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 <I/SIGMA(I)> 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 <I/SIGMA(I)> FOR SHELL : NULL
REMARK 200
REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH
REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT
REMARK 200 SOFTWARE USED: 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
(ATOM LINES ARE NOT SHOWN.)
END
