 1 AND C 2 DOMAINS; 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_VECTOR_TYPE: PLASMID; SOURCE 9 EXPRESSION_SYSTEM_PLASMID: PET15B KEYWDS VEGF RECEPTOR, SEMAPHORIN RECEPTOR, DEVELOPMENTAL PROTEIN, KEYWDS 2 DIFFERENTIATION, GLYCOPROTEIN, MEMBRANE, NEUROGENESIS, KEYWDS 3 TRANSMEMBRANE, HORMONE, SIGNALING PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR B.A.APPLETON,C.WIESMANN REVDAT 6 30-AUG-23 2QQJ 1 REMARK SEQADV REVDAT 5 25-OCT-17 2QQJ 1 REMARK REVDAT 4 13-JUL-11 2QQJ 1 VERSN REVDAT 3 24-FEB-09 2QQJ 1 VERSN REVDAT 2 15-JAN-08 2QQJ 1 JRNL REVDAT 1 20-NOV-07 2QQJ 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. 1.95 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) : 1.95 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 20.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 3 NUMBER OF REFLECTIONS : 22404 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) : 0.176 REMARK 3 R VALUE (WORKING SET) : 0.172 REMARK 3 FREE R VALUE : 0.235 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.100 REMARK 3 FREE R VALUE TEST SET COUNT : 1216 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) : 1.95 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.99 REMARK 3 REFLECTION IN BIN (WORKING SET) : 1296 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 99.20 REMARK 3 BIN R VALUE (WORKING SET) : 0.1960 REMARK 3 BIN FREE R VALUE SET COUNT : 63 REMARK 3 BIN FREE R VALUE : 0.2780 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 2503 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 6 REMARK 3 SOLVENT ATOMS : 239 REMARK 3 REMARK 3 B VALUES. REMARK 3 B VALUE TYPE : LIKELY RESIDUAL REMARK 3 FROM WILSON PLOT (A**2) : 32.60 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 22.46 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 2.74000 REMARK 3 B22 (A**2) : -1.22000 REMARK 3 B33 (A**2) : -1.52000 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): 0.168 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.164 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.114 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 7.486 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.961 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.931 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 2579 ; 0.013 ; 0.022 REMARK 3 BOND LENGTHS OTHERS (A): 1789 ; 0.001 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 3503 ; 1.454 ; 1.943 REMARK 3 BOND ANGLES OTHERS (DEGREES): 4319 ; 0.935 ; 3.002 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 316 ; 7.326 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 124 ;35.482 ;23.387 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 425 ;12.992 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 23 ;16.608 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 371 ; 0.091 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 2882 ; 0.005 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): 539 ; 0.001 ; 0.020 REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): 374 ; 0.181 ; 0.200 REMARK 3 NON-BONDED CONTACTS OTHERS (A): 1816 ; 0.201 ; 0.200 REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): 1157 ; 0.174 ; 0.200 REMARK 3 NON-BONDED TORSION OTHERS (A): 1360 ; 0.084 ; 0.200 REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): 172 ; 0.121 ; 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): 10 ; 0.148 ; 0.200 REMARK 3 SYMMETRY VDW OTHERS (A): 52 ; 0.234 ; 0.200 REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): 20 ; 0.191 ; 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): 2023 ; 3.430 ; 2.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): 638 ; 0.720 ; 2.500 REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 2536 ; 4.033 ; 5.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 1205 ; 3.358 ; 2.500 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 965 ; 4.494 ; 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 : 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 276 A 428 REMARK 3 ORIGIN FOR THE GROUP (A): 0.9324 -8.7558 47.6435 REMARK 3 T TENSOR REMARK 3 T11: -0.0633 T22: -0.0746 REMARK 3 T33: -0.0751 T12: -0.0171 REMARK 3 T13: 0.0095 T23: 0.0175 REMARK 3 L TENSOR REMARK 3 L11: 0.5303 L22: 1.4666 REMARK 3 L33: 1.8163 L12: 0.0354 REMARK 3 L13: -0.0168 L23: -0.2776 REMARK 3 S TENSOR REMARK 3 S11: 0.0394 S12: -0.0288 S13: -0.0231 REMARK 3 S21: -0.0206 S22: -0.0046 S23: 0.0380 REMARK 3 S31: -0.0269 S32: 0.0574 S33: -0.0348 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 : A 429 A 595 REMARK 3 ORIGIN FOR THE GROUP (A): 2.6565 23.7085 45.2506 REMARK 3 T TENSOR REMARK 3 T11: -0.0794 T22: -0.0541 REMARK 3 T33: -0.0359 T12: -0.0641 REMARK 3 T13: -0.0298 T23: 0.0066 REMARK 3 L TENSOR REMARK 3 L11: 1.6942 L22: 2.9144 REMARK 3 L33: 2.2929 L12: -0.6933 REMARK 3 L13: -0.1977 L23: -0.1254 REMARK 3 S TENSOR REMARK 3 S11: -0.0861 S12: 0.0132 S13: 0.1101 REMARK 3 S21: 0.3366 S22: 0.0319 S23: -0.0969 REMARK 3 S31: -0.0658 S32: 0.0634 S33: 0.0542 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 2QQJ COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 03-AUG-07. REMARK 100 THE DEPOSITION ID IS D_1000043929. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 09-NOV-05 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 6.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : ALS REMARK 200 BEAMLINE : 5.0.1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.00 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 210 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO, HKL-2000 REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 23691 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.950 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 (%) : 99.8 REMARK 200 DATA REDUNDANCY : 5.300 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : 0.08900 REMARK 200 FOR THE DATA SET : 16.8000 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 (%) : 99.9 REMARK 200 DATA REDUNDANCY IN SHELL : 5.20 REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : 0.53000 REMARK 200 FOR SHELL : 3.100 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: PDB ENTRY 2QQI REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 42.40 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.14 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1 M BIS-TRIS, 20% PEG 5000 MME, PH REMARK 280 6.5, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 297K 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 18.22800 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 60.96450 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 35.25050 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 60.96450 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 18.22800 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 35.25050 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: 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 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 271 REMARK 465 SER A 272 REMARK 465 HIS A 273 REMARK 465 MET A 274 REMARK 465 PHE A 275 REMARK 465 TYR A 458 REMARK 465 ASP A 510 REMARK 465 SER A 511 REMARK 465 ILE A 512 REMARK 465 THR A 513 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 -139.20 51.68 REMARK 500 ARG A 334 -36.62 79.86 REMARK 500 ALA A 386 -126.65 -114.36 REMARK 500 ARG A 405 -51.05 -122.89 REMARK 500 SER A 416 -47.14 78.39 REMARK 500 SER A 416 -44.71 75.66 REMARK 500 VAL A 468 -42.04 70.97 REMARK 500 SER A 472 -101.37 -119.72 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 1 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 2QQI 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: 2QQN RELATED DB: PDB REMARK 900 RELATED ID: 2QQO RELATED DB: PDB DBREF 2QQJ A 275 595 UNP O60462 NRP2_HUMAN 275 595 SEQADV 2QQJ GLY A 271 UNP O60462 EXPRESSION TAG SEQADV 2QQJ SER A 272 UNP O60462 EXPRESSION TAG SEQADV 2QQJ HIS A 273 UNP O60462 EXPRESSION TAG SEQADV 2QQJ MET A 274 UNP O60462 EXPRESSION TAG SEQRES 1 A 325 GLY SER HIS MET PHE GLN CYS ASN VAL PRO LEU GLY MET SEQRES 2 A 325 GLU SER GLY ARG ILE ALA ASN GLU GLN ILE SER ALA SER SEQRES 3 A 325 SER THR TYR SER ASP GLY ARG TRP THR PRO GLN GLN SER SEQRES 4 A 325 ARG LEU HIS GLY ASP ASP ASN GLY TRP THR PRO ASN LEU SEQRES 5 A 325 ASP SER ASN LYS GLU TYR LEU GLN VAL ASP LEU ARG PHE SEQRES 6 A 325 LEU THR MET LEU THR ALA ILE ALA THR GLN GLY ALA ILE SEQRES 7 A 325 SER ARG GLU THR GLN ASN GLY TYR TYR VAL LYS SER TYR SEQRES 8 A 325 LYS LEU GLU VAL SER THR ASN GLY GLU ASP TRP MET VAL SEQRES 9 A 325 TYR ARG HIS GLY LYS ASN HIS LYS VAL PHE GLN ALA ASN SEQRES 10 A 325 ASN ASP ALA THR GLU VAL VAL LEU ASN LYS LEU HIS ALA SEQRES 11 A 325 PRO LEU LEU THR ARG PHE VAL ARG ILE ARG PRO GLN THR SEQRES 12 A 325 TRP HIS SER GLY ILE ALA LEU ARG LEU GLU LEU PHE GLY SEQRES 13 A 325 CYS ARG VAL THR ASP ALA PRO CYS SER ASN MET LEU GLY SEQRES 14 A 325 MET LEU SER GLY LEU ILE ALA ASP SER GLN ILE SER ALA SEQRES 15 A 325 SER SER THR GLN GLU TYR LEU TRP SER PRO SER ALA ALA SEQRES 16 A 325 ARG LEU VAL SER SER ARG SER GLY TRP PHE PRO ARG ILE SEQRES 17 A 325 PRO GLN ALA GLN PRO GLY GLU GLU TRP LEU GLN VAL ASP SEQRES 18 A 325 LEU GLY THR PRO LYS THR VAL LYS GLY VAL ILE ILE GLN SEQRES 19 A 325 GLY ALA ARG GLY GLY ASP SER ILE THR ALA VAL GLU ALA SEQRES 20 A 325 ARG ALA PHE VAL ARG LYS PHE LYS VAL SER TYR SER LEU SEQRES 21 A 325 ASN GLY LYS ASP TRP GLU TYR ILE GLN ASP PRO ARG THR SEQRES 22 A 325 GLN GLN PRO LYS LEU PHE GLU GLY ASN MET HIS TYR ASP SEQRES 23 A 325 THR PRO ASP ILE ARG ARG PHE ASP PRO ILE PRO ALA GLN SEQRES 24 A 325 TYR VAL ARG VAL TYR PRO GLU ARG TRP SER PRO ALA GLY SEQRES 25 A 325 ILE GLY MET ARG LEU GLU VAL LEU GLY CYS ASP TRP THR HET GOL A 1 6 HETNAM GOL GLYCEROL HETSYN GOL GLYCERIN; PROPANE-1,2,3-TRIOL FORMUL 2 GOL C3 H8 O3 FORMUL 3 HOH *239(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 SHEET 1 A 9 ILE A 293 ALA A 295 0 SHEET 2 A 9 LEU A 329 GLN A 345 -1 O GLN A 330 N SER A 294 SHEET 3 A 9 VAL A 394 HIS A 415 -1 O LEU A 402 N LEU A 339 SHEET 4 A 9 GLY A 355 SER A 366 -1 N TYR A 357 O HIS A 415 SHEET 5 A 9 ALA A 347 ILE A 348 -1 N ALA A 347 O TYR A 356 SHEET 6 A 9 GLY A 355 SER A 366 -1 O TYR A 356 N ALA A 347 SHEET 7 A 9 MET A 373 VAL A 374 -1 O MET A 373 N VAL A 365 SHEET 8 A 9 GLY A 355 SER A 366 -1 N VAL A 365 O MET A 373 SHEET 9 A 9 PHE A 384 GLN A 385 -1 O PHE A 384 N TYR A 361 SHEET 1 B 3 LEU A 329 GLN A 345 0 SHEET 2 B 3 ARG A 421 CYS A 427 -1 O CYS A 427 N MET A 338 SHEET 3 B 3 VAL A 279 PRO A 280 -1 N VAL A 279 O GLY A 426 SHEET 1 C 2 ARG A 376 HIS A 377 0 SHEET 2 C 2 ASN A 380 HIS A 381 -1 O ASN A 380 N HIS A 377 SHEET 1 D 6 ASN A 436 MET A 437 0 SHEET 2 D 6 ARG A 586 ASP A 593 -1 O GLY A 591 N ASN A 436 SHEET 3 D 6 LEU A 488 GLN A 504 -1 N THR A 497 O CYS A 592 SHEET 4 D 6 ASP A 559 TRP A 578 -1 O GLN A 569 N LEU A 492 SHEET 5 D 6 VAL A 521 SER A 529 -1 N LYS A 523 O GLU A 576 SHEET 6 D 6 GLU A 536 TYR A 537 -1 O GLU A 536 N TYR A 528 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 2 GLN A 539 ASP A 540 0 SHEET 2 F 2 GLN A 545 PRO A 546 -1 O GLN A 545 N ASP A 540 SSBOND 1 CYS A 277 CYS A 427 1555 1555 2.01 SSBOND 2 CYS A 434 CYS A 592 1555 1555 2.04 SITE 1 AC1 8 ASN A 278 TYR A 528 ILE A 538 GLN A 539 SITE 2 AC1 8 HOH A 641 HOH A 690 HOH A 710 HOH A 810 CRYST1 36.456 70.501 121.929 90.00 90.00 90.00 P 21 21 21 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 0.027430 0.000000 0.000000 0.00000 SCALE2 0.000000 0.014184 0.000000 0.00000 SCALE3 0.000000 0.000000 0.008201 0.00000