HEADER VIRAL PROTEIN 14-JAN-09 3FUS TITLE IMPROVED STRUCTURE OF THE UNLIGANDED SIMIAN IMMUNODEFICIENCY VIRUS TITLE 2 GP120 CORE CAVEAT 3FUS NAG B 1 HAS WRONG CHIRALITY AT ATOM C1 NAG D 1 HAS WRONG CAVEAT 2 3FUS CHIRALITY AT ATOM C1 NAG G 1 HAS WRONG CHIRALITY AT ATOM C1 CAVEAT 3 3FUS NAG H 1 HAS WRONG CHIRALITY AT ATOM C1 NAG A 1 HAS WRONG CAVEAT 4 3FUS CHIRALITY AT ATOM C1 COMPND MOL_ID: 1; COMPND 2 MOLECULE: EXTERIOR MEMBRANE GLYCOPROTEIN GP120; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: GP120 CORE, RESIDUES 66-109, 209-311, 342-502; COMPND 5 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: SIMIAN IMMUNODEFICIENCY VIRUS; SOURCE 3 ORGANISM_COMMON: SIV-CPZ; SOURCE 4 ORGANISM_TAXID: 11723; SOURCE 5 GENE: ENV; SOURCE 6 EXPRESSION_SYSTEM: TRICHOPLUSIA NI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 7111; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: HI5; SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PFAST-BAC1; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PSIVGP120CORE KEYWDS SIV, AIDS, GP120, STRUCTURAL REFINEMENT, NORMAL MODE, APOPTOSIS, CELL KEYWDS 2 MEMBRANE, ENVELOPE PROTEIN, FUSION PROTEIN, HOST-VIRUS INTERACTION, KEYWDS 3 MEMBRANE, TRANSMEMBRANE, VIRION, VIRAL PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR X.CHEN,B.POON,Q.WANG,J.MA REVDAT 7 16-OCT-24 3FUS 1 HETSYN REVDAT 6 29-JUL-20 3FUS 1 CAVEAT COMPND REMARK HET REVDAT 6 2 1 HETNAM FORMUL LINK SITE REVDAT 6 3 1 ATOM REVDAT 5 26-JUL-17 3FUS 1 SOURCE REVDAT 4 05-OCT-11 3FUS 1 JRNL REMARK REVDAT 3 13-JUL-11 3FUS 1 VERSN REVDAT 2 09-FEB-11 3FUS 1 JRNL REVDAT 1 30-JUN-09 3FUS 0 JRNL AUTH X.CHEN,M.LU,B.K.POON,Q.WANG,J.MA JRNL TITL STRUCTURAL IMPROVEMENT OF UNLIGANDED SIMIAN IMMUNODEFICIENCY JRNL TITL 2 VIRUS GP120 CORE BY NORMAL-MODE-BASED X-RAY CRYSTALLOGRAPHIC JRNL TITL 3 REFINEMENT. JRNL REF ACTA CRYSTALLOGR.,SECT.D V. 65 339 2009 JRNL REFN ISSN 0907-4449 JRNL PMID 19307715 JRNL DOI 10.1107/S0907444909003539 REMARK 0 REMARK 0 THIS ENTRY 3FUS REFLECTS AN ALTERNATIVE MODELING OF THE ORIGINAL REMARK 0 STRUCTURAL DATA (R2BF1SF) DETERMINED BY AUTHORS OF THE PDB ENTRY REMARK 0 2BF1:B.CHEN,E.M.VOGAN,H.GONG,J.J.SKEHEL,D.C.WILEY,S.C.HARRISON REMARK 0 ORIGINAL DATA REFERENCE 1 REMARK 0 PDB ID: 2BF1 REMARK 0 AUTH B.CHEN,E.M.VOGAN,H.GONG,J.J.SKEHEL,D.C.WILEY,S.C.HARRISON REMARK 0 TITL DETERMINING THE STRUCTURE OF AN UNLIGANDED AND FULLY REMARK 0 TITL 2 GLYCOSYLATED SIV GP120 ENVELOPE GLYCOPROTEIN. REMARK 0 REF STRUCTURE V. 13 197 2005 REMARK 0 REFN ISSN 0969-2126 REMARK 0 PMID 15698564 REMARK 0 DOI 10.1016/J.STR.2004.12.004 REMARK 2 REMARK 2 RESOLUTION. 4.00 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.2.0019 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) : 4.00 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 25.58 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 3 NUMBER OF REFLECTIONS : 5842 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) : 0.346 REMARK 3 R VALUE (WORKING SET) : 0.346 REMARK 3 FREE R VALUE : 0.354 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.600 REMARK 3 FREE R VALUE TEST SET COUNT : 279 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) : 4.00 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 4.10 REMARK 3 REFLECTION IN BIN (WORKING SET) : 400 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 100.0 REMARK 3 BIN R VALUE (WORKING SET) : 0.3700 REMARK 3 BIN FREE R VALUE SET COUNT : 19 REMARK 3 BIN FREE R VALUE : 0.3810 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 2470 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 670 REMARK 3 SOLVENT ATOMS : 0 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 131.8 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -0.61000 REMARK 3 B22 (A**2) : -0.61000 REMARK 3 B33 (A**2) : 1.21000 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): NULL REMARK 3 ESU BASED ON FREE R VALUE (A): 1.053 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 1.516 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 244.543 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.854 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.883 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 3267 ; 0.011 ; 0.021 REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 4517 ; 2.055 ; 2.173 REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 302 ; 7.717 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 125 ;45.590 ;23.600 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 426 ;24.328 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 19 ;17.950 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 629 ; 0.173 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 2049 ; 0.004 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): 1750 ; 0.307 ; 0.200 REMARK 3 NON-BONDED CONTACTS OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): 2191 ; 0.342 ; 0.200 REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): 119 ; 0.261 ; 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): 84 ; 0.430 ; 0.200 REMARK 3 SYMMETRY VDW OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): 10 ; 0.322 ; 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): 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 : NULL REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : BABINET MODEL WITH MASK REMARK 3 PARAMETERS FOR MASK CALCULATION REMARK 3 VDW PROBE RADIUS : 3.00 REMARK 3 ION PROBE RADIUS : 0.80 REMARK 3 SHRINKAGE RADIUS : 2.80 REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 3FUS COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 23-MAR-09. REMARK 100 THE DEPOSITION ID IS D_1000051067. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : NULL REMARK 200 TEMPERATURE (KELVIN) : NULL REMARK 200 PH : NULL REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : NULL REMARK 200 RADIATION SOURCE : NULL REMARK 200 BEAMLINE : NULL REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : NULL REMARK 200 WAVELENGTH OR RANGE (A) : NULL REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : NULL REMARK 200 DETECTOR MANUFACTURER : NULL REMARK 200 INTENSITY-INTEGRATION SOFTWARE : NULL REMARK 200 DATA SCALING SOFTWARE : NULL REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : NULL REMARK 200 RESOLUTION RANGE HIGH (A) : NULL REMARK 200 RESOLUTION RANGE LOW (A) : NULL REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : NULL REMARK 200 DATA REDUNDANCY : NULL REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : NULL REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : NULL REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : NULL REMARK 200 COMPLETENESS FOR SHELL (%) : NULL REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : NULL REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: NULL REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MIRAS REMARK 200 SOFTWARE USED: NULL REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: AUTHOR USED THE SF DATA FROM ENTRY 2BF1. REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 73.62 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 4.66 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: NULL REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 43 21 2 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 -Y+1/2,X+1/2,Z+3/4 REMARK 290 4555 Y+1/2,-X+1/2,Z+1/4 REMARK 290 5555 -X+1/2,Y+1/2,-Z+3/4 REMARK 290 6555 X+1/2,-Y+1/2,-Z+1/4 REMARK 290 7555 Y,X,-Z REMARK 290 8555 -Y,-X,-Z+1/2 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 58.85050 REMARK 290 SMTRY1 3 0.000000 -1.000000 0.000000 54.02400 REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 54.02400 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 88.27575 REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 54.02400 REMARK 290 SMTRY2 4 -1.000000 0.000000 0.000000 54.02400 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 29.42525 REMARK 290 SMTRY1 5 -1.000000 0.000000 0.000000 54.02400 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 54.02400 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 88.27575 REMARK 290 SMTRY1 6 1.000000 0.000000 0.000000 54.02400 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 54.02400 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 29.42525 REMARK 290 SMTRY1 7 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY2 7 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 8 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY2 8 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 8 0.000000 0.000000 -1.000000 58.85050 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 300 REMARK: GP120 CORE, RESIDUES 66-109, 209-311, 342-502 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, B, C, D, E, F, G, H, I, J, REMARK 350 AND CHAINS: K, 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 ASP A 220 REMARK 465 LYS A 221 REMARK 465 HIS A 222 REMARK 465 TYR A 223 REMARK 465 TRP A 224 REMARK 465 ASP A 225 REMARK 465 THR A 226 REMARK 465 ILE A 227 REMARK 465 ARG A 228 REMARK 465 GLU A 500 REMARK 465 ILE A 501 REMARK 465 THR A 502 REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS IN SAME ASYMMETRIC UNIT REMARK 500 REMARK 500 THE FOLLOWING ATOMS ARE IN CLOSE CONTACT. REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI DISTANCE REMARK 500 O TRP A 91 OH TYR A 448 1.80 REMARK 500 N LEU A 107 O ASN A 211 2.12 REMARK 500 O SER A 105 N SER A 213 2.14 REMARK 500 ND2 ASN A 283 O5 NAG D 1 2.14 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS REMARK 500 REMARK 500 THE FOLLOWING ATOMS THAT ARE RELATED BY CRYSTALLOGRAPHIC REMARK 500 SYMMETRY ARE IN CLOSE CONTACT. AN ATOM LOCATED WITHIN 0.15 REMARK 500 ANGSTROMS OF A SYMMETRY RELATED ATOM IS ASSUMED TO BE ON A REMARK 500 SPECIAL POSITION AND IS, THEREFORE, LISTED IN REMARK 375 REMARK 500 INSTEAD OF REMARK 500. ATOMS WITH NON-BLANK ALTERNATE REMARK 500 LOCATION INDICATORS ARE NOT INCLUDED IN THE CALCULATIONS. REMARK 500 REMARK 500 DISTANCE CUTOFF: REMARK 500 2.2 ANGSTROMS FOR CONTACTS NOT INVOLVING HYDROGEN ATOMS REMARK 500 1.6 ANGSTROMS FOR CONTACTS INVOLVING HYDROGEN ATOMS REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI SSYMOP DISTANCE REMARK 500 O LEU A 67 CD1 ILE A 436 4455 1.88 REMARK 500 OE1 GLU A 66 CB LYS A 445 4455 2.02 REMARK 500 O3 FUL B 5 O3 FUL B 5 8555 2.14 REMARK 500 O3 MAN C 4 O3 FUL E 4 6555 2.17 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 ASN A 70 69.77 -163.83 REMARK 500 SER A 74 -134.62 -157.35 REMARK 500 PHE A 75 -113.87 -108.34 REMARK 500 ASP A 76 179.95 50.44 REMARK 500 ALA A 77 -34.77 178.80 REMARK 500 ASN A 80 -138.29 47.52 REMARK 500 SER A 97 -32.21 -149.89 REMARK 500 ILE A 98 169.92 179.76 REMARK 500 LYS A 99 -72.29 166.00 REMARK 500 PRO A 100 -104.91 -97.55 REMARK 500 CYS A 101 51.19 -175.72 REMARK 500 VAL A 102 -143.99 -141.57 REMARK 500 LYS A 103 -50.29 -141.08 REMARK 500 CYS A 108 -156.23 -151.47 REMARK 500 ILE A 109 100.83 60.13 REMARK 500 GLU A 217 -161.51 174.22 REMARK 500 CYS A 232 -84.31 -78.76 REMARK 500 ALA A 233 -53.63 -173.56 REMARK 500 PRO A 235 78.68 -67.62 REMARK 500 CYS A 242 -114.59 -80.49 REMARK 500 ASN A 243 -164.09 173.26 REMARK 500 THR A 245 -178.27 178.91 REMARK 500 ASN A 246 -76.72 -52.42 REMARK 500 TYR A 247 149.45 176.69 REMARK 500 SER A 248 -62.10 -132.38 REMARK 500 PHE A 250 -166.90 -116.83 REMARK 500 SER A 255 -97.91 -154.70 REMARK 500 SER A 260 157.87 161.03 REMARK 500 SER A 261 -70.87 -165.36 REMARK 500 CYS A 262 138.31 -38.70 REMARK 500 MET A 265 -62.43 -16.54 REMARK 500 THR A 268 -139.42 -97.70 REMARK 500 TRP A 273 -74.00 -113.18 REMARK 500 PHE A 276 -106.43 -76.52 REMARK 500 THR A 279 101.44 63.35 REMARK 500 ARG A 280 59.91 38.07 REMARK 500 ARG A 284 102.44 -55.22 REMARK 500 ARG A 292 33.18 -149.89 REMARK 500 ASP A 293 -129.55 67.32 REMARK 500 SER A 299 109.66 -162.51 REMARK 500 TYR A 304 156.72 -25.45 REMARK 500 PRO A 364 96.73 -60.77 REMARK 500 TYR A 366 94.19 -20.52 REMARK 500 ALA A 379 -61.49 -124.17 REMARK 500 PRO A 385 -126.20 -90.60 REMARK 500 GLU A 386 14.32 169.46 REMARK 500 CYS A 394 128.33 -170.85 REMARK 500 ASN A 404 -53.04 -132.46 REMARK 500 PRO A 420 178.96 -52.35 REMARK 500 TRP A 440 -72.63 -74.40 REMARK 500 REMARK 500 THIS ENTRY HAS 63 RAMACHANDRAN OUTLIERS. REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 2BF1 RELATED DB: PDB REMARK 900 THE ORIGINAL UNLIGANDED SIMIAN IMMUNODEFICIENCY VIRUS GP120 CORE REMARK 900 STRUCTURE. THIS ENTRY 2B6P REFLECTS AN ALTERNATIVE MODELING OF X- REMARK 900 RAY DATA R2BF1SF DBREF 3FUS A 66 109 UNP Q07374 Q07374_SIVCZ 66 109 DBREF 3FUS A 209 311 UNP Q07374 Q07374_SIVCZ 209 311 DBREF 3FUS A 342 502 UNP Q07374 Q07374_SIVCZ 342 502 SEQADV 3FUS HIS A 64 UNP Q07374 EXPRESSION TAG SEQADV 3FUS MET A 65 UNP Q07374 EXPRESSION TAG SEQADV 3FUS GLY A 110 UNP Q07374 LINKER SEQADV 3FUS ALA A 207 UNP Q07374 LINKER SEQADV 3FUS GLY A 208 UNP Q07374 LINKER SEQADV 3FUS GLY A 312 UNP Q07374 LINKER SEQADV 3FUS ALA A 313 UNP Q07374 LINKER SEQADV 3FUS GLY A 341 UNP Q07374 LINKER SEQRES 1 A 316 HIS MET GLU LEU ALA LEU ASN VAL THR GLU SER PHE ASP SEQRES 2 A 316 ALA TRP GLU ASN THR VAL THR GLU GLN ALA ILE GLU ASP SEQRES 3 A 316 VAL TRP GLN LEU PHE GLU THR SER ILE LYS PRO CYS VAL SEQRES 4 A 316 LYS LEU SER PRO LEU CYS ILE GLY ALA GLY HIS CYS ASN SEQRES 5 A 316 THR SER ILE ILE GLN GLU SER CYS ASP LYS HIS TYR TRP SEQRES 6 A 316 ASP THR ILE ARG PHE ARG TYR CYS ALA PRO PRO GLY TYR SEQRES 7 A 316 ALA LEU LEU ARG CYS ASN ASP THR ASN TYR SER GLY PHE SEQRES 8 A 316 MET PRO LYS CYS SER LYS VAL VAL VAL SER SER CYS THR SEQRES 9 A 316 ARG MET MET GLU THR GLN THR SER THR TRP PHE GLY PHE SEQRES 10 A 316 ASN GLY THR ARG ALA GLU ASN ARG THR TYR ILE TYR TRP SEQRES 11 A 316 HIS GLY ARG ASP ASN ARG THR ILE ILE SER LEU ASN LYS SEQRES 12 A 316 TYR TYR ASN LEU THR MET LYS CYS ARG GLY ALA GLY TRP SEQRES 13 A 316 CYS TRP PHE GLY GLY ASN TRP LYS ASP ALA ILE LYS GLU SEQRES 14 A 316 MET LYS GLN THR ILE VAL LYS HIS PRO ARG TYR THR GLY SEQRES 15 A 316 THR ASN ASN THR ASP LYS ILE ASN LEU THR ALA PRO ARG SEQRES 16 A 316 GLY GLY ASP PRO GLU VAL THR PHE MET TRP THR ASN CYS SEQRES 17 A 316 ARG GLY GLU PHE LEU TYR CYS LYS MET ASN TRP PHE LEU SEQRES 18 A 316 ASN TRP VAL GLU ASP ARG ASP VAL THR ASN GLN ARG PRO SEQRES 19 A 316 LYS GLU ARG HIS ARG ARG ASN TYR VAL PRO CYS HIS ILE SEQRES 20 A 316 ARG GLN ILE ILE ASN THR TRP HIS LYS VAL GLY LYS ASN SEQRES 21 A 316 VAL TYR LEU PRO PRO ARG GLU GLY ASP LEU THR CYS ASN SEQRES 22 A 316 SER THR VAL THR SER LEU ILE ALA ASN ILE ASP TRP THR SEQRES 23 A 316 ASP GLY ASN GLN THR ASN ILE THR MET SER ALA GLU VAL SEQRES 24 A 316 ALA GLU LEU TYR ARG LEU GLU LEU GLY ASP TYR LYS LEU SEQRES 25 A 316 VAL GLU ILE THR MODRES 3FUS ASN A 70 ASN GLYCOSYLATION SITE MODRES 3FUS ASN A 211 ASN GLYCOSYLATION SITE MODRES 3FUS ASN A 243 ASN GLYCOSYLATION SITE MODRES 3FUS ASN A 277 ASN GLYCOSYLATION SITE MODRES 3FUS ASN A 305 ASN GLYCOSYLATION SITE MODRES 3FUS ASN A 459 ASN GLYCOSYLATION SITE MODRES 3FUS ASN A 475 ASN GLYCOSYLATION SITE MODRES 3FUS ASN A 294 ASN GLYCOSYLATION SITE MODRES 3FUS ASN A 478 ASN GLYCOSYLATION SITE MODRES 3FUS ASN A 283 ASN GLYCOSYLATION SITE MODRES 3FUS ASN A 370 ASN GLYCOSYLATION SITE MODRES 3FUS ASN A 246 ASN GLYCOSYLATION SITE MODRES 3FUS ASN A 376 ASN GLYCOSYLATION SITE HET NAG B 1 14 HET NAG B 2 14 HET BMA B 3 11 HET BMA B 4 11 HET FUL B 5 10 HET NAG C 1 14 HET NAG C 2 14 HET BMA C 3 11 HET MAN C 4 11 HET MAN C 5 11 HET FUL C 6 10 HET NAG D 1 14 HET NAG D 2 14 HET FUL D 3 10 HET NAG E 1 14 HET NAG E 2 14 HET MAN E 3 11 HET FUL E 4 10 HET NAG F 1 14 HET NAG F 2 14 HET BMA F 3 11 HET FUL F 4 10 HET NAG G 1 14 HET NAG G 2 14 HET NAG H 1 14 HET NAG H 2 14 HET BMA H 3 11 HET BMA H 4 11 HET MAN H 5 11 HET FUL H 6 10 HET NAG I 1 14 HET NAG I 2 14 HET BMA I 3 11 HET BMA I 4 11 HET MAN I 5 11 HET BMA I 6 11 HET MAN I 7 11 HET NAG J 1 14 HET NAG J 2 14 HET BMA J 3 11 HET MAN J 4 11 HET MAN J 5 11 HET MAN J 6 11 HET NAG K 1 14 HET NAG K 2 14 HET BMA K 3 11 HET MAN K 4 11 HET MAN K 5 11 HET FUL K 6 10 HET NAG L 1 14 HET NAG L 2 14 HET BMA L 3 11 HET MAN L 4 11 HET NAG A 1 14 HET NAG A 2 14 HETNAM NAG 2-ACETAMIDO-2-DEOXY-BETA-D-GLUCOPYRANOSE HETNAM BMA BETA-D-MANNOPYRANOSE HETNAM FUL BETA-L-FUCOPYRANOSE HETNAM MAN ALPHA-D-MANNOPYRANOSE HETSYN NAG N-ACETYL-BETA-D-GLUCOSAMINE; 2-ACETAMIDO-2-DEOXY-BETA- HETSYN 2 NAG D-GLUCOSE; 2-ACETAMIDO-2-DEOXY-D-GLUCOSE; 2-ACETAMIDO- HETSYN 3 NAG 2-DEOXY-GLUCOSE; N-ACETYL-D-GLUCOSAMINE HETSYN BMA BETA-D-MANNOSE; D-MANNOSE; MANNOSE HETSYN FUL BETA-L-FUCOSE; 6-DEOXY-BETA-L-GALACTOPYRANOSE; L- HETSYN 2 FUL FUCOSE; FUCOSE; 6-DEOXY-BETA-L-GALACTOSE HETSYN MAN ALPHA-D-MANNOSE; D-MANNOSE; MANNOSE FORMUL 2 NAG 24(C8 H15 N O6) FORMUL 2 BMA 12(C6 H12 O6) FORMUL 2 FUL 7(C6 H12 O5) FORMUL 3 MAN 12(C6 H12 O6) HELIX 1 1 THR A 81 GLU A 95 1 15 HELIX 2 2 ARG A 264 THR A 268 5 5 HELIX 3 3 ASN A 348 VAL A 361 1 14 HELIX 4 4 ASN A 404 ASN A 408 5 5 HELIX 5 5 GLU A 484 ARG A 490 1 7 SHEET 1 A 2 PRO A 106 LEU A 107 0 SHEET 2 A 2 ASN A 211 THR A 212 -1 O ASN A 211 N LEU A 107 SHEET 1 B 3 THR A 270 SER A 271 0 SHEET 2 B 3 MET A 390 ASN A 393 -1 O ASN A 393 N THR A 270 SHEET 3 B 3 LEU A 399 CYS A 401 -1 O CYS A 401 N MET A 390 SHEET 1 C 4 PHE A 274 GLY A 275 0 SHEET 2 C 4 SER A 464 ALA A 467 -1 O SER A 464 N GLY A 275 SHEET 3 C 4 ILE A 297 ASN A 301 -1 N ILE A 298 O ALA A 467 SHEET 4 C 4 TYR A 286 HIS A 290 -1 N TYR A 286 O ASN A 301 SHEET 1 D 3 TRP A 342 GLY A 347 0 SHEET 2 D 3 LEU A 306 ARG A 311 -1 N LYS A 309 O TRP A 344 SHEET 3 D 3 ASN A 459 SER A 460 -1 O SER A 460 N MET A 308 SHEET 1 E 2 ASN A 376 LEU A 377 0 SHEET 2 E 2 ASN A 478 ILE A 479 1 O ILE A 479 N ASN A 376 SSBOND 1 CYS A 101 CYS A 219 1555 1555 2.00 SSBOND 2 CYS A 108 CYS A 210 1555 1555 2.24 SSBOND 3 CYS A 232 CYS A 262 1555 1555 2.04 SSBOND 4 CYS A 242 CYS A 254 1555 1555 2.03 SSBOND 5 CYS A 310 CYS A 343 1555 1555 2.03 SSBOND 6 CYS A 394 CYS A 458 1555 1555 2.19 SSBOND 7 CYS A 401 CYS A 431 1555 1555 2.03 LINK C1 NAG A 1 ND2 ASN A 70 1555 1555 1.45 LINK C1 NAG A 2 ND2 ASN A 211 1555 1555 1.48 LINK ND2 ASN A 243 C1 NAG K 1 1555 1555 1.44 LINK ND2 ASN A 246 C1 NAG B 1 1555 1555 1.46 LINK ND2 ASN A 277 C1 NAG C 1 1555 1555 1.43 LINK ND2 ASN A 283 C1 NAG D 1 1555 1555 1.45 LINK ND2 ASN A 294 C1 NAG E 1 1555 1555 1.44 LINK ND2 ASN A 305 C1 NAG F 1 1555 1555 1.45 LINK ND2 ASN A 370 C1 NAG G 1 1555 1555 1.45 LINK ND2 ASN A 376 C1 NAG H 1 1555 1555 1.47 LINK ND2 ASN A 459 C1 NAG I 1 1555 1555 1.45 LINK ND2 ASN A 475 C1 NAG J 1 1555 1555 1.46 LINK ND2 ASN A 478 C1 NAG L 1 1555 1555 1.45 LINK O4 NAG B 1 C1 NAG B 2 1555 1555 1.46 LINK O6 NAG B 1 C1 FUL B 5 1555 1555 1.43 LINK O4 NAG B 2 C1 BMA B 3 1555 1555 1.44 LINK O3 BMA B 3 C1 BMA B 4 1555 1555 1.45 LINK O4 NAG C 1 C1 NAG C 2 1555 1555 1.44 LINK O6 NAG C 1 C1 FUL C 6 1555 1555 1.43 LINK O4 NAG C 2 C1 BMA C 3 1555 1555 1.45 LINK O3 BMA C 3 C1 MAN C 4 1555 1555 1.45 LINK O6 BMA C 3 C1 MAN C 5 1555 1555 1.45 LINK O4 NAG D 1 C1 NAG D 2 1555 1555 1.45 LINK O6 NAG D 1 C1 FUL D 3 1555 1555 1.44 LINK O4 NAG E 1 C1 NAG E 2 1555 1555 1.46 LINK O6 NAG E 1 C1 FUL E 4 1555 1555 1.44 LINK O4 NAG E 2 C1 MAN E 3 1555 1555 1.45 LINK O4 NAG F 1 C1 NAG F 2 1555 1555 1.44 LINK O6 NAG F 1 C1 FUL F 4 1555 1555 1.43 LINK O4 NAG F 2 C1 BMA F 3 1555 1555 1.45 LINK O4 NAG G 1 C1 NAG G 2 1555 1555 1.42 LINK O4 NAG H 1 C1 NAG H 2 1555 1555 1.44 LINK O6 NAG H 1 C1 FUL H 6 1555 1555 1.43 LINK O4 NAG H 2 C1 BMA H 3 1555 1555 1.45 LINK O6 BMA H 3 C1 BMA H 4 1555 1555 1.45 LINK O3 BMA H 4 C1 MAN H 5 1555 1555 1.44 LINK O4 NAG I 1 C1 NAG I 2 1555 1555 1.45 LINK O4 NAG I 2 C1 BMA I 3 1555 1555 1.45 LINK O3 BMA I 3 C1 BMA I 4 1555 1555 1.46 LINK O6 BMA I 3 C1 MAN I 7 1555 1555 1.45 LINK O2 BMA I 4 C1 MAN I 5 1555 1555 1.45 LINK O2 MAN I 5 C1 BMA I 6 1555 1555 1.45 LINK O4 NAG J 1 C1 NAG J 2 1555 1555 1.46 LINK O4 NAG J 2 C1 BMA J 3 1555 1555 1.46 LINK O3 BMA J 3 C1 MAN J 4 1555 1555 1.45 LINK O6 BMA J 3 C1 MAN J 6 1555 1555 1.44 LINK O2 MAN J 4 C1 MAN J 5 1555 1555 1.44 LINK O4 NAG K 1 C1 NAG K 2 1555 1555 1.46 LINK O6 NAG K 1 C1 FUL K 6 1555 1555 1.44 LINK O4 NAG K 2 C1 BMA K 3 1555 1555 1.44 LINK O3 BMA K 3 C1 MAN K 4 1555 1555 1.44 LINK O6 BMA K 3 C1 MAN K 5 1555 1555 1.45 LINK O4 NAG L 1 C1 NAG L 2 1555 1555 1.46 LINK O4 NAG L 2 C1 BMA L 3 1555 1555 1.42 LINK O6 BMA L 3 C1 MAN L 4 1555 1555 1.46 CRYST1 108.048 108.048 117.701 90.00 90.00 90.00 P 43 21 2 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 0.009255 0.000000 0.000000 0.00000 SCALE2 0.000000 0.009255 0.000000 0.00000 SCALE3 0.000000 0.000000 0.008496 0.00000