HEADER IMMUNE SYSTEM 23-MAR-10 3MA9
TITLE CRYSTAL STRUCTURE OF GP41 DERIVED PROTEIN COMPLEXED WITH FAB 8066
COMPND MOL_ID: 1;
COMPND 2 MOLECULE: TRANSMEMBRANE GLYCOPROTEIN;
COMPND 3 CHAIN: A;
COMPND 4 SYNONYM: GP41;
COMPND 5 ENGINEERED: YES;
COMPND 6 MOL_ID: 2;
COMPND 7 MOLECULE: FAB8066 FAB ANTIBODY FRAGMENT, HEAVY CHAIN;
COMPND 8 CHAIN: H;
COMPND 9 ENGINEERED: YES;
COMPND 10 MOL_ID: 3;
COMPND 11 MOLECULE: FAB8066 FAB ANTIBODY FRAGMENT, LIGHT CHAIN;
COMPND 12 CHAIN: L;
COMPND 13 ENGINEERED: YES
SOURCE MOL_ID: 1;
SOURCE 2 ORGANISM_SCIENTIFIC: HUMAN IMMUNODEFICIENCY VIRUS 1;
SOURCE 3 ORGANISM_TAXID: 11676;
SOURCE 4 EXPRESSION_SYSTEM: ESCHERICHIA COLI;
SOURCE 5 EXPRESSION_SYSTEM_TAXID: 562;
SOURCE 6 MOL_ID: 2;
SOURCE 7 ORGANISM_SCIENTIFIC: HOMO SAPIENS;
SOURCE 8 ORGANISM_COMMON: HUMAN;
SOURCE 9 ORGANISM_TAXID: 9606;
SOURCE 10 MOL_ID: 3;
SOURCE 11 ORGANISM_SCIENTIFIC: HOMO SAPIENS;
SOURCE 12 ORGANISM_COMMON: HUMAN;
SOURCE 13 ORGANISM_TAXID: 9606
KEYWDS GP41, IMMUNE SYSTEM
EXPDTA X-RAY DIFFRACTION
AUTHOR M.LI,E.GUSTCHINA,J.LOUIS,A.GUSTCHINA,A.WLODAWER,M.CLORE
REVDAT 3 06-SEP-23 3MA9 1 REMARK LINK
REVDAT 2 08-NOV-17 3MA9 1 REMARK
REVDAT 1 01-DEC-10 3MA9 0
JRNL AUTH E.GUSTCHINA,M.LI,J.M.LOUIS,D.E.ANDERSON,J.LLOYD,C.FRISCH,
JRNL AUTH 2 C.A.BEWLEY,A.GUSTCHINA,A.WLODAWER,G.M.CLORE
JRNL TITL STRUCTURAL BASIS OF HIV-1 NEUTRALIZATION BY AFFINITY MATURED
JRNL TITL 2 FABS DIRECTED AGAINST THE INTERNAL TRIMERIC COILED-COIL OF
JRNL TITL 3 GP41.
JRNL REF PLOS PATHOG. V. 6 01182 2010
JRNL REFN ISSN 1553-7366
JRNL PMID 21085615
JRNL DOI 10.1371/JOURNAL.PPAT.1001182
REMARK 2
REMARK 2 RESOLUTION. 2.05 ANGSTROMS.
REMARK 3
REMARK 3 REFINEMENT.
REMARK 3 PROGRAM : REFMAC 5.5.0102
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) : 2.05
REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 29.45
REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL
REMARK 3 COMPLETENESS FOR RANGE (%) : 98.6
REMARK 3 NUMBER OF REFLECTIONS : 43032
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) : 0.194
REMARK 3 R VALUE (WORKING SET) : 0.193
REMARK 3 FREE R VALUE : 0.245
REMARK 3 FREE R VALUE TEST SET SIZE (%) : 3.200
REMARK 3 FREE R VALUE TEST SET COUNT : 1414
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) : 2.05
REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.10
REMARK 3 REFLECTION IN BIN (WORKING SET) : 2779
REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 87.60
REMARK 3 BIN R VALUE (WORKING SET) : 0.2880
REMARK 3 BIN FREE R VALUE SET COUNT : 97
REMARK 3 BIN FREE R VALUE : 0.3300
REMARK 3
REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT.
REMARK 3 PROTEIN ATOMS : 4781
REMARK 3 NUCLEIC ACID ATOMS : 0
REMARK 3 HETEROGEN ATOMS : 2
REMARK 3 SOLVENT ATOMS : 442
REMARK 3
REMARK 3 B VALUES.
REMARK 3 FROM WILSON PLOT (A**2) : NULL
REMARK 3 MEAN B VALUE (OVERALL, A**2) : 32.47
REMARK 3 OVERALL ANISOTROPIC B VALUE.
REMARK 3 B11 (A**2) : -1.62000
REMARK 3 B22 (A**2) : -2.41000
REMARK 3 B33 (A**2) : 4.03000
REMARK 3 B12 (A**2) : 0.00000
REMARK 3 B13 (A**2) : 0.00000
REMARK 3 B23 (A**2) : 0.00000
REMARK 3
REMARK 3 ESTIMATED OVERALL COORDINATE ERROR.
REMARK 3 ESU BASED ON R VALUE (A): 0.195
REMARK 3 ESU BASED ON FREE R VALUE (A): 0.177
REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.149
REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 12.432
REMARK 3
REMARK 3 CORRELATION COEFFICIENTS.
REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.959
REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.938
REMARK 3
REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT
REMARK 3 BOND LENGTHS REFINED ATOMS (A): 4904 ; 0.010 ; 0.022
REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL
REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 6679 ; 1.209 ; 1.944
REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL
REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 617 ; 6.060 ; 5.000
REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 215 ;37.635 ;25.628
REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 808 ;17.062 ;15.000
REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 16 ;16.649 ;15.000
REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 758 ; 0.085 ; 0.200
REMARK 3 GENERAL PLANES REFINED ATOMS (A): 3699 ; 0.005 ; 0.021
REMARK 3 GENERAL PLANES OTHERS (A): NULL ; NULL ; NULL
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): 3087 ; 4.829 ; 2.000
REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL
REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 4985 ; 6.332 ; 3.000
REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL
REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 1817 ; 6.893 ; 2.000
REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL
REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 1692 ; 8.621 ; 3.000
REMARK 3 SIDE-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL
REMARK 3 LONG RANGE B REFINED ATOMS (A**2): NULL ; NULL ; NULL
REMARK 3 LONG RANGE B OTHER ATOMS (A**2): NULL ; NULL ; NULL
REMARK 3
REMARK 3 ANISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT
REMARK 3 RIGID-BOND RESTRAINTS (A**2): NULL ; NULL ; NULL
REMARK 3 SPHERICITY; FREE ATOMS (A**2): NULL ; NULL ; NULL
REMARK 3 SPHERICITY; BONDED ATOMS (A**2): NULL ; NULL ; NULL
REMARK 3
REMARK 3 NCS RESTRAINTS STATISTICS
REMARK 3 NUMBER OF DIFFERENT NCS GROUPS : NULL
REMARK 3
REMARK 3 TLS DETAILS
REMARK 3 NUMBER OF TLS GROUPS : 3
REMARK 3
REMARK 3 TLS GROUP : 1
REMARK 3 NUMBER OF COMPONENTS GROUP : 1
REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI
REMARK 3 RESIDUE RANGE : A 1 A 218
REMARK 3 ORIGIN FOR THE GROUP (A): 17.5473 81.3008 73.0550
REMARK 3 T TENSOR
REMARK 3 T11: 0.0238 T22: 0.0773
REMARK 3 T33: 0.0456 T12: 0.0131
REMARK 3 T13: 0.0026 T23: -0.0035
REMARK 3 L TENSOR
REMARK 3 L11: 0.3123 L22: 1.6887
REMARK 3 L33: 0.8911 L12: -0.0844
REMARK 3 L13: -0.0291 L23: -0.4570
REMARK 3 S TENSOR
REMARK 3 S11: -0.0015 S12: -0.0658 S13: 0.0716
REMARK 3 S21: 0.1482 S22: -0.0084 S23: 0.0719
REMARK 3 S31: 0.0111 S32: 0.0635 S33: 0.0099
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 : H 1 H 218
REMARK 3 ORIGIN FOR THE GROUP (A): 21.5975 39.8143 53.7211
REMARK 3 T TENSOR
REMARK 3 T11: 0.0647 T22: 0.0698
REMARK 3 T33: 0.0486 T12: 0.0067
REMARK 3 T13: -0.0263 T23: 0.0220
REMARK 3 L TENSOR
REMARK 3 L11: 0.1477 L22: 1.0630
REMARK 3 L33: 0.7911 L12: 0.0586
REMARK 3 L13: -0.1214 L23: 0.7961
REMARK 3 S TENSOR
REMARK 3 S11: -0.0527 S12: 0.0684 S13: 0.0374
REMARK 3 S21: 0.0597 S22: 0.0957 S23: -0.0161
REMARK 3 S31: 0.0983 S32: -0.0060 S33: -0.0431
REMARK 3
REMARK 3 TLS GROUP : 3
REMARK 3 NUMBER OF COMPONENTS GROUP : 1
REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI
REMARK 3 RESIDUE RANGE : L 1 L 209
REMARK 3 ORIGIN FOR THE GROUP (A): 5.9023 42.4157 45.6383
REMARK 3 T TENSOR
REMARK 3 T11: 0.0578 T22: 0.1260
REMARK 3 T33: 0.0950 T12: -0.0024
REMARK 3 T13: -0.0505 T23: 0.0518
REMARK 3 L TENSOR
REMARK 3 L11: 0.2720 L22: 1.4958
REMARK 3 L33: 0.5561 L12: 0.3720
REMARK 3 L13: -0.1010 L23: 0.5040
REMARK 3 S TENSOR
REMARK 3 S11: -0.0685 S12: 0.0490 S13: 0.0330
REMARK 3 S21: -0.1607 S22: 0.0608 S23: 0.1238
REMARK 3 S31: -0.0413 S32: -0.1269 S33: 0.0076
REMARK 3
REMARK 3 BULK SOLVENT MODELLING.
REMARK 3 METHOD USED : MASK
REMARK 3 PARAMETERS FOR MASK CALCULATION
REMARK 3 VDW PROBE RADIUS : 1.20
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 3MA9 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11
REMARK 100
REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 23-MAR-10.
REMARK 100 THE DEPOSITION ID IS D_1000058304.
REMARK 200
REMARK 200 EXPERIMENTAL DETAILS
REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION
REMARK 200 DATE OF DATA COLLECTION : 03-APR-09
REMARK 200 TEMPERATURE (KELVIN) : 100
REMARK 200 PH : 8.0
REMARK 200 NUMBER OF CRYSTALS USED : 1
REMARK 200
REMARK 200 SYNCHROTRON (Y/N) : Y
REMARK 200 RADIATION SOURCE : APS
REMARK 200 BEAMLINE : 22-ID
REMARK 200 X-RAY GENERATOR MODEL : NULL
REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M
REMARK 200 WAVELENGTH OR RANGE (A) : 1.0
REMARK 200 MONOCHROMATOR : GRAPHITE
REMARK 200 OPTICS : MIRROR
REMARK 200
REMARK 200 DETECTOR TYPE : CCD
REMARK 200 DETECTOR MANUFACTURER : MARCCD 300
REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-3000
REMARK 200 DATA SCALING SOFTWARE : HKL-3000
REMARK 200
REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 44497
REMARK 200 RESOLUTION RANGE HIGH (A) : 2.050
REMARK 200 RESOLUTION RANGE LOW (A) : 30.000
REMARK 200 REJECTION CRITERIA (SIGMA(I)) : -3.000
REMARK 200
REMARK 200 OVERALL.
REMARK 200 COMPLETENESS FOR RANGE (%) : 99.2
REMARK 200 DATA REDUNDANCY : 4.800
REMARK 200 R MERGE (I) : NULL
REMARK 200 R SYM (I) : 0.09900
REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 15.2400
REMARK 200
REMARK 200 IN THE HIGHEST RESOLUTION SHELL.
REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.05
REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.12
REMARK 200 COMPLETENESS FOR SHELL (%) : 96.6
REMARK 200 DATA REDUNDANCY IN SHELL : 3.50
REMARK 200 R MERGE FOR SHELL (I) : NULL
REMARK 200 R SYM FOR SHELL (I) : 0.66200
REMARK 200 <I/SIGMA(I)> FOR SHELL : 1.920
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: 2CMR
REMARK 200
REMARK 200 REMARK: NULL
REMARK 280
REMARK 280 CRYSTAL
REMARK 280 SOLVENT CONTENT, VS (%): 47.80
REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.36
REMARK 280
REMARK 280 CRYSTALLIZATION CONDITIONS: 1.2M DIBASIC AMMONIUM PHOSPHATE, PH
REMARK 280 8.0, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 293K
REMARK 290
REMARK 290 CRYSTALLOGRAPHIC SYMMETRY
REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 21 21 21
REMARK 290
REMARK 290 SYMOP SYMMETRY
REMARK 290 NNNMMM OPERATOR
REMARK 290 1555 X,Y,Z
REMARK 290 2555 -X+1/2,-Y,Z+1/2
REMARK 290 3555 -X,Y+1/2,-Z+1/2
REMARK 290 4555 X+1/2,-Y+1/2,-Z
REMARK 290
REMARK 290 WHERE NNN -> OPERATOR NUMBER
REMARK 290 MMM -> TRANSLATION VECTOR
REMARK 290
REMARK 290 CRYSTALLOGRAPHIC SYMMETRY TRANSFORMATIONS
REMARK 290 THE FOLLOWING TRANSFORMATIONS OPERATE ON THE ATOM/HETATM
REMARK 290 RECORDS IN THIS ENTRY TO PRODUCE CRYSTALLOGRAPHICALLY
REMARK 290 RELATED MOLECULES.
REMARK 290 SMTRY1 1 1.000000 0.000000 0.000000 0.00000
REMARK 290 SMTRY2 1 0.000000 1.000000 0.000000 0.00000
REMARK 290 SMTRY3 1 0.000000 0.000000 1.000000 0.00000
REMARK 290 SMTRY1 2 -1.000000 0.000000 0.000000 20.76350
REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000
REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 66.82850
REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000
REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 62.34900
REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 66.82850
REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 20.76350
REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 62.34900
REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000
REMARK 290
REMARK 290 REMARK: NULL
REMARK 300
REMARK 300 BIOMOLECULE: 1
REMARK 300 SEE REMARK 350 FOR THE AUTHOR PROVIDED AND/OR PROGRAM
REMARK 300 GENERATED ASSEMBLY INFORMATION FOR THE STRUCTURE IN
REMARK 300 THIS ENTRY. THE REMARK MAY ALSO PROVIDE INFORMATION ON
REMARK 300 BURIED SURFACE AREA.
REMARK 350
REMARK 350 COORDINATES FOR A COMPLETE MULTIMER REPRESENTING THE KNOWN
REMARK 350 BIOLOGICALLY SIGNIFICANT OLIGOMERIZATION STATE OF THE
REMARK 350 MOLECULE CAN BE GENERATED BY APPLYING BIOMT TRANSFORMATIONS
REMARK 350 GIVEN BELOW. BOTH NON-CRYSTALLOGRAPHIC AND
REMARK 350 CRYSTALLOGRAPHIC OPERATIONS ARE GIVEN.
REMARK 350
REMARK 350 BIOMOLECULE: 1
REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: TRIMERIC
REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: TRIMERIC
REMARK 350 SOFTWARE USED: PISA
REMARK 350 TOTAL BURIED SURFACE AREA: 5790 ANGSTROM**2
REMARK 350 SURFACE AREA OF THE COMPLEX: 28440 ANGSTROM**2
REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -57.0 KCAL/MOL
REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, H, 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 GLY A 43
REMARK 465 SER A 44
REMARK 465 GLY A 45
REMARK 465 GLY A 46
REMARK 465 GLY A 85
REMARK 465 SER A 86
REMARK 465 SER A 87
REMARK 465 GLY A 88
REMARK 465 ALA A 129
REMARK 465 GLY A 130
REMARK 465 GLY A 131
REMARK 465 SER A 132
REMARK 465 GLY A 133
REMARK 465 GLY A 134
REMARK 465 HIS A 135
REMARK 465 GLY A 173
REMARK 465 SER A 174
REMARK 465 SER A 175
REMARK 465 GLY A 176
REMARK 465 ALA A 217
REMARK 465 GLN H 1
REMARK 465 VAL H 2
REMARK 465 SER H 135
REMARK 465 LYS H 136
REMARK 465 SER H 137
REMARK 465 THR H 138
REMARK 465 SER H 139
REMARK 465 LYS H 221
REMARK 465 SER H 222
REMARK 465 GLU H 223
REMARK 465 PHE H 224
REMARK 465 GLU H 225
REMARK 465 GLN H 226
REMARK 465 LYS H 227
REMARK 465 LEU H 228
REMARK 465 ILE H 229
REMARK 465 SER H 230
REMARK 465 GLU H 231
REMARK 465 GLU H 232
REMARK 465 ASP H 233
REMARK 465 LEU H 234
REMARK 465 ASN H 235
REMARK 465 GLY H 236
REMARK 465 ALA H 237
REMARK 465 PRO H 238
REMARK 465 HIS H 239
REMARK 465 HIS H 240
REMARK 465 HIS H 241
REMARK 465 HIS H 242
REMARK 465 HIS H 243
REMARK 465 HIS H 244
REMARK 465 ASP L 1
REMARK 465 THR L 211
REMARK 465 GLU L 212
REMARK 465 ALA L 213
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 GLN H 199 CB CG CD OE1 NE2
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 OE2 GLU A 172 O HOH A 386 1.82
REMARK 500 O HOH A 233 O HOH A 332 1.94
REMARK 500 OE1 GLN H 3 O HOH H 317 2.02
REMARK 500 O HOH L 348 O HOH L 440 2.19
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 CE MET A 1 OH TYR A 60 4566 2.13
REMARK 500 O HOH H 269 O HOH L 312 1655 2.15
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 LEU H 185 CA - CB - CG ANGL. DEV. = 15.7 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 H 151 63.03 63.74
REMARK 500 ALA L 83 170.79 178.69
REMARK 500 VAL L 95 29.90 48.16
REMARK 500 PRO L 143 172.53 -57.38
REMARK 500 SER L 154 15.38 58.61
REMARK 500
REMARK 500 REMARK: NULL
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 NA H 245 NA
REMARK 620 N RES CSSEQI ATOM
REMARK 620 1 SER H 50 OG
REMARK 620 2 ASN H 58 OD1 97.6
REMARK 620 3 VAL L 95 O 123.6 97.3
REMARK 620 N 1 2
REMARK 620
REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL
REMARK 620 NA L 214 NA
REMARK 620 N RES CSSEQI ATOM
REMARK 620 1 GLY L 24 O
REMARK 620 2 ASN L 26 OD1 72.4
REMARK 620 N 1
REMARK 800
REMARK 800 SITE
REMARK 800 SITE_IDENTIFIER: AC1
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE NA H 245
REMARK 800
REMARK 800 SITE_IDENTIFIER: AC2
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE NA L 214
REMARK 900
REMARK 900 RELATED ENTRIES
REMARK 900 RELATED ID: 3MAC RELATED DB: PDB
REMARK 900 CRYSTAL STRUCTURE OF GP41-DERIVED PROTEIN COMPLEXED WITH FAB 8062
DBREF 3MA9 A 1 217 UNP D0VWW0 D0VWW0_9HIV1 1 217
DBREF 3MA9 H 1 244 PDB 3MA9 3MA9 1 244
DBREF 3MA9 L 1 213 PDB 3MA9 3MA9 1 213
SEQRES 1 A 217 MET GLN LEU LEU SER GLY ILE VAL GLN GLN GLN ASN ASN
SEQRES 2 A 217 LEU LEU ARG ALA ILE GLU ALA GLN GLN HIS LEU LEU GLN
SEQRES 3 A 217 LEU THR VAL TRP GLY ILE LYS GLN LEU GLN ALA ARG ILE
SEQRES 4 A 217 LEU ALA GLY GLY SER GLY GLY HIS THR THR TRP MET GLU
SEQRES 5 A 217 TRP ASP ARG GLU ILE ASN ASN TYR THR SER LEU ILE HIS
SEQRES 6 A 217 SER LEU ILE GLU GLU SER GLN ASN GLN GLN GLU LYS ASN
SEQRES 7 A 217 GLU GLN GLU LEU LEU GLU GLY SER SER GLY GLY GLN LEU
SEQRES 8 A 217 LEU SER GLY ILE VAL GLN GLN GLN ASN ASN LEU LEU ARG
SEQRES 9 A 217 ALA ILE GLU ALA GLN GLN HIS LEU LEU GLN LEU THR VAL
SEQRES 10 A 217 TRP GLY ILE LYS GLN LEU GLN ALA ARG ILE LEU ALA GLY
SEQRES 11 A 217 GLY SER GLY GLY HIS THR THR TRP MET GLU TRP ASP ARG
SEQRES 12 A 217 GLU ILE ASN ASN TYR THR SER LEU ILE HIS SER LEU ILE
SEQRES 13 A 217 GLU GLU SER GLN ASN GLN GLN GLU LYS ASN GLU GLN GLU
SEQRES 14 A 217 LEU LEU GLU GLY SER SER GLY GLY GLN LEU LEU SER GLY
SEQRES 15 A 217 ILE VAL GLN GLN GLN ASN ASN LEU LEU ARG ALA ILE GLU
SEQRES 16 A 217 ALA GLN GLN HIS LEU LEU GLN LEU THR VAL TRP GLY ILE
SEQRES 17 A 217 LYS GLN LEU GLN ALA ARG ILE LEU ALA
SEQRES 1 H 245 GLN VAL GLN LEU VAL GLN SER GLY ALA GLU VAL LYS LYS
SEQRES 2 H 245 PRO GLY SER SER VAL LYS VAL SER CYS LYS ALA SER GLY
SEQRES 3 H 245 GLY THR PHE ASN SER TYR ALA PHE SER TRP VAL ARG GLN
SEQRES 4 H 245 ALA PRO GLY GLN GLY LEU GLU TRP MET GLY SER ILE ILE
SEQRES 5 H 245 PRO ILE PHE GLY THR THR ASN TYR ALA GLN LYS PHE GLN
SEQRES 6 H 245 GLY ARG VAL THR ILE THR ALA ASP GLU SER THR SER THR
SEQRES 7 H 245 ALA TYR MET GLU LEU SER SER LEU ARG SER GLU ASP THR
SEQRES 8 H 245 ALA VAL TYR TYR CYS ALA ARG TYR PHE ASP THR TYR ASN
SEQRES 9 H 245 ASN TYR GLY PHE ALA ASN TRP GLY GLN GLY THR LEU VAL
SEQRES 10 H 245 THR VAL SER SER ALA SER THR LYS GLY PRO SER VAL PHE
SEQRES 11 H 245 PRO LEU ALA PRO SER SER LYS SER THR SER GLY GLY THR
SEQRES 12 H 245 ALA ALA LEU GLY CYS LEU VAL LYS ASP TYR PHE PRO GLU
SEQRES 13 H 245 PRO VAL THR VAL SER TRP ASN SER GLY ALA LEU THR SER
SEQRES 14 H 245 GLY VAL HIS THR PHE PRO ALA VAL LEU GLN SER SER GLY
SEQRES 15 H 245 LEU TYR SER LEU SER SER VAL VAL THR VAL PRO SER SER
SEQRES 16 H 245 SER LEU GLY THR GLN THR TYR ILE CYS ASN VAL ASN HIS
SEQRES 17 H 245 LYS PRO SER ASN THR LYS VAL ASP LYS LYS VAL GLU PRO
SEQRES 18 H 245 LYS SER GLU PHE GLU GLN LYS LEU ILE SER GLU GLU ASP
SEQRES 19 H 245 LEU ASN GLY ALA PRO HIS HIS HIS HIS HIS HIS
SEQRES 1 L 213 ASP ILE GLU LEU THR GLN PRO PRO SER VAL SER VAL VAL
SEQRES 2 L 213 PRO GLY GLN THR ALA ARG ILE SER CYS SER GLY ASP ASN
SEQRES 3 L 213 ILE PRO TYR GLU TYR ALA SER TRP TYR GLN GLN LYS PRO
SEQRES 4 L 213 GLY GLN ALA PRO VAL LEU VAL ILE TYR GLY ASP ASN ASN
SEQRES 5 L 213 ARG PRO SER GLY ILE PRO GLU ARG PHE SER GLY SER ASN
SEQRES 6 L 213 SER GLY ASN THR ALA THR LEU THR ILE SER GLY THR GLN
SEQRES 7 L 213 ALA GLU ASP GLU ALA ASP TYR TYR CYS ALA SER TRP ASP
SEQRES 8 L 213 SER MET THR VAL ASP GLY VAL PHE GLY GLY GLY THR LYS
SEQRES 9 L 213 LEU THR VAL LEU GLY GLN PRO LYS ALA ALA PRO SER VAL
SEQRES 10 L 213 THR LEU PHE PRO PRO SER SER GLU GLU LEU GLN ALA ASN
SEQRES 11 L 213 LYS ALA THR LEU VAL CYS LEU ILE SER ASP PHE TYR PRO
SEQRES 12 L 213 GLY ALA VAL THR VAL ALA TRP LYS ALA ASP SER SER PRO
SEQRES 13 L 213 VAL LYS ALA GLY VAL GLU THR THR THR PRO SER LYS GLN
SEQRES 14 L 213 SER ASN ASN LYS TYR ALA ALA SER SER TYR LEU SER LEU
SEQRES 15 L 213 THR PRO GLU GLN TRP LYS SER HIS ARG SER TYR SER CYS
SEQRES 16 L 213 GLN VAL THR HIS GLU GLY SER THR VAL GLU LYS THR VAL
SEQRES 17 L 213 ALA PRO THR GLU ALA
HET NA H 245 1
HET NA L 214 1
HETNAM NA SODIUM ION
FORMUL 4 NA 2(NA 1+)
FORMUL 6 HOH *442(H2 O)
HELIX 1 1 MET A 1 LEU A 40 1 40
HELIX 2 2 HIS A 47 GLU A 84 1 38
HELIX 3 3 GLY A 89 ALA A 125 1 37
HELIX 4 4 THR A 137 GLU A 172 1 36
HELIX 5 5 GLY A 177 ILE A 215 1 39
HELIX 6 6 THR H 28 TYR H 32 5 5
HELIX 7 7 GLN H 61 GLN H 64 5 4
HELIX 8 8 ARG H 86 THR H 90 5 5
HELIX 9 9 SER H 163 ALA H 165 5 3
HELIX 10 10 SER H 194 LEU H 196 5 3
HELIX 11 11 LYS H 208 ASN H 211 5 4
HELIX 12 12 PRO L 28 TYR L 31 5 4
HELIX 13 13 GLN L 78 GLU L 82 5 5
HELIX 14 14 SER L 123 ALA L 129 1 7
HELIX 15 15 THR L 183 SER L 189 1 7
SHEET 1 A 4 LEU H 4 GLN H 6 0
SHEET 2 A 4 VAL H 18 ALA H 24 -1 O LYS H 23 N VAL H 5
SHEET 3 A 4 THR H 77 LEU H 82 -1 O MET H 80 N VAL H 20
SHEET 4 A 4 VAL H 67 ASP H 72 -1 N THR H 70 O TYR H 79
SHEET 1 B 6 GLU H 10 LYS H 12 0
SHEET 2 B 6 THR H 114 VAL H 118 1 O THR H 117 N LYS H 12
SHEET 3 B 6 ALA H 91 ARG H 97 -1 N TYR H 93 O THR H 114
SHEET 4 B 6 PHE H 34 GLN H 39 -1 N VAL H 37 O TYR H 94
SHEET 5 B 6 GLU H 46 ILE H 51 -1 O MET H 48 N TRP H 36
SHEET 6 B 6 THR H 57 TYR H 59 -1 O ASN H 58 N SER H 50
SHEET 1 C 4 GLU H 10 LYS H 12 0
SHEET 2 C 4 THR H 114 VAL H 118 1 O THR H 117 N LYS H 12
SHEET 3 C 4 ALA H 91 ARG H 97 -1 N TYR H 93 O THR H 114
SHEET 4 C 4 ASN H 109 TRP H 110 -1 O ASN H 109 N ARG H 97
SHEET 1 D 4 SER H 127 LEU H 131 0
SHEET 2 D 4 THR H 142 TYR H 152 -1 O GLY H 146 N LEU H 131
SHEET 3 D 4 TYR H 183 PRO H 192 -1 O TYR H 183 N TYR H 152
SHEET 4 D 4 VAL H 170 THR H 172 -1 N HIS H 171 O VAL H 188
SHEET 1 E 4 SER H 127 LEU H 131 0
SHEET 2 E 4 THR H 142 TYR H 152 -1 O GLY H 146 N LEU H 131
SHEET 3 E 4 TYR H 183 PRO H 192 -1 O TYR H 183 N TYR H 152
SHEET 4 E 4 VAL H 176 LEU H 177 -1 N VAL H 176 O SER H 184
SHEET 1 F 3 THR H 158 TRP H 161 0
SHEET 2 F 3 ILE H 202 HIS H 207 -1 O ASN H 204 N SER H 160
SHEET 3 F 3 THR H 212 LYS H 217 -1 O VAL H 214 N VAL H 205
SHEET 1 G 5 SER L 9 VAL L 12 0
SHEET 2 G 5 THR L 103 VAL L 107 1 O THR L 106 N VAL L 10
SHEET 3 G 5 ALA L 83 TRP L 90 -1 N ALA L 83 O LEU L 105
SHEET 4 G 5 SER L 33 GLN L 37 -1 N GLN L 37 O ASP L 84
SHEET 5 G 5 VAL L 44 TYR L 48 -1 O VAL L 44 N GLN L 36
SHEET 1 H 4 SER L 9 VAL L 12 0
SHEET 2 H 4 THR L 103 VAL L 107 1 O THR L 106 N VAL L 10
SHEET 3 H 4 ALA L 83 TRP L 90 -1 N ALA L 83 O LEU L 105
SHEET 4 H 4 GLY L 97 PHE L 99 -1 O VAL L 98 N SER L 89
SHEET 1 I 3 ALA L 18 SER L 23 0
SHEET 2 I 3 THR L 69 ILE L 74 -1 O ALA L 70 N CYS L 22
SHEET 3 I 3 PHE L 61 SER L 66 -1 N SER L 62 O THR L 73
SHEET 1 J 4 SER L 116 PHE L 120 0
SHEET 2 J 4 ALA L 132 PHE L 141 -1 O LEU L 137 N THR L 118
SHEET 3 J 4 TYR L 174 LEU L 182 -1 O SER L 178 N CYS L 136
SHEET 4 J 4 VAL L 161 THR L 163 -1 N GLU L 162 O TYR L 179
SHEET 1 K 4 SER L 116 PHE L 120 0
SHEET 2 K 4 ALA L 132 PHE L 141 -1 O LEU L 137 N THR L 118
SHEET 3 K 4 TYR L 174 LEU L 182 -1 O SER L 178 N CYS L 136
SHEET 4 K 4 SER L 167 LYS L 168 -1 N SER L 167 O ALA L 175
SHEET 1 L 4 SER L 155 VAL L 157 0
SHEET 2 L 4 THR L 147 ALA L 152 -1 N ALA L 152 O SER L 155
SHEET 3 L 4 TYR L 193 HIS L 199 -1 O GLN L 196 N ALA L 149
SHEET 4 L 4 SER L 202 VAL L 208 -1 O VAL L 204 N VAL L 197
SSBOND 1 CYS H 22 CYS H 95 1555 1555 2.06
SSBOND 2 CYS H 147 CYS H 203 1555 1555 2.04
SSBOND 3 CYS L 22 CYS L 87 1555 1555 2.07
SSBOND 4 CYS L 136 CYS L 195 1555 1555 2.04
LINK OG SER H 50 NA NA H 245 1555 1555 2.88
LINK OD1 ASN H 58 NA NA H 245 1555 1555 2.73
LINK NA NA H 245 O VAL L 95 1555 1555 2.73
LINK O GLY L 24 NA NA L 214 1555 1555 2.95
LINK OD1 ASN L 26 NA NA L 214 1555 1555 3.10
CISPEP 1 PHE H 153 PRO H 154 0 -8.94
CISPEP 2 GLU H 155 PRO H 156 0 -2.50
CISPEP 3 ILE L 27 PRO L 28 0 -1.30
CISPEP 4 TYR L 142 PRO L 143 0 -2.61
SITE 1 AC1 5 TRP A 30 SER H 50 ASN H 58 TRP L 90
SITE 2 AC1 5 VAL L 95
SITE 1 AC2 5 SER H 74 SER H 76 GLY L 24 ASN L 26
SITE 2 AC2 5 ASN L 68
CRYST1 41.527 124.698 133.657 90.00 90.00 90.00 P 21 21 21 4
ORIGX1 1.000000 0.000000 0.000000 0.00000
ORIGX2 0.000000 1.000000 0.000000 0.00000
ORIGX3 0.000000 0.000000 1.000000 0.00000
SCALE1 0.024081 0.000000 0.000000 0.00000
SCALE2 0.000000 0.008019 0.000000 0.00000
SCALE3 0.000000 0.000000 0.007482 0.00000
(ATOM LINES ARE NOT SHOWN.)
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