PDB Short entry for 3NVN HEADER VIRAL PROTEIN/SIGNALING PROTEIN 08-JUL-10 3NVN TITLE MOLECULAR MECHANISM OF GUIDANCE CUE RECOGNITION COMPND MOL_ID: 1; COMPND 2 MOLECULE: EVM139; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: UNP RESIDUES 15-399; COMPND 5 SYNONYM: SEMAPHORIN; COMPND 6 ENGINEERED: YES; COMPND 7 MOL_ID: 2; COMPND 8 MOLECULE: PLEXIN-C1; COMPND 9 CHAIN: B; COMPND 10 FRAGMENT: UNP RESIDUES 35-507; COMPND 11 SYNONYM: VIRUS-ENCODED SEMAPHORIN PROTEIN RECEPTOR; COMPND 12 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: ECTROMELIA VIRUS; SOURCE 3 ORGANISM_TAXID: 12643; SOURCE 4 GENE: SEMA; SOURCE 5 EXPRESSION_SYSTEM: HOMO SAPIENS; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 9606; SOURCE 7 EXPRESSION_SYSTEM_CELL: HEK293S; SOURCE 8 MOL_ID: 2; SOURCE 9 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 10 ORGANISM_COMMON: HUMAN; SOURCE 11 ORGANISM_TAXID: 9606; SOURCE 12 GENE: PLXNC1, VESPR; SOURCE 13 EXPRESSION_SYSTEM: HOMO SAPIENS; SOURCE 14 EXPRESSION_SYSTEM_TAXID: 9606; SOURCE 15 EXPRESSION_SYSTEM_CELL: HEK293S KEYWDS BETA-PROPELLER, SIGNALING, VIRAL PROTEIN-SIGNALING PROTEIN COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR H.LIU,Z.JUO,A.SHIM,P.FOCIA,X.CHEN,C.GARCIA,X.HE REVDAT 2 29-JUL-20 3NVN 1 COMPND REMARK SEQADV HETNAM REVDAT 2 2 1 LINK SITE ATOM REVDAT 1 15-SEP-10 3NVN 0 JRNL AUTH H.LIU,Z.S.JUO,A.H.SHIM,P.J.FOCIA,X.CHEN,K.C.GARCIA,X.HE JRNL TITL STRUCTURAL BASIS OF SEMAPHORIN-PLEXIN RECOGNITION AND VIRAL JRNL TITL 2 MIMICRY FROM SEMA7A AND A39R COMPLEXES WITH PLEXINC1. JRNL REF CELL(CAMBRIDGE,MASS.) V. 142 749 2010 JRNL REFN ISSN 0092-8674 JRNL PMID 20727575 JRNL DOI 10.1016/J.CELL.2010.07.040 REMARK 2 REMARK 2 RESOLUTION. 2.26 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : CNS 1.1 REMARK 3 AUTHORS : BRUNGER,ADAMS,CLORE,DELANO,GROS,GROSSE- REMARK 3 : KUNSTLEVE,JIANG,KUSZEWSKI,NILGES,PANNU, REMARK 3 : READ,RICE,SIMONSON,WARREN REMARK 3 REMARK 3 REFINEMENT TARGET : ENGH & HUBER REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.26 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 43.53 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 DATA CUTOFF HIGH (ABS(F)) : 6766291.520 REMARK 3 DATA CUTOFF LOW (ABS(F)) : 0.0000 REMARK 3 COMPLETENESS (WORKING+TEST) (%) : 99.5 REMARK 3 NUMBER OF REFLECTIONS : 51699 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 SET) : 0.239 REMARK 3 FREE R VALUE : 0.276 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 2595 REMARK 3 ESTIMATED ERROR OF FREE R VALUE : 0.005 REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : 6 REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 2.26 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.40 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 99.00 REMARK 3 REFLECTIONS IN BIN (WORKING SET) : 8049 REMARK 3 BIN R VALUE (WORKING SET) : 0.3870 REMARK 3 BIN FREE R VALUE : 0.3980 REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : 5.10 REMARK 3 BIN FREE R VALUE TEST SET COUNT : 431 REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : 0.019 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 6674 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 113 REMARK 3 SOLVENT ATOMS : 509 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 13.20 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 47.90 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 10.80000 REMARK 3 B22 (A**2) : -6.94000 REMARK 3 B33 (A**2) : -3.86000 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 COORDINATE ERROR. REMARK 3 ESD FROM LUZZATI PLOT (A) : 0.34 REMARK 3 ESD FROM SIGMAA (A) : 0.54 REMARK 3 LOW RESOLUTION CUTOFF (A) : 5.00 REMARK 3 REMARK 3 CROSS-VALIDATED ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM C-V LUZZATI PLOT (A) : 0.40 REMARK 3 ESD FROM C-V SIGMAA (A) : 0.58 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.008 REMARK 3 BOND ANGLES (DEGREES) : 1.300 REMARK 3 DIHEDRAL ANGLES (DEGREES) : 26.10 REMARK 3 IMPROPER ANGLES (DEGREES) : 1.010 REMARK 3 REMARK 3 ISOTROPIC THERMAL MODEL : RESTRAINED REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. RMS SIGMA REMARK 3 MAIN-CHAIN BOND (A**2) : NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE (A**2) : NULL ; NULL REMARK 3 SIDE-CHAIN BOND (A**2) : NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE (A**2) : NULL ; NULL REMARK 3 REMARK 3 BULK SOLVENT MODELING. REMARK 3 METHOD USED : FLAT MODEL REMARK 3 KSOL : 0.31 REMARK 3 BSOL : 39.78 REMARK 3 REMARK 3 NCS MODEL : NONE REMARK 3 REMARK 3 NCS RESTRAINTS. RMS SIGMA/WEIGHT REMARK 3 GROUP 1 POSITIONAL (A) : NULL ; NULL REMARK 3 GROUP 1 B-FACTOR (A**2) : NULL ; NULL REMARK 3 REMARK 3 PARAMETER FILE 1 : PROTEIN_REP.PARAM REMARK 3 PARAMETER FILE 2 : WATER_REP.PARAM REMARK 3 PARAMETER FILE 3 : CARBOHYDRATE.PARAM REMARK 3 PARAMETER FILE 4 : ION.PARAM REMARK 3 PARAMETER FILE 5 : NULL REMARK 3 TOPOLOGY FILE 1 : PROTEIN.TOP REMARK 3 TOPOLOGY FILE 2 : WATER.TOP REMARK 3 TOPOLOGY FILE 3 : CARBOHYDRATE.TOP REMARK 3 TOPOLOGY FILE 4 : ION.TOP REMARK 3 TOPOLOGY FILE 5 : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: BULK SOLVENT MODEL USED REMARK 4 REMARK 4 3NVN COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 20-JUL-10. REMARK 100 THE DEPOSITION ID IS D_1000060335. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 06-FEB-10 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 7.0 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : APS REMARK 200 BEAMLINE : 21-ID-G REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.97856 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : IMAGE PLATE REMARK 200 DETECTOR MANUFACTURER : MAR SCANNER 300 MM PLATE REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 73704 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.000 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : NULL REMARK 200 DATA REDUNDANCY : 8.400 REMARK 200 R MERGE (I) : 0.08800 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 14.8900 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.00 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.10 REMARK 200 COMPLETENESS FOR SHELL (%) : 95.5 REMARK 200 DATA REDUNDANCY IN SHELL : 4.00 REMARK 200 R MERGE FOR SHELL (I) : 0.29300 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> FOR SHELL : 2.970 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: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 56.79 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.85 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 6% PEG8000, 0.1M HEPES PH7.0, 0.2M REMARK 280 NACL, 0.1M CACL2, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 295K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: C 2 2 21 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,-Y,Z+1/2 REMARK 290 3555 -X,Y,-Z+1/2 REMARK 290 4555 X,-Y,-Z REMARK 290 5555 X+1/2,Y+1/2,Z REMARK 290 6555 -X+1/2,-Y+1/2,Z+1/2 REMARK 290 7555 -X+1/2,Y+1/2,-Z+1/2 REMARK 290 8555 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 0.00000 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 86.11550 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 86.11550 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 5 1.000000 0.000000 0.000000 47.87450 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 66.74700 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 6 -1.000000 0.000000 0.000000 47.87450 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 66.74700 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 86.11550 REMARK 290 SMTRY1 7 -1.000000 0.000000 0.000000 47.87450 REMARK 290 SMTRY2 7 0.000000 1.000000 0.000000 66.74700 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 86.11550 REMARK 290 SMTRY1 8 1.000000 0.000000 0.000000 47.87450 REMARK 290 SMTRY2 8 0.000000 -1.000000 0.000000 66.74700 REMARK 290 SMTRY3 8 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 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 PRO A 12 REMARK 465 GLY A 13 REMARK 465 THR A 14 REMARK 465 LEU A 398 REMARK 465 LYS A 399 REMARK 465 MET A 400 REMARK 465 ALA B 35 REMARK 465 ASP B 36 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 ILE A 397 CG1 CG2 CD1 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 ND2 ASN A 54 C1 NDG A 1 1.44 REMARK 500 ND2 ASN B 407 C1 NDG B 7 1.45 REMARK 500 ND2 ASN B 141 C1 NDG B 2 1.45 REMARK 500 ND2 ASN B 241 C1 NAG B 4 1.62 REMARK 500 ND2 ASN B 149 O5 NAG B 3 1.78 REMARK 500 ND2 ASN B 86 O5 NAG B 1 1.94 REMARK 500 CG ASN B 86 C1 NAG B 1 2.00 REMARK 500 ND2 ASN B 386 O5 NAG B 6 2.03 REMARK 500 OD1 ASN B 86 O HOH B 563 2.11 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND LENGTHS REMARK 500 REMARK 500 THE STEREOCHEMICAL PARAMETERS OF THE FOLLOWING RESIDUES REMARK 500 HAVE VALUES WHICH DEVIATE FROM EXPECTED VALUES BY MORE REMARK 500 THAN 6*RMSD (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 500 IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT: (10X,I3,1X,2(A3,1X,A1,I4,A1,1X,A4,3X),1X,F6.3) REMARK 500 REMARK 500 EXPECTED VALUES PROTEIN: ENGH AND HUBER, 1999 REMARK 500 EXPECTED VALUES NUCLEIC ACID: CLOWNEY ET AL 1996 REMARK 500 REMARK 500 M RES CSSEQI ATM1 RES CSSEQI ATM2 DEVIATION REMARK 500 SER A 201 CB SER A 201 OG -0.289 REMARK 500 ASN B 86 CB ASN B 86 CG -0.149 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 200 C - N - CD ANGL. DEV. = -18.2 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 ILE A 33 -81.89 -123.36 REMARK 500 ASP A 34 54.80 -99.91 REMARK 500 THR A 59 104.23 -52.87 REMARK 500 ASN A 61 -92.33 -159.16 REMARK 500 VAL A 71 -119.56 -103.85 REMARK 500 ASN A 80 -155.03 57.20 REMARK 500 ASN A 81 50.58 -98.62 REMARK 500 ASP A 90 63.71 -103.90 REMARK 500 SER A 92 178.62 61.61 REMARK 500 ASP A 94 98.67 84.13 REMARK 500 HIS A 115 -87.03 -79.35 REMARK 500 GLU A 117 0.01 -153.54 REMARK 500 ILE A 130 84.30 45.69 REMARK 500 ASP A 179 79.09 -117.46 REMARK 500 THR A 180 -78.33 -93.46 REMARK 500 CYS A 218 82.92 -153.49 REMARK 500 ASP A 239 -151.92 -156.33 REMARK 500 TYR A 250 -141.63 -101.85 REMARK 500 GLU A 335 109.16 48.65 REMARK 500 ASN A 336 89.61 -43.79 REMARK 500 GLU A 337 -24.08 -175.02 REMARK 500 LYS A 347 -156.02 -121.41 REMARK 500 ASP A 367 53.63 -93.97 REMARK 500 THR A 376 -100.40 -111.26 REMARK 500 SER B 61 -83.42 -109.52 REMARK 500 ASP B 82 -74.27 -82.08 REMARK 500 ASN B 86 120.91 -33.60 REMARK 500 GLU B 89 106.50 -44.93 REMARK 500 PRO B 95 95.83 -53.19 REMARK 500 PRO B 96 -161.49 -58.75 REMARK 500 PRO B 188 -80.48 -70.62 REMARK 500 ARG B 193 106.22 -18.84 REMARK 500 TRP B 240 -71.88 -141.83 REMARK 500 THR B 259 44.48 -103.86 REMARK 500 GLU B 316 -61.31 -157.10 REMARK 500 GLN B 318 16.59 171.57 REMARK 500 GLU B 319 -82.48 -42.18 REMARK 500 ARG B 320 57.95 -68.04 REMARK 500 PRO B 323 9.55 -65.03 REMARK 500 TRP B 345 -55.09 -132.25 REMARK 500 HIS B 353 -100.86 -72.22 REMARK 500 GLU B 356 62.08 -104.08 REMARK 500 PRO B 365 39.96 -87.11 REMARK 500 ILE B 366 105.15 58.13 REMARK 500 THR B 377 -16.51 -140.38 REMARK 500 VAL B 384 -80.00 -93.94 REMARK 500 ASN B 386 1.46 -166.56 REMARK 500 GLU B 406 -80.85 -58.05 REMARK 500 ASN B 407 44.26 -91.47 REMARK 500 ALA B 509 119.71 -10.73 REMARK 500 REMARK 500 REMARK: NULL REMARK 610 REMARK 610 MISSING HETEROATOM REMARK 610 THE FOLLOWING RESIDUES HAVE MISSING ATOMS (M=MODEL NUMBER; REMARK 610 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 610 I=INSERTION CODE): REMARK 610 M RES C SSEQI REMARK 610 NDG A 1 REMARK 610 NDG B 2 REMARK 610 NAG B 4 REMARK 610 NDG B 7 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 B 801 CA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 GLU B 301 O REMARK 620 2 ASP B 304 OD1 99.3 REMARK 620 3 HOH B 571 O 98.1 145.7 REMARK 620 4 HOH B 655 O 103.5 90.9 56.2 REMARK 620 5 HOH B 656 O 76.4 127.0 85.8 141.9 REMARK 620 6 HOH B 706 O 112.5 78.1 121.3 143.5 57.1 REMARK 620 N 1 2 3 4 5 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 3NVX RELATED DB: PDB REMARK 900 RELATED ID: 3NVQ RELATED DB: PDB DBREF 3NVN A 16 400 UNP Q8JL80 Q8JL80_9POXV 15 399 DBREF 3NVN B 35 507 UNP O60486 PLXC1_HUMAN 35 507 SEQADV 3NVN PRO A 12 UNP Q8JL80 EXPRESSION TAG SEQADV 3NVN GLY A 13 UNP Q8JL80 EXPRESSION TAG SEQADV 3NVN THR A 14 UNP Q8JL80 EXPRESSION TAG SEQADV 3NVN SER A 15 UNP Q8JL80 EXPRESSION TAG SEQADV 3NVN GLY B 508 UNP O60486 EXPRESSION TAG SEQADV 3NVN ALA B 509 UNP O60486 EXPRESSION TAG SEQADV 3NVN PRO B 510 UNP O60486 EXPRESSION TAG SEQRES 1 A 389 PRO GLY THR SER ILE GLU TRP HIS LYS PHE GLU THR SER SEQRES 2 A 389 GLU GLU ILE ILE SER THR TYR LEU ILE ASP ASP VAL LEU SEQRES 3 A 389 TYR THR GLY VAL ASN GLY ALA VAL TYR THR PHE SER ASN SEQRES 4 A 389 ASN GLU LEU ASN LYS THR GLY LEU THR ASN ASN ASN ASN SEQRES 5 A 389 TYR ILE THR THR SER ILE LYS VAL GLU ASP THR LEU VAL SEQRES 6 A 389 CYS GLY THR ASN ASN GLY ASN PRO LYS CYS TRP LYS ILE SEQRES 7 A 389 ASP GLY SER GLU ASP PRO LYS TYR ARG GLY ARG GLY TYR SEQRES 8 A 389 ALA PRO TYR GLN ASN SER LYS VAL THR ILE ILE SER HIS SEQRES 9 A 389 ASN GLU CYS VAL LEU SER ASP ILE ASN ILE SER LYS GLU SEQRES 10 A 389 GLY ILE LYS ARG TRP ARG ARG PHE ASP GLY PRO CYS GLY SEQRES 11 A 389 TYR ASP LEU TYR THR ALA ASP ASN VAL ILE PRO LYS ASP SEQRES 12 A 389 GLY VAL ARG GLY ALA PHE VAL ASP LYS ASP GLY THR TYR SEQRES 13 A 389 ASP LYS VAL TYR ILE LEU PHE THR ASP THR ILE ASP THR SEQRES 14 A 389 LYS ARG ILE VAL LYS ILE PRO TYR ILE ALA GLN MET CYS SEQRES 15 A 389 LEU ASN ASP GLU GLY GLY PRO SER SER LEU SER SER HIS SEQRES 16 A 389 ARG TRP SER THR PHE LEU LYS VAL GLU LEU GLU CYS ASP SEQRES 17 A 389 ILE ASP GLY ARG SER TYR ARG GLN ILE ILE HIS SER LYS SEQRES 18 A 389 ALA ILE LYS THR ASP ASN ASP THR ILE LEU TYR VAL PHE SEQRES 19 A 389 PHE ASP SER PRO TYR SER LYS SER ALA LEU CYS THR TYR SEQRES 20 A 389 SER MET ASN ALA ILE LYS HIS SER PHE SER THR SER LYS SEQRES 21 A 389 LEU GLY GLY TYR THR LYS GLN LEU PRO SER PRO ALA PRO SEQRES 22 A 389 GLY ILE CYS LEU PRO ALA GLY LYS VAL VAL PRO HIS THR SEQRES 23 A 389 THR PHE ASP ILE ILE GLU GLN TYR ASN GLU LEU ASP ASP SEQRES 24 A 389 ILE ILE LYS PRO LEU SER GLN PRO ILE PHE GLU GLY PRO SEQRES 25 A 389 SER GLY VAL LYS TRP PHE ASP ILE LYS GLU LYS GLU ASN SEQRES 26 A 389 GLU HIS ARG GLU TYR ARG ILE TYR PHE ILE LYS GLU ASN SEQRES 27 A 389 THR ILE TYR SER PHE ASP THR LYS SER LYS GLN THR ARG SEQRES 28 A 389 SER ALA GLN VAL ASP ALA ARG LEU PHE SER VAL MET VAL SEQRES 29 A 389 THR SER LYS PRO LEU PHE ILE ALA ASP ILE GLY ILE GLY SEQRES 30 A 389 VAL GLY ILE PRO ARG MET LYS LYS ILE LEU LYS MET SEQRES 1 B 476 ALA ASP GLU PRO VAL TRP ARG SER GLU GLN ALA ILE GLY SEQRES 2 B 476 ALA ILE ALA ALA SER GLN GLU ASP GLY VAL PHE VAL ALA SEQRES 3 B 476 SER GLY SER CYS LEU ASP GLN LEU ASP TYR SER LEU GLU SEQRES 4 B 476 HIS SER LEU SER ARG LEU TYR ARG ASP GLN ALA GLY ASN SEQRES 5 B 476 CYS THR GLU PRO VAL SER LEU ALA PRO PRO ALA ARG PRO SEQRES 6 B 476 ARG PRO GLY SER SER PHE SER LYS LEU LEU LEU PRO TYR SEQRES 7 B 476 ARG GLU GLY ALA ALA GLY LEU GLY GLY LEU LEU LEU THR SEQRES 8 B 476 GLY TRP THR PHE ASP ARG GLY ALA CYS GLU VAL ARG PRO SEQRES 9 B 476 LEU GLY ASN LEU SER ARG ASN SER LEU ARG ASN GLY THR SEQRES 10 B 476 GLU VAL VAL SER CYS HIS PRO GLN GLY SER THR ALA GLY SEQRES 11 B 476 VAL VAL TYR ARG ALA GLY ARG ASN ASN ARG TRP TYR LEU SEQRES 12 B 476 ALA VAL ALA ALA THR TYR VAL LEU PRO GLU PRO GLU THR SEQRES 13 B 476 ALA SER ARG CYS ASN PRO ALA ALA SER ASP HIS ASP THR SEQRES 14 B 476 ALA ILE ALA LEU LYS ASP THR GLU GLY ARG SER LEU ALA SEQRES 15 B 476 THR GLN GLU LEU GLY ARG LEU LYS LEU CYS GLU GLY ALA SEQRES 16 B 476 GLY SER LEU HIS PHE VAL ASP ALA PHE LEU TRP ASN GLY SEQRES 17 B 476 SER ILE TYR PHE PRO TYR TYR PRO TYR ASN TYR THR SER SEQRES 18 B 476 GLY ALA ALA THR GLY TRP PRO SER MET ALA ARG ILE ALA SEQRES 19 B 476 GLN SER THR GLU VAL LEU PHE GLN GLY GLN ALA SER LEU SEQRES 20 B 476 ASP CYS GLY HIS GLY HIS PRO ASP GLY ARG ARG LEU LEU SEQRES 21 B 476 LEU SER SER SER LEU VAL GLU ALA LEU ASP VAL TRP ALA SEQRES 22 B 476 GLY VAL PHE SER ALA ALA ALA GLY GLU GLY GLN GLU ARG SEQRES 23 B 476 ARG SER PRO THR THR THR ALA LEU CYS LEU PHE ARG MET SEQRES 24 B 476 SER GLU ILE GLN ALA ARG ALA LYS ARG VAL SER TRP ASP SEQRES 25 B 476 PHE LYS THR ALA GLU SER HIS CYS LYS GLU GLY ASP GLN SEQRES 26 B 476 PRO GLU ARG VAL GLN PRO ILE ALA SER SER THR LEU ILE SEQRES 27 B 476 HIS SER ASP LEU THR SER VAL TYR GLY THR VAL VAL MET SEQRES 28 B 476 ASN ARG THR VAL LEU PHE LEU GLY THR GLY ASP GLY GLN SEQRES 29 B 476 LEU LEU LYS VAL ILE LEU GLY GLU ASN LEU THR SER ASN SEQRES 30 B 476 CYS PRO GLU VAL ILE TYR GLU ILE LYS GLU GLU THR PRO SEQRES 31 B 476 VAL PHE TYR LYS LEU VAL PRO ASP PRO VAL LYS ASN ILE SEQRES 32 B 476 TYR ILE TYR LEU THR ALA GLY LYS GLU VAL ARG ARG ILE SEQRES 33 B 476 ARG VAL ALA ASN CYS ASN LYS HIS LYS SER CYS SER GLU SEQRES 34 B 476 CYS LEU THR ALA THR ASP PRO HIS CYS GLY TRP CYS HIS SEQRES 35 B 476 SER LEU GLN ARG CYS THR PHE GLN GLY ASP CYS VAL HIS SEQRES 36 B 476 SER GLU ASN LEU GLU ASN TRP LEU ASP ILE SER SER GLY SEQRES 37 B 476 ALA LYS LYS CYS PRO GLY ALA PRO MODRES 3NVN ASN B 86 ASN GLYCOSYLATION SITE MODRES 3NVN ASN B 386 ASN GLYCOSYLATION SITE MODRES 3NVN ASN B 252 ASN GLYCOSYLATION SITE MODRES 3NVN ASN B 149 ASN GLYCOSYLATION SITE HET NDG A 1 14 HET CA B 801 1 HET NAG B 1 14 HET NDG B 2 14 HET NAG B 3 14 HET NAG B 4 14 HET NAG B 5 14 HET NAG B 6 14 HET NDG B 7 14 HETNAM NDG 2-ACETAMIDO-2-DEOXY-ALPHA-D-GLUCOPYRANOSE HETNAM CA CALCIUM ION HETNAM NAG 2-ACETAMIDO-2-DEOXY-BETA-D-GLUCOPYRANOSE FORMUL 3 NDG 3(C8 H15 N O6) FORMUL 4 CA CA 2+ FORMUL 5 NAG 5(C8 H15 N O6) FORMUL 12 HOH *509(H2 O) HELIX 1 1 MET A 260 SER A 270 1 11 HELIX 2 2 PRO A 295 TYR A 305 1 11 HELIX 3 3 THR B 128 ALA B 133 1 6 HELIX 4 4 ALA B 197 HIS B 201 5 5 HELIX 5 5 GLY B 212 ALA B 216 5 5 HELIX 6 6 MET B 333 ALA B 340 1 8 HELIX 7 7 SER B 460 THR B 466 1 7 HELIX 8 8 GLY B 485 CYS B 487 5 3 HELIX 9 9 GLY B 502 CYS B 506 5 5 SHEET 1 A 4 GLU A 17 LYS A 20 0 SHEET 2 A 4 GLY A 386 VAL A 389 -1 O VAL A 389 N GLU A 17 SHEET 3 A 4 PRO A 379 ALA A 383 -1 N ALA A 383 O GLY A 386 SHEET 4 A 4 LEU A 370 VAL A 375 -1 N PHE A 371 O ILE A 382 SHEET 1 B 4 ILE A 27 LEU A 32 0 SHEET 2 B 4 LEU A 37 VAL A 41 -1 O GLY A 40 N SER A 29 SHEET 3 B 4 ALA A 44 SER A 49 -1 O TYR A 46 N THR A 39 SHEET 4 B 4 GLU A 52 GLY A 57 -1 O ASN A 54 N THR A 47 SHEET 1 C 3 ILE A 65 LYS A 70 0 SHEET 2 C 3 THR A 74 GLY A 78 -1 O LEU A 75 N ILE A 69 SHEET 3 C 3 LYS A 85 LYS A 88 -1 O TRP A 87 N VAL A 76 SHEET 1 D 4 ILE A 112 SER A 114 0 SHEET 2 D 4 VAL A 119 SER A 121 -1 O LEU A 120 N ILE A 113 SHEET 3 D 4 ARG A 134 ARG A 135 -1 O ARG A 134 N SER A 121 SHEET 4 D 4 LEU A 144 TYR A 145 -1 O LEU A 144 N ARG A 135 SHEET 1 E 5 GLY A 158 ASP A 164 0 SHEET 2 E 5 TYR A 167 ASP A 179 -1 O TYR A 171 N PHE A 160 SHEET 3 E 5 ILE A 183 CYS A 193 -1 O ILE A 186 N ASP A 176 SHEET 4 E 5 LEU A 212 LEU A 216 -1 O LEU A 212 N GLN A 191 SHEET 5 E 5 GLU A 307 ILE A 312 1 O ILE A 312 N GLU A 215 SHEET 1 F 4 GLN A 227 LYS A 235 0 SHEET 2 F 4 THR A 240 ASP A 247 -1 O TYR A 243 N LYS A 232 SHEET 3 F 4 ALA A 254 SER A 259 -1 O ALA A 254 N PHE A 246 SHEET 4 F 4 PHE A 320 GLU A 321 -1 O PHE A 320 N LEU A 255 SHEET 1 G 5 TRP A 328 GLU A 333 0 SHEET 2 G 5 TYR A 341 ILE A 346 -1 O TYR A 344 N ASP A 330 SHEET 3 G 5 THR A 350 ASP A 355 -1 O PHE A 354 N ILE A 343 SHEET 4 G 5 THR A 361 GLN A 365 -1 O ALA A 364 N ILE A 351 SHEET 5 G 5 LYS A 395 LYS A 396 -1 O LYS A 395 N SER A 363 SHEET 1 H 4 VAL B 39 ARG B 41 0 SHEET 2 H 4 GLU B 446 ARG B 451 -1 O VAL B 447 N TRP B 40 SHEET 3 H 4 TYR B 438 ALA B 443 -1 N LEU B 441 O ARG B 448 SHEET 4 H 4 VAL B 430 PRO B 431 -1 N VAL B 430 O TYR B 440 SHEET 1 I 4 ALA B 48 ALA B 51 0 SHEET 2 I 4 VAL B 57 ALA B 60 -1 O ALA B 60 N ALA B 48 SHEET 3 I 4 CYS B 64 LEU B 68 -1 O ASP B 66 N VAL B 59 SHEET 4 I 4 SER B 75 TYR B 80 -1 O SER B 77 N GLN B 67 SHEET 1 J 4 SER B 106 TYR B 112 0 SHEET 2 J 4 LEU B 122 TRP B 127 -1 O LEU B 122 N TYR B 112 SHEET 3 J 4 CYS B 134 PRO B 138 -1 O ARG B 137 N LEU B 123 SHEET 4 J 4 ASN B 149 GLY B 150 -1 O GLY B 150 N CYS B 134 SHEET 1 K 4 THR B 162 ALA B 169 0 SHEET 2 K 4 ARG B 174 ALA B 181 -1 O TYR B 176 N TYR B 167 SHEET 3 K 4 THR B 203 ASP B 209 -1 O LYS B 208 N LEU B 177 SHEET 4 K 4 ARG B 222 LYS B 224 -1 O LEU B 223 N ILE B 205 SHEET 1 L 3 LEU B 232 PHE B 234 0 SHEET 2 L 3 SER B 243 ASN B 252 -1 O TYR B 249 N HIS B 233 SHEET 3 L 3 ALA B 257 ALA B 258 -1 O ALA B 257 N ASN B 252 SHEET 1 M 5 PHE B 238 LEU B 239 0 SHEET 2 M 5 SER B 243 ASN B 252 -1 O TYR B 245 N PHE B 238 SHEET 3 M 5 SER B 263 ALA B 268 -1 O ILE B 267 N ILE B 244 SHEET 4 M 5 PHE B 275 LEU B 281 -1 O GLN B 276 N ARG B 266 SHEET 5 M 5 GLU B 361 VAL B 363 1 O GLU B 361 N SER B 280 SHEET 1 N 4 LEU B 293 LEU B 299 0 SHEET 2 N 4 VAL B 305 SER B 311 -1 O ALA B 307 N SER B 298 SHEET 3 N 4 THR B 326 ARG B 332 -1 O PHE B 331 N TRP B 306 SHEET 4 N 4 LEU B 371 HIS B 373 -1 O HIS B 373 N THR B 326 SHEET 1 O 4 LEU B 376 VAL B 383 0 SHEET 2 O 4 THR B 388 THR B 394 -1 O VAL B 389 N THR B 382 SHEET 3 O 4 GLN B 398 ILE B 403 -1 O VAL B 402 N LEU B 390 SHEET 4 O 4 GLU B 414 GLU B 418 -1 O TYR B 417 N LEU B 399 SHEET 1 P 3 ARG B 480 PHE B 483 0 SHEET 2 P 3 CYS B 472 CYS B 475 -1 N CYS B 475 O ARG B 480 SHEET 3 P 3 TRP B 496 LEU B 497 -1 O LEU B 497 N TRP B 474 SSBOND 1 CYS A 77 CYS A 86 1555 1555 2.04 SSBOND 2 CYS A 118 CYS A 140 1555 1555 2.03 SSBOND 3 CYS A 193 CYS A 287 1555 1555 2.05 SSBOND 4 CYS A 218 CYS A 256 1555 1555 2.04 SSBOND 5 CYS B 64 CYS B 87 1555 1555 2.03 SSBOND 6 CYS B 156 CYS B 194 1555 1555 2.03 SSBOND 7 CYS B 226 CYS B 354 1555 1555 2.04 SSBOND 8 CYS B 283 CYS B 329 1555 1555 2.03 SSBOND 9 CYS B 455 CYS B 472 1555 1555 2.04 SSBOND 10 CYS B 461 CYS B 506 1555 1555 2.04 SSBOND 11 CYS B 464 CYS B 481 1555 1555 2.01 SSBOND 12 CYS B 475 CYS B 487 1555 1555 2.03 LINK C1 NAG B 1 ND2 ASN B 86 1555 1555 1.37 LINK C1 NAG B 3 ND2 ASN B 149 1555 1555 1.53 LINK C1 NAG B 5 ND2 ASN B 252 1555 1555 1.52 LINK C1 NAG B 6 ND2 ASN B 386 1555 1555 1.45 LINK O GLU B 301 CA CA B 801 1555 1555 2.22 LINK OD1 ASP B 304 CA CA B 801 1555 1555 2.22 LINK O HOH B 571 CA CA B 801 1555 1555 3.20 LINK O HOH B 655 CA CA B 801 1555 1555 2.68 LINK O HOH B 656 CA CA B 801 1555 1555 2.58 LINK O HOH B 706 CA CA B 801 1555 1555 3.06 CISPEP 1 GLN A 317 PRO A 318 0 1.36 CISPEP 2 GLY A 322 PRO A 323 0 -0.61 CRYST1 95.749 133.494 172.231 90.00 90.00 90.00 C 2 2 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 0.010444 0.000000 0.000000 0.00000 SCALE2 0.000000 0.007491 0.000000 0.00000 SCALE3 0.000000 0.000000 0.005806 0.00000