HEADER VIRAL PROTEIN/IMMUNE SYSTEM 30-JUN-15 5CAY TITLE ENVELOPE GLYCOPROTEIN GP120 CORE FROM HIV TYPE 2 BOUND TO THE FIRST TITLE 2 TWO DOMAINS OF HUMAN SOLUBLE CD4 RECEPTOR COMPND MOL_ID: 1; COMPND 2 MOLECULE: ENVELOPE GLYCOPROTEIN GP120 CORE FROM ST STRAIN OF HIV-2; COMPND 3 CHAIN: G; COMPND 4 ENGINEERED: YES; COMPND 5 MUTATION: YES; COMPND 6 MOL_ID: 2; COMPND 7 MOLECULE: T-CELL SURFACE GLYCOPROTEIN CD4; COMPND 8 CHAIN: B; COMPND 9 FRAGMENT: DOMAINS 1 AND 2 (UNP RESIDUES 26-208); COMPND 10 SYNONYM: T-CELL SURFACE ANTIGEN T4/LEU-3; COMPND 11 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HUMAN IMMUNODEFICIENCY VIRUS TYPE 2 (ISOLATE SOURCE 3 ST); SOURCE 4 ORGANISM_TAXID: 11721; SOURCE 5 EXPRESSION_SYSTEM: HOMO SAPIENS; SOURCE 6 EXPRESSION_SYSTEM_COMMON: HUMAN; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 9606; SOURCE 8 MOL_ID: 2; SOURCE 9 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 10 ORGANISM_COMMON: HUMAN; SOURCE 11 ORGANISM_TAXID: 9606; SOURCE 12 GENE: CD4; SOURCE 13 EXPRESSION_SYSTEM: SPODOPTERA FRUGIPERDA; SOURCE 14 EXPRESSION_SYSTEM_COMMON: FALL ARMYWORM; SOURCE 15 EXPRESSION_SYSTEM_TAXID: 7108; SOURCE 16 EXPRESSION_SYSTEM_VECTOR_TYPE: BACULOVIRUS KEYWDS HIV-2, GP120, GLYCOPROTEIN, CD4, VIRAL PROTEIN-IMMUNE SYSTEM COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR Y.W.DAVENPORT,P.J.BJORKMAN REVDAT 6 27-SEP-23 5CAY 1 HETSYN REVDAT 5 29-JUL-20 5CAY 1 COMPND REMARK HETNAM LINK REVDAT 5 2 1 SITE ATOM REVDAT 4 11-DEC-19 5CAY 1 REMARK REVDAT 3 27-SEP-17 5CAY 1 JRNL REMARK REVDAT 2 10-FEB-16 5CAY 1 JRNL REVDAT 1 09-DEC-15 5CAY 0 JRNL AUTH Y.W.DAVENPORT,A.P.WEST,P.J.BJORKMAN JRNL TITL STRUCTURE OF AN HIV-2 GP120 IN COMPLEX WITH CD4. JRNL REF J.VIROL. V. 90 2112 2015 JRNL REFN ESSN 1098-5514 JRNL PMID 26608312 JRNL DOI 10.1128/JVI.02678-15 REMARK 2 REMARK 2 RESOLUTION. 3.00 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.8.0123 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) : 3.00 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 99.57 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 99.1 REMARK 3 NUMBER OF REFLECTIONS : 17394 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) : 0.235 REMARK 3 R VALUE (WORKING SET) : 0.231 REMARK 3 FREE R VALUE : 0.287 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 9.000 REMARK 3 FREE R VALUE TEST SET COUNT : 1721 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) : 3.00 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 3.08 REMARK 3 REFLECTION IN BIN (WORKING SET) : 1249 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 99.64 REMARK 3 BIN R VALUE (WORKING SET) : 0.3600 REMARK 3 BIN FREE R VALUE SET COUNT : 130 REMARK 3 BIN FREE R VALUE : 0.3990 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 3708 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 151 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) : 103.1 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.51000 REMARK 3 B22 (A**2) : 4.81000 REMARK 3 B33 (A**2) : -5.32000 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): 1.018 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.420 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.356 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 43.331 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.928 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.888 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 3970 ; 0.008 ; 0.020 REMARK 3 BOND LENGTHS OTHERS (A): 3673 ; 0.002 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 5387 ; 1.486 ; 1.978 REMARK 3 BOND ANGLES OTHERS (DEGREES): 8474 ; 1.058 ; 3.000 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 452 ; 7.987 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 182 ;36.426 ;24.341 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 664 ;16.135 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 23 ;15.190 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 610 ; 0.180 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 4332 ; 0.005 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): 907 ; 0.001 ; 0.020 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): 1835 ; 1.263 ; 7.131 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): 1834 ; 1.262 ; 7.129 REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 2278 ; 2.302 ;10.683 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): 2279 ; 2.302 ;10.685 REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 2135 ; 1.391 ; 7.494 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): 2136 ; 1.391 ; 7.495 REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE OTHER ATOMS (A**2): 3110 ; 2.392 ;11.181 REMARK 3 LONG RANGE B REFINED ATOMS (A**2): 15688 ; 6.781 ;67.742 REMARK 3 LONG RANGE B OTHER ATOMS (A**2): 15689 ; 6.781 ;67.744 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 : G 41 G 503 REMARK 3 ORIGIN FOR THE GROUP (A): -33.3390 -43.2430 24.1190 REMARK 3 T TENSOR REMARK 3 T11: 0.4224 T22: 0.1647 REMARK 3 T33: 0.0219 T12: -0.0277 REMARK 3 T13: -0.0165 T23: -0.0299 REMARK 3 L TENSOR REMARK 3 L11: 0.8281 L22: 0.7423 REMARK 3 L33: 4.4000 L12: -0.0838 REMARK 3 L13: -0.5501 L23: -0.0585 REMARK 3 S TENSOR REMARK 3 S11: -0.0021 S12: -0.1450 S13: 0.1303 REMARK 3 S21: 0.0375 S22: 0.0800 S23: -0.0080 REMARK 3 S31: -0.2760 S32: 0.4025 S33: -0.0779 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 : B 2 B 174 REMARK 3 ORIGIN FOR THE GROUP (A): -18.4210 -72.5270 7.7280 REMARK 3 T TENSOR REMARK 3 T11: 0.6930 T22: 0.3036 REMARK 3 T33: 0.0410 T12: 0.3089 REMARK 3 T13: -0.1284 T23: -0.0418 REMARK 3 L TENSOR REMARK 3 L11: 5.0432 L22: 6.4921 REMARK 3 L33: 2.0716 L12: -4.9795 REMARK 3 L13: -3.1852 L23: 3.3956 REMARK 3 S TENSOR REMARK 3 S11: 0.1173 S12: 0.0739 S13: -0.2889 REMARK 3 S21: -0.1024 S22: -0.2690 S23: 0.2196 REMARK 3 S31: 0.0359 S32: -0.0091 S33: 0.1517 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : MASK REMARK 3 PARAMETERS FOR MASK CALCULATION REMARK 3 VDW PROBE RADIUS : 1.00 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 5CAY COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 30-JUN-15. REMARK 100 THE DEPOSITION ID IS D_1000210717. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 23-JAN-14 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 : SSRL REMARK 200 BEAMLINE : BL12-2 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.0332 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS 6M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : AIMLESS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 19116 REMARK 200 RESOLUTION RANGE HIGH (A) : 3.000 REMARK 200 RESOLUTION RANGE LOW (A) : 99.570 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.2 REMARK 200 DATA REDUNDANCY : 4.500 REMARK 200 R MERGE (I) : 0.08100 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 12.8000 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: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHASER REMARK 200 STARTING MODEL: 2NXY,3LQA REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 68.64 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.92 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.15M DL-MALIC ACID 7.0, 0.1M REMARK 280 IMIDAZOLE PH 7.0, 22% PEGMME 550, VAPOR DIFFUSION, SITTING DROP, REMARK 280 TEMPERATURE 293K 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 99.56950 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 99.56950 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 47.13800 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 50.11150 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 6 -1.000000 0.000000 0.000000 47.13800 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 50.11150 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 99.56950 REMARK 290 SMTRY1 7 -1.000000 0.000000 0.000000 47.13800 REMARK 290 SMTRY2 7 0.000000 1.000000 0.000000 50.11150 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 99.56950 REMARK 290 SMTRY1 8 1.000000 0.000000 0.000000 47.13800 REMARK 290 SMTRY2 8 0.000000 -1.000000 0.000000 50.11150 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 APPLY THE FOLLOWING TO CHAINS: G, B, A, C 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 VAL G 34 REMARK 465 TRP G 35 REMARK 465 ARG G 36 REMARK 465 ASN G 37 REMARK 465 ALA G 38 REMARK 465 SER G 39 REMARK 465 ILE G 40 REMARK 465 ASN G 48 REMARK 465 ARG G 49 REMARK 465 ASP G 50 REMARK 465 THR G 51 REMARK 465 TRP G 52 REMARK 465 GLY G 53 REMARK 465 THR G 54 REMARK 465 ILE G 55 REMARK 465 GLN G 56 REMARK 465 CYS G 57 REMARK 465 LEU G 58 REMARK 465 PRO G 59 REMARK 465 ASN G 336 REMARK 465 ARG G 421 REMARK 465 THR G 422 REMARK 465 ASN G 423 REMARK 465 GLN G 424 REMARK 465 THR G 425 REMARK 465 ASN G 476 REMARK 465 PRO G 504 REMARK 465 ILE G 505 REMARK 465 HIS G 506 REMARK 465 HIS G 507 REMARK 465 HIS G 508 REMARK 465 HIS G 509 REMARK 465 HIS G 510 REMARK 465 HIS G 511 REMARK 465 MET B 0 REMARK 465 LYS B 1 REMARK 465 ASN B 103 REMARK 465 SER B 104 REMARK 465 ASP B 105 REMARK 465 THR B 106 REMARK 465 HIS B 107 REMARK 465 LEU B 108 REMARK 465 LEU B 109 REMARK 465 GLN B 110 REMARK 465 GLY B 111 REMARK 465 GLN B 112 REMARK 465 SER B 113 REMARK 465 SER B 145 REMARK 465 VAL B 146 REMARK 465 SER B 147 REMARK 465 GLN B 148 REMARK 465 LEU B 149 REMARK 465 GLU B 150 REMARK 465 LEU B 151 REMARK 465 GLN B 152 REMARK 465 ASP B 153 REMARK 465 SER B 154 REMARK 465 GLY B 155 REMARK 465 THR B 156 REMARK 465 VAL B 175 REMARK 465 VAL B 176 REMARK 465 LEU B 177 REMARK 465 ALA B 178 REMARK 465 PHE B 179 REMARK 465 GLN B 180 REMARK 465 LYS B 181 REMARK 465 ALA B 182 REMARK 465 SER B 183 REMARK 465 HIS B 184 REMARK 465 HIS B 185 REMARK 465 HIS B 186 REMARK 465 HIS B 187 REMARK 465 HIS B 188 REMARK 465 HIS B 189 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 PHE G 43 CG CD1 CD2 CE1 CE2 CZ REMARK 470 GLN G 65 CG CD OE1 NE2 REMARK 470 LYS G 99 CG CD CE NZ REMARK 470 LYS B 167 CB CG CD CE NZ 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 NH2 ARG G 340 OE1 GLN G 436 1.95 REMARK 500 ND2 ASN G 212 C1 NAG B 201 2.18 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 TYR G 402 CE1 TYR G 402 CZ -0.091 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 THR G 370 N - CA - C ANGL. DEV. = 23.8 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 ASP G 62 33.30 72.02 REMARK 500 TYR G 64 69.28 -110.98 REMARK 500 TRP G 78 -63.51 -92.15 REMARK 500 ASN G 80 113.74 -173.29 REMARK 500 ASP G 221 -154.05 -170.51 REMARK 500 PHE G 251 118.40 -166.03 REMARK 500 TRP G 274 -70.34 67.86 REMARK 500 ASP G 294 161.32 69.02 REMARK 500 ASP G 372 99.36 79.94 REMARK 500 THR G 373 169.76 68.73 REMARK 500 GLU G 374 -59.35 66.84 REMARK 500 GLU G 413 -65.53 -142.34 REMARK 500 VAL G 486 -60.57 64.37 REMARK 500 SER B 19 68.75 -113.20 REMARK 500 ASP B 53 -66.52 97.58 REMARK 500 ASN B 73 72.70 54.37 REMARK 500 GLU B 87 -68.33 -144.07 REMARK 500 LYS B 90 119.52 -160.51 REMARK 500 LYS B 136 -169.50 -125.34 REMARK 500 ASN B 164 -131.00 57.05 REMARK 500 LYS B 167 -164.46 -118.77 REMARK 500 PHE B 170 -133.31 -138.22 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 NAG B 201 DBREF 5CAY G 34 511 PDB 5CAY 5CAY 34 511 DBREF 5CAY B 1 183 UNP P01730 CD4_HUMAN 26 208 SEQADV 5CAY MET B 0 UNP P01730 INITIATING METHIONINE SEQADV 5CAY HIS B 184 UNP P01730 EXPRESSION TAG SEQADV 5CAY HIS B 185 UNP P01730 EXPRESSION TAG SEQADV 5CAY HIS B 186 UNP P01730 EXPRESSION TAG SEQADV 5CAY HIS B 187 UNP P01730 EXPRESSION TAG SEQADV 5CAY HIS B 188 UNP P01730 EXPRESSION TAG SEQADV 5CAY HIS B 189 UNP P01730 EXPRESSION TAG SEQRES 1 G 345 VAL TRP ARG ASN ALA SER ILE PRO LEU PHE CYS ALA THR SEQRES 2 G 345 LYS ASN ARG ASP THR TRP GLY THR ILE GLN CYS LEU PRO SEQRES 3 G 345 ASP ASN ASP ASP TYR GLN GLU ILE ALA LEU ASN VAL ILE SEQRES 4 G 345 GLU ALA PHE ASP ALA TRP ASN ASN THR VAL THR GLU GLN SEQRES 5 G 345 ALA VAL GLU ASP VAL TRP SER LEU PHE GLU THR SER ILE SEQRES 6 G 345 LYS PRO CYS VAL LYS LEU THR ASN THR SER VAL ILE THR SEQRES 7 G 345 GLU SER CYS ASP LYS HIS TYR TRP ASP THR MET ARG PHE SEQRES 8 G 345 ARG TYR CYS ALA PRO PRO GLY PHE ALA LEU LEU ARG CYS SEQRES 9 G 345 ASN ASP THR ASN TYR SER GLY PHE GLU PRO ASN CYS SER SEQRES 10 G 345 LYS VAL VAL ALA ALA THR CYS THR ARG MET MET GLU THR SEQRES 11 G 345 GLN THR SER THR TRP PHE GLY PHE ASN GLY THR ARG ALA SEQRES 12 G 345 GLU ASN ARG THR TYR ILE TYR TRP HIS GLY ARG ASP ASN SEQRES 13 G 345 ARG THR ILE ILE SER LEU ASN LYS PHE TYR ASN LEU THR SEQRES 14 G 345 VAL HIS CYS LYS ARG PRO GLY ASN ARG ARG PRO ARG GLN SEQRES 15 G 345 ALA TRP CYS TRP PHE LYS GLY GLU TRP LYS GLU ALA MET SEQRES 16 G 345 LYS GLU VAL LYS LEU THR LEU ALA LYS HIS PRO ARG TYR SEQRES 17 G 345 LYS GLY THR ASN ASP THR GLU LYS ILE ARG PHE ILE ALA SEQRES 18 G 345 PRO GLY GLU ARG SER ASP PRO GLU VAL ALA TYR MET TRP SEQRES 19 G 345 THR ASN CYS ARG GLY GLU PHE LEU TYR CYS ASN MET THR SEQRES 20 G 345 TRP PHE LEU ASN TRP VAL GLU ASN ARG THR ASN GLN THR SEQRES 21 G 345 GLN HIS ASN TYR VAL PRO CYS HIS ILE LYS GLN ILE ILE SEQRES 22 G 345 ASN THR TRP HIS LYS VAL GLY LYS ASN VAL TYR LEU PRO SEQRES 23 G 345 PRO ARG GLU GLY GLN LEU THR CYS ASN SER THR VAL THR SEQRES 24 G 345 SER ILE ILE ALA ASN ILE ASP GLY GLY GLU ASN GLN THR SEQRES 25 G 345 ASN ILE THR PHE SER ALA GLU VAL ALA GLU LEU TYR ARG SEQRES 26 G 345 LEU GLU LEU GLY ASP TYR LYS LEU ILE GLU VAL THR PRO SEQRES 27 G 345 ILE HIS HIS HIS HIS HIS HIS SEQRES 1 B 190 MET LYS LYS VAL VAL LEU GLY LYS LYS GLY ASP THR VAL SEQRES 2 B 190 GLU LEU THR CYS THR ALA SER GLN LYS LYS SER ILE GLN SEQRES 3 B 190 PHE HIS TRP LYS ASN SER ASN GLN ILE LYS ILE LEU GLY SEQRES 4 B 190 ASN GLN GLY SER PHE LEU THR LYS GLY PRO SER LYS LEU SEQRES 5 B 190 ASN ASP ARG ALA ASP SER ARG ARG SER LEU TRP ASP GLN SEQRES 6 B 190 GLY ASN PHE PRO LEU ILE ILE LYS ASN LEU LYS ILE GLU SEQRES 7 B 190 ASP SER ASP THR TYR ILE CYS GLU VAL GLU ASP GLN LYS SEQRES 8 B 190 GLU GLU VAL GLN LEU LEU VAL PHE GLY LEU THR ALA ASN SEQRES 9 B 190 SER ASP THR HIS LEU LEU GLN GLY GLN SER LEU THR LEU SEQRES 10 B 190 THR LEU GLU SER PRO PRO GLY SER SER PRO SER VAL GLN SEQRES 11 B 190 CYS ARG SER PRO ARG GLY LYS ASN ILE GLN GLY GLY LYS SEQRES 12 B 190 THR LEU SER VAL SER GLN LEU GLU LEU GLN ASP SER GLY SEQRES 13 B 190 THR TRP THR CYS THR VAL LEU GLN ASN GLN LYS LYS VAL SEQRES 14 B 190 GLU PHE LYS ILE ASP ILE VAL VAL LEU ALA PHE GLN LYS SEQRES 15 B 190 ALA SER HIS HIS HIS HIS HIS HIS HET NAG A 1 14 HET NAG A 2 14 HET NAG C 1 14 HET NAG C 2 14 HET BMA C 3 11 HET NAG G 601 14 HET NAG G 604 14 HET NAG G 608 14 HET NAG G 609 14 HET NAG G 610 14 HET NAG B 201 14 HETNAM NAG 2-ACETAMIDO-2-DEOXY-BETA-D-GLUCOPYRANOSE HETNAM BMA BETA-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 FORMUL 3 NAG 10(C8 H15 N O6) FORMUL 4 BMA C6 H12 O6 HELIX 1 AA1 ASN G 80 ILE G 98 1 19 HELIX 2 AA2 GLU G 349 LYS G 363 1 15 HELIX 3 AA3 ASP G 386 TYR G 391 1 6 HELIX 4 AA4 MET G 405 TRP G 411 1 7 HELIX 5 AA5 VAL G 486 GLY G 495 1 10 HELIX 6 AA6 ARG B 58 GLY B 65 5 8 HELIX 7 AA7 LYS B 75 SER B 79 5 5 SHEET 1 AA1 3 PHE G 43 ALA G 45 0 SHEET 2 AA1 3 ARG G 229 CYS G 233 -1 O ARG G 231 N ALA G 45 SHEET 3 AA1 3 MET G 267 GLU G 268 -1 O MET G 267 N PHE G 230 SHEET 1 AA2 4 GLU G 66 LEU G 69 0 SHEET 2 AA2 4 VAL G 258 ALA G 261 -1 O ALA G 260 N ILE G 67 SHEET 3 AA2 4 PHE G 238 CYS G 243 -1 N ARG G 242 O VAL G 259 SHEET 4 AA2 4 TYR G 497 GLU G 501 -1 O LYS G 498 N LEU G 241 SHEET 1 AA3 2 GLU G 73 ASP G 76 0 SHEET 2 AA3 2 PHE G 251 CYS G 255 -1 O GLU G 252 N PHE G 75 SHEET 1 AA4 4 VAL G 215 THR G 217 0 SHEET 2 AA4 4 VAL G 102 LEU G 104 -1 N LYS G 103 O ILE G 216 SHEET 3 AA4 4 LYS G 446 VAL G 448 -1 O LYS G 446 N LEU G 104 SHEET 4 AA4 4 ILE G 437 ASN G 439 -1 N ILE G 438 O ASN G 447 SHEET 1 AA5 4 PHE G 275 PHE G 277 0 SHEET 2 AA5 4 LEU G 457 ASP G 471 -1 O SER G 465 N GLY G 276 SHEET 3 AA5 4 THR G 478 PHE G 482 -1 O ASN G 479 N ASP G 471 SHEET 4 AA5 4 ILE G 376 ILE G 379 1 N ARG G 377 O ILE G 480 SHEET 1 AA6 8 TYR G 287 TRP G 290 0 SHEET 2 AA6 8 ARG G 296 SER G 300 -1 O ILE G 298 N TYR G 289 SHEET 3 AA6 8 LEU G 457 ASP G 471 -1 O ILE G 466 N ILE G 299 SHEET 4 AA6 8 THR G 308 ARG G 313 -1 N VAL G 309 O SER G 461 SHEET 5 AA6 8 GLN G 341 TRP G 345 -1 O TRP G 345 N HIS G 310 SHEET 6 AA6 8 TYR G 429 LYS G 435 -1 O CYS G 432 N ALA G 342 SHEET 7 AA6 8 GLU G 399 CYS G 403 -1 N TYR G 402 O HIS G 433 SHEET 8 AA6 8 MET G 392 CYS G 396 -1 N CYS G 396 O GLU G 399 SHEET 1 AA7 6 VAL B 3 GLY B 6 0 SHEET 2 AA7 6 LYS B 90 VAL B 97 1 O GLN B 94 N VAL B 4 SHEET 3 AA7 6 ASP B 80 GLU B 85 -1 N ASP B 80 O LEU B 95 SHEET 4 AA7 6 HIS B 27 LYS B 29 -1 N LYS B 29 O ILE B 83 SHEET 5 AA7 6 LYS B 35 GLN B 40 -1 O LEU B 37 N TRP B 28 SHEET 6 AA7 6 PHE B 43 THR B 45 -1 O THR B 45 N GLY B 38 SHEET 1 AA8 3 VAL B 12 LEU B 14 0 SHEET 2 AA8 3 LEU B 69 ILE B 71 -1 O LEU B 69 N LEU B 14 SHEET 3 AA8 3 ALA B 55 ASP B 56 -1 N ASP B 56 O ILE B 70 SHEET 1 AA9 2 GLY B 99 THR B 101 0 SHEET 2 AA9 2 THR B 117 GLU B 119 -1 O THR B 117 N THR B 101 SHEET 1 AB1 4 ILE B 138 GLN B 139 0 SHEET 2 AB1 4 SER B 127 ARG B 131 -1 N CYS B 130 O ILE B 138 SHEET 3 AB1 4 THR B 158 LEU B 162 -1 O THR B 160 N GLN B 129 SHEET 4 AB1 4 LYS B 167 VAL B 168 -1 O VAL B 168 N VAL B 161 SSBOND 1 CYS G 101 CYS G 220 1555 1555 2.06 SSBOND 2 CYS G 233 CYS G 263 1555 1555 2.05 SSBOND 3 CYS G 243 CYS G 255 1555 1555 2.11 SSBOND 4 CYS G 311 CYS G 344 1555 1555 1.97 SSBOND 5 CYS G 396 CYS G 459 1555 1555 2.07 SSBOND 6 CYS G 403 CYS G 432 1555 1555 1.91 SSBOND 7 CYS B 16 CYS B 84 1555 1555 2.04 SSBOND 8 CYS B 130 CYS B 159 1555 1555 2.04 LINK ND2 ASN G 79 C1 NAG G 601 1555 1555 1.45 LINK ND2 ASN G 244 C1 NAG G 604 1555 1555 1.44 LINK ND2 ASN G 278 C1 NAG C 1 1555 1555 1.45 LINK ND2 ASN G 284 C1 NAG G 610 1555 1555 1.45 LINK ND2 ASN G 295 C1 NAG A 1 1555 1555 1.45 LINK ND2 ASN G 306 C1 NAG G 609 1555 1555 1.44 LINK ND2 ASN G 404 C1 NAG G 608 1555 1555 1.49 LINK O4 NAG A 1 C1 NAG A 2 1555 1555 1.45 LINK O4 NAG C 1 C1 NAG C 2 1555 1555 1.45 LINK O4 NAG C 2 C1 BMA C 3 1555 1555 1.45 CISPEP 1 ASP G 60 ASN G 61 0 0.03 CISPEP 2 PRO G 314 GLY G 315 0 15.81 CISPEP 3 TYR G 367 LYS G 368 0 -8.13 CRYST1 94.276 100.223 199.139 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 0.010607 0.000000 0.000000 0.00000 SCALE2 0.000000 0.009978 0.000000 0.00000 SCALE3 0.000000 0.000000 0.005022 0.00000