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 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 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