HEADER IMMUNE SYSTEM 10-FEB-20 6VRY TITLE STRUCTURE OF NCI09 FAB IN COMPLEX WITH SIV V2 PEPTIDE COMPND MOL_ID: 1; COMPND 2 MOLECULE: NCI09 LIGHT CHAIN; COMPND 3 CHAIN: L; COMPND 4 ENGINEERED: YES; COMPND 5 MOL_ID: 2; COMPND 6 MOLECULE: SIV V2 PEPTIDE; COMPND 7 CHAIN: G; COMPND 8 ENGINEERED: YES; COMPND 9 MOL_ID: 3; COMPND 10 MOLECULE: NCI09 HEAVY CHAIN; COMPND 11 CHAIN: H; COMPND 12 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: MACACA MULATTA; SOURCE 3 ORGANISM_COMMON: RHESUS MONKEY; SOURCE 4 ORGANISM_TAXID: 9544; SOURCE 5 EXPRESSION_SYSTEM: HOMO SAPIENS; SOURCE 6 EXPRESSION_SYSTEM_COMMON: HUMAN; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 9606; SOURCE 8 EXPRESSION_SYSTEM_CELL_LINE: HEK293; SOURCE 9 MOL_ID: 2; SOURCE 10 SYNTHETIC: YES; SOURCE 11 ORGANISM_SCIENTIFIC: SIMIAN IMMUNODEFICIENCY VIRUS; SOURCE 12 ORGANISM_COMMON: SIV; SOURCE 13 ORGANISM_TAXID: 11723; SOURCE 14 MOL_ID: 3; SOURCE 15 ORGANISM_SCIENTIFIC: MACACA MULATTA; SOURCE 16 ORGANISM_COMMON: RHESUS MONKEY; SOURCE 17 ORGANISM_TAXID: 9544; SOURCE 18 EXPRESSION_SYSTEM: HOMO SAPIENS; SOURCE 19 EXPRESSION_SYSTEM_COMMON: HUMAN; SOURCE 20 EXPRESSION_SYSTEM_TAXID: 9606; SOURCE 21 EXPRESSION_SYSTEM_CELL_LINE: HEK293 KEYWDS SIV, V1V2, V2, ENV, GP120, ANTIBODY, NCI09, IMMUNE SYSTEM EXPDTA X-RAY DIFFRACTION AUTHOR J.GORMAN,M.AHMADI,P.D.KWONG REVDAT 2 11-OCT-23 6VRY 1 REMARK REVDAT 1 30-DEC-20 6VRY 0 JRNL AUTH J.GORMAN,M.AHMADI,P.D.KWONG JRNL TITL HIV VACCINE CANDIDATE WITH V1 DELETION REVEALS VIRUS JRNL TITL 2 VULNERABILITY TO V2 ANTIBODIES JRNL REF ISCIENCE 2020 JRNL REFN ESSN 2589-0042 REMARK 2 REMARK 2 RESOLUTION. 1.40 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (1.14_3260: ???) REMARK 3 AUTHORS : PAUL ADAMS,PAVEL AFONINE,VINCENT CHEN,IAN REMARK 3 : DAVIS,KRESHNA GOPAL,RALF GROSSE-KUNSTLEVE, REMARK 3 : LI-WEI HUNG,ROBERT IMMORMINO,TOM IOERGER, REMARK 3 : AIRLIE MCCOY,ERIK MCKEE,NIGEL MORIARTY, REMARK 3 : REETAL PAI,RANDY READ,JANE RICHARDSON, REMARK 3 : DAVID RICHARDSON,TOD ROMO,JIM SACCHETTINI, REMARK 3 : NICHOLAS SAUTER,JACOB SMITH,LAURENT REMARK 3 : STORONI,TOM TERWILLIGER,PETER ZWART REMARK 3 REMARK 3 REFINEMENT TARGET : NULL REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.40 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 31.26 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.360 REMARK 3 COMPLETENESS FOR RANGE (%) : 88.0 REMARK 3 NUMBER OF REFLECTIONS : 83495 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.148 REMARK 3 R VALUE (WORKING SET) : 0.147 REMARK 3 FREE R VALUE : 0.168 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 4175 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT (IN BINS). REMARK 3 BIN RESOLUTION RANGE COMPL. NWORK NFREE RWORK RFREE REMARK 3 1 31.2600 - 4.3466 0.80 2585 136 0.1710 0.1953 REMARK 3 2 4.3466 - 3.4514 0.91 2816 148 0.1309 0.1532 REMARK 3 3 3.4514 - 3.0156 0.95 2930 155 0.1422 0.1550 REMARK 3 4 3.0156 - 2.7400 0.96 2921 154 0.1461 0.1575 REMARK 3 5 2.7400 - 2.5437 0.97 2944 155 0.1463 0.1629 REMARK 3 6 2.5437 - 2.3938 0.97 2963 155 0.1418 0.1690 REMARK 3 7 2.3938 - 2.2740 0.98 2924 154 0.1349 0.1607 REMARK 3 8 2.2740 - 2.1750 0.97 2941 155 0.1336 0.1615 REMARK 3 9 2.1750 - 2.0913 0.98 2958 155 0.1388 0.1434 REMARK 3 10 2.0913 - 2.0191 0.98 2938 155 0.1385 0.1616 REMARK 3 11 2.0191 - 1.9560 0.98 2943 155 0.1374 0.1622 REMARK 3 12 1.9560 - 1.9001 0.98 2929 155 0.1441 0.1429 REMARK 3 13 1.9001 - 1.8501 0.98 2924 153 0.1377 0.1511 REMARK 3 14 1.8501 - 1.8050 0.98 2930 155 0.1439 0.1765 REMARK 3 15 1.8050 - 1.7639 0.98 2936 154 0.1430 0.1806 REMARK 3 16 1.7639 - 1.7264 0.97 2894 153 0.1517 0.1570 REMARK 3 17 1.7264 - 1.6919 0.97 2915 152 0.1528 0.1741 REMARK 3 18 1.6919 - 1.6599 0.97 2911 154 0.1518 0.1712 REMARK 3 19 1.6599 - 1.6303 0.97 2868 151 0.1544 0.2060 REMARK 3 20 1.6303 - 1.6027 0.97 2889 152 0.1529 0.1977 REMARK 3 21 1.6027 - 1.5768 0.96 2902 153 0.1588 0.1731 REMARK 3 22 1.5768 - 1.5526 0.95 2829 149 0.1663 0.2054 REMARK 3 23 1.5526 - 1.5297 0.93 2743 144 0.1673 0.1957 REMARK 3 24 1.5297 - 1.5082 0.88 2616 138 0.1825 0.2079 REMARK 3 25 1.5082 - 1.4878 0.77 2319 121 0.1885 0.2270 REMARK 3 26 1.4878 - 1.4685 0.70 2078 110 0.1950 0.1837 REMARK 3 27 1.4685 - 1.4501 0.62 1843 97 0.1959 0.2424 REMARK 3 28 1.4501 - 1.4326 0.53 1552 82 0.2084 0.2104 REMARK 3 29 1.4326 - 1.4160 0.45 1330 70 0.1970 0.2382 REMARK 3 30 1.4160 - 1.4001 0.36 1049 55 0.2102 0.1899 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : NULL REMARK 3 SOLVENT RADIUS : 1.11 REMARK 3 SHRINKAGE RADIUS : 0.90 REMARK 3 K_SOL : NULL REMARK 3 B_SOL : NULL REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.100 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 16.250 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : NULL REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : NULL REMARK 3 B22 (A**2) : NULL REMARK 3 B33 (A**2) : NULL REMARK 3 B12 (A**2) : NULL REMARK 3 B13 (A**2) : NULL REMARK 3 B23 (A**2) : NULL REMARK 3 REMARK 3 TWINNING INFORMATION. REMARK 3 FRACTION: NULL REMARK 3 OPERATOR: NULL REMARK 3 REMARK 3 DEVIATIONS FROM IDEAL VALUES. REMARK 3 RMSD COUNT REMARK 3 BOND : 0.010 3671 REMARK 3 ANGLE : 1.127 5041 REMARK 3 CHIRALITY : 0.090 583 REMARK 3 PLANARITY : 0.007 636 REMARK 3 DIHEDRAL : 17.811 1378 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 5 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: CHAIN 'L' AND (RESID 1 THROUGH 113 ) REMARK 3 ORIGIN FOR THE GROUP (A): 7.2313 -10.3714 -13.0497 REMARK 3 T TENSOR REMARK 3 T11: 0.1145 T22: 0.0916 REMARK 3 T33: 0.1050 T12: -0.0087 REMARK 3 T13: 0.0058 T23: -0.0028 REMARK 3 L TENSOR REMARK 3 L11: 0.3193 L22: 0.5675 REMARK 3 L33: 1.4575 L12: -0.2455 REMARK 3 L13: -0.1764 L23: -0.4374 REMARK 3 S TENSOR REMARK 3 S11: 0.0686 S12: -0.0001 S13: 0.1003 REMARK 3 S21: 0.0639 S22: -0.0302 S23: 0.0534 REMARK 3 S31: -0.2030 S32: 0.0275 S33: -0.0016 REMARK 3 TLS GROUP : 2 REMARK 3 SELECTION: CHAIN 'L' AND (RESID 114 THROUGH 214 ) REMARK 3 ORIGIN FOR THE GROUP (A): 10.6849 -9.1716 -49.4856 REMARK 3 T TENSOR REMARK 3 T11: 0.1034 T22: 0.1212 REMARK 3 T33: 0.1122 T12: -0.0108 REMARK 3 T13: 0.0065 T23: 0.0102 REMARK 3 L TENSOR REMARK 3 L11: 1.1886 L22: 1.5428 REMARK 3 L33: 1.0734 L12: -0.0223 REMARK 3 L13: 0.3421 L23: 0.0813 REMARK 3 S TENSOR REMARK 3 S11: -0.0055 S12: 0.1620 S13: 0.0108 REMARK 3 S21: -0.0947 S22: 0.0151 S23: -0.0102 REMARK 3 S31: 0.0290 S32: -0.0086 S33: 0.0001 REMARK 3 TLS GROUP : 3 REMARK 3 SELECTION: CHAIN 'G' AND (RESID 163 THROUGH 173 ) REMARK 3 ORIGIN FOR THE GROUP (A): 16.0980 -27.0293 4.1564 REMARK 3 T TENSOR REMARK 3 T11: 0.1571 T22: 0.2174 REMARK 3 T33: 0.1315 T12: -0.0111 REMARK 3 T13: -0.0391 T23: 0.0478 REMARK 3 L TENSOR REMARK 3 L11: 0.1623 L22: 0.1991 REMARK 3 L33: 0.0605 L12: -0.0583 REMARK 3 L13: -0.0087 L23: 0.0871 REMARK 3 S TENSOR REMARK 3 S11: -0.0155 S12: -0.4821 S13: -0.2293 REMARK 3 S21: 0.3249 S22: 0.0277 S23: -0.0559 REMARK 3 S31: 0.0179 S32: -0.1681 S33: -0.0049 REMARK 3 TLS GROUP : 4 REMARK 3 SELECTION: CHAIN 'H' AND (RESID 1 THROUGH 119 ) REMARK 3 ORIGIN FOR THE GROUP (A): 17.6407 -30.6282 -15.5345 REMARK 3 T TENSOR REMARK 3 T11: 0.0803 T22: 0.0835 REMARK 3 T33: 0.0908 T12: -0.0068 REMARK 3 T13: -0.0089 T23: 0.0074 REMARK 3 L TENSOR REMARK 3 L11: 0.5994 L22: 0.8413 REMARK 3 L33: 1.6398 L12: -0.0950 REMARK 3 L13: 0.0854 L23: 0.2189 REMARK 3 S TENSOR REMARK 3 S11: 0.0040 S12: -0.0244 S13: -0.0477 REMARK 3 S21: -0.0013 S22: 0.0056 S23: -0.0690 REMARK 3 S31: 0.0238 S32: 0.0606 S33: 0.0001 REMARK 3 TLS GROUP : 5 REMARK 3 SELECTION: CHAIN 'H' AND (RESID 120 THROUGH 214 ) REMARK 3 ORIGIN FOR THE GROUP (A): 23.4342 -15.4150 -42.8262 REMARK 3 T TENSOR REMARK 3 T11: 0.1163 T22: 0.1188 REMARK 3 T33: 0.1089 T12: 0.0034 REMARK 3 T13: 0.0101 T23: -0.0056 REMARK 3 L TENSOR REMARK 3 L11: 1.2895 L22: 1.2604 REMARK 3 L33: 0.7164 L12: -0.0040 REMARK 3 L13: 0.1554 L23: -0.0729 REMARK 3 S TENSOR REMARK 3 S11: -0.0886 S12: 0.0705 S13: 0.0761 REMARK 3 S21: -0.0920 S22: 0.0383 S23: -0.0873 REMARK 3 S31: 0.0296 S32: 0.0820 S33: -0.0000 REMARK 3 REMARK 3 NCS DETAILS REMARK 3 NUMBER OF NCS GROUPS : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 6VRY COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 11-FEB-20. REMARK 100 THE DEPOSITION ID IS D_1000246967. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 28-DEC-17 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 4.6 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 : SI(111) REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : MARMOSAIC 300 MM CCD REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 87297 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.400 REMARK 200 RESOLUTION RANGE LOW (A) : 40.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 92.0 REMARK 200 DATA REDUNDANCY : 3.400 REMARK 200 R MERGE (I) : 0.04400 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 17.6000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.40 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.42 REMARK 200 COMPLETENESS FOR SHELL (%) : 65.8 REMARK 200 DATA REDUNDANCY IN SHELL : 1.60 REMARK 200 R MERGE FOR SHELL (I) : 0.41400 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: PHENIX REMARK 200 STARTING MODEL: PDB ENTRY 5WT9 REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 47.88 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.36 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 22% W/V PEG4000, 0.1 M SODIUM ACETATE, REMARK 280 PH 4.6, CRYOPROTECTANT: 20% ETHYLENE GLYCOL, VAPOR DIFFUSION, REMARK 280 HANGING DROP, TEMPERATURE 273K 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 32.88000 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 50.41650 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 36.04350 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 50.41650 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 32.88000 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 36.04350 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: 6180 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 19890 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -24.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: L, G, H, A 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 LYS G 158 REMARK 465 PHE G 159 REMARK 465 THR G 160 REMARK 465 MET G 161 REMARK 465 THR G 162 REMARK 465 SER H 215 REMARK 465 CYS H 216 REMARK 465 ASP H 217 REMARK 465 LYS H 218 REMARK 465 GLY H 219 REMARK 465 LEU H 220 REMARK 465 GLU H 221 REMARK 465 VAL H 222 REMARK 465 LEU H 223 REMARK 465 PHE H 224 REMARK 465 GLN H 225 REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS IN SAME ASYMMETRIC UNIT REMARK 500 REMARK 500 THE FOLLOWING ATOMS ARE IN CLOSE CONTACT. REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI DISTANCE REMARK 500 O HOH H 543 O HOH H 563 1.86 REMARK 500 O HOH H 389 O HOH H 495 1.87 REMARK 500 O HOH L 532 O HOH L 622 1.88 REMARK 500 O HOH H 329 O HOH H 381 1.92 REMARK 500 O HOH H 321 O HOH H 454 1.95 REMARK 500 O HOH H 308 O HOH H 378 2.04 REMARK 500 O HOH L 558 O HOH L 620 2.05 REMARK 500 O HOH H 477 O HOH H 569 2.07 REMARK 500 O HOH L 574 O HOH L 671 2.10 REMARK 500 O HOH L 573 O HOH L 635 2.11 REMARK 500 O HOH H 403 O HOH H 503 2.14 REMARK 500 O HOH L 496 O HOH L 655 2.14 REMARK 500 O HOH L 406 O HOH L 657 2.15 REMARK 500 O HOH L 616 O HOH L 661 2.15 REMARK 500 O HOH H 455 O HOH H 535 2.16 REMARK 500 OG SER L 127 O HOH L 401 2.17 REMARK 500 O HOH H 435 O HOH H 566 2.18 REMARK 500 O HOH H 587 O HOH H 595 2.18 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS REMARK 500 REMARK 500 THE FOLLOWING ATOMS THAT ARE RELATED BY CRYSTALLOGRAPHIC REMARK 500 SYMMETRY ARE IN CLOSE CONTACT. AN ATOM LOCATED WITHIN 0.15 REMARK 500 ANGSTROMS OF A SYMMETRY RELATED ATOM IS ASSUMED TO BE ON A REMARK 500 SPECIAL POSITION AND IS, THEREFORE, LISTED IN REMARK 375 REMARK 500 INSTEAD OF REMARK 500. ATOMS WITH NON-BLANK ALTERNATE REMARK 500 LOCATION INDICATORS ARE NOT INCLUDED IN THE CALCULATIONS. REMARK 500 REMARK 500 DISTANCE CUTOFF: REMARK 500 2.2 ANGSTROMS FOR CONTACTS NOT INVOLVING HYDROGEN ATOMS REMARK 500 1.6 ANGSTROMS FOR CONTACTS INVOLVING HYDROGEN ATOMS REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI SSYMOP DISTANCE REMARK 500 O HOH L 645 O HOH H 540 3554 1.84 REMARK 500 O HOH L 659 O HOH H 552 3554 2.02 REMARK 500 O HOH L 612 O HOH H 507 2544 2.06 REMARK 500 O HOH L 656 O HOH H 555 4444 2.10 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 CYS H 196 CA - CB - SG ANGL. DEV. = 9.0 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 ASN L 30 -107.67 53.69 REMARK 500 ALA L 51 -37.85 71.30 REMARK 500 ALA L 84 170.01 178.82 REMARK 500 TYR L 91 41.37 -140.82 REMARK 500 SER H 15 -11.99 84.19 REMARK 500 LYS H 43 1.20 85.69 REMARK 500 ASP H 144 58.02 71.38 REMARK 500 REMARK 500 REMARK: NULL REMARK 525 REMARK 525 SOLVENT REMARK 525 REMARK 525 THE SOLVENT MOLECULES HAVE CHAIN IDENTIFIERS THAT REMARK 525 INDICATE THE POLYMER CHAIN WITH WHICH THEY ARE MOST REMARK 525 CLOSELY ASSOCIATED. THE REMARK LISTS ALL THE SOLVENT REMARK 525 MOLECULES WHICH ARE MORE THAN 5A AWAY FROM THE REMARK 525 NEAREST POLYMER CHAIN (M = MODEL NUMBER; REMARK 525 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE REMARK 525 NUMBER; I=INSERTION CODE): REMARK 525 REMARK 525 M RES CSSEQI REMARK 525 HOH L 700 DISTANCE = 6.23 ANGSTROMS REMARK 525 HOH H 607 DISTANCE = 6.05 ANGSTROMS REMARK 525 HOH H 608 DISTANCE = 7.61 ANGSTROMS DBREF 6VRY L 1 214 PDB 6VRY 6VRY 1 214 DBREF 6VRY G 158 172 UNP P08810 ENV_SIVM2 171 185 DBREF 6VRY H 1 225 PDB 6VRY 6VRY 1 225 SEQADV 6VRY ASN G 173 UNP P08810 EXPRESSION TAG SEQRES 1 L 214 GLU ILE VAL MET THR GLN SER PRO VAL THR LEU SER LEU SEQRES 2 L 214 SER PRO GLY GLU ARG ALA THR LEU SER CYS ARG ALA SER SEQRES 3 L 214 GLN SER VAL ASN ALA SER LEU ALA TRP TYR GLN GLN LYS SEQRES 4 L 214 PRO GLY GLN ALA PRO ARG LEU LEU ILE TYR ASP ALA SER SEQRES 5 L 214 THR ARG ALA THR GLY LEU PRO ASP ARG PHE SER GLY SER SEQRES 6 L 214 GLY SER GLY THR GLU PHE THR LEU SER ILE SER SER LEU SEQRES 7 L 214 GLU PRO GLU ASP PHE ALA VAL TYR TYR CYS GLN HIS TYR SEQRES 8 L 214 PHE ASN TRP PRO LEU THR PHE GLY GLY GLY THR LYS VAL SEQRES 9 L 214 GLU ILE LYS ARG THR VAL ALA ALA PRO SER VAL PHE ILE SEQRES 10 L 214 PHE PRO PRO SER ASP GLU GLN LEU LYS SER GLY THR ALA SEQRES 11 L 214 SER VAL VAL CYS LEU LEU ASN ASN PHE TYR PRO ARG GLU SEQRES 12 L 214 ALA LYS VAL GLN TRP LYS VAL ASP ASN ALA LEU GLN SER SEQRES 13 L 214 GLY ASN SER GLN GLU SER VAL THR GLU GLN ASP SER LYS SEQRES 14 L 214 ASP SER THR TYR SER LEU SER SER THR LEU THR LEU SER SEQRES 15 L 214 LYS ALA ASP TYR GLU LYS HIS LYS VAL TYR ALA CYS GLU SEQRES 16 L 214 VAL THR HIS GLN GLY LEU SER SER PRO VAL THR LYS SER SEQRES 17 L 214 PHE ASN ARG GLY GLU CYS SEQRES 1 G 16 LYS PHE THR MET THR GLY LEU LYS ARG ASP LYS THR LYS SEQRES 2 G 16 GLU TYR ASN SEQRES 1 H 236 GLN VAL GLN LEU GLN GLU SER GLY PRO GLY LEU VAL LYS SEQRES 2 H 236 PRO SER GLU THR LEU SER LEU THR CYS ALA VAL SER GLY SEQRES 3 H 236 GLY SER ILE SER ASP TYR TYR TYR TRP ASN TRP ILE ARG SEQRES 4 H 236 GLN PHE PRO GLY LYS GLY LEU GLU TRP ILE GLY ASN ILE SEQRES 5 H 236 TYR GLY LYS SER ALA SER THR TYR TYR ASN PRO SER LEU SEQRES 6 H 236 LYS SER ARG VAL SER ILE SER LYS ASP THR SER LYS ASN SEQRES 7 H 236 GLN PHE PHE LEU LYS LEU SER SER VAL THR ALA ALA ASP SEQRES 8 H 236 THR ALA VAL TYR TYR CYS ALA ARG GLU TYR CYS ILE GLY SEQRES 9 H 236 SER THR CYS TYR PRO ILE LEU ASP SER TRP GLY GLN GLY SEQRES 10 H 236 ALA VAL VAL THR VAL SER SER ALA SER THR LYS GLY PRO SEQRES 11 H 236 SER VAL PHE PRO LEU ALA PRO SER SER LYS SER THR SER SEQRES 12 H 236 GLY GLY THR ALA ALA LEU GLY CYS LEU VAL LYS ASP TYR SEQRES 13 H 236 PHE PRO GLU PRO VAL THR VAL SER TRP ASN SER GLY ALA SEQRES 14 H 236 LEU THR SER GLY VAL HIS THR PHE PRO ALA VAL LEU GLN SEQRES 15 H 236 SER SER GLY LEU TYR SER LEU SER SER VAL VAL THR VAL SEQRES 16 H 236 PRO SER SER SER LEU GLY THR GLN THR TYR ILE CYS ASN SEQRES 17 H 236 VAL ASN HIS LYS PRO SER ASN THR LYS VAL ASP LYS ARG SEQRES 18 H 236 VAL GLU PRO LYS SER CYS ASP LYS GLY LEU GLU VAL LEU SEQRES 19 H 236 PHE GLN HET NAG A 1 26 HET NAG A 2 26 HET BMA A 3 11 HET FUC A 4 20 HETNAM NAG 2-ACETAMIDO-2-DEOXY-BETA-D-GLUCOPYRANOSE HETNAM BMA BETA-D-MANNOPYRANOSE HETNAM FUC ALPHA-L-FUCOPYRANOSE HETSYN NAG N-ACETYL-BETA-D-GLUCOSAMINE; 2-ACETAMIDO-2-DEOXY-BETA- HETSYN 2 NAG D-GLUCOSE; 2-ACETAMIDO-2-DEOXY-D-GLUCOSE; 2-ACETAMIDO- HETSYN 3 NAG 2-DEOXY-GLUCOSE; N-ACETYL-D-GLUCOSAMINE HETSYN BMA BETA-D-MANNOSE; D-MANNOSE; MANNOSE HETSYN FUC ALPHA-L-FUCOSE; 6-DEOXY-ALPHA-L-GALACTOPYRANOSE; L- HETSYN 2 FUC FUCOSE; FUCOSE FORMUL 4 NAG 2(C8 H15 N O6) FORMUL 4 BMA C6 H12 O6 FORMUL 4 FUC C6 H12 O5 FORMUL 5 HOH *634(H2 O) HELIX 1 AA1 GLU L 79 PHE L 83 5 5 HELIX 2 AA2 SER L 121 LYS L 126 1 6 HELIX 3 AA3 LYS L 183 GLU L 187 1 5 HELIX 4 AA4 THR H 83 THR H 87 5 5 HELIX 5 AA5 SER H 127 LYS H 129 5 3 HELIX 6 AA6 SER H 156 ALA H 158 5 3 HELIX 7 AA7 SER H 187 LEU H 189 5 3 HELIX 8 AA8 LYS H 201 ASN H 204 5 4 SHEET 1 AA1 4 MET L 4 SER L 7 0 SHEET 2 AA1 4 ALA L 19 ALA L 25 -1 O SER L 22 N SER L 7 SHEET 3 AA1 4 GLU L 70 ILE L 75 -1 O LEU L 73 N LEU L 21 SHEET 4 AA1 4 PHE L 62 SER L 67 -1 N SER L 63 O SER L 74 SHEET 1 AA2 6 THR L 10 LEU L 13 0 SHEET 2 AA2 6 THR L 102 ILE L 106 1 O GLU L 105 N LEU L 11 SHEET 3 AA2 6 ALA L 84 HIS L 90 -1 N ALA L 84 O VAL L 104 SHEET 4 AA2 6 LEU L 33 GLN L 38 -1 N GLN L 38 O VAL L 85 SHEET 5 AA2 6 ARG L 45 TYR L 49 -1 O LEU L 47 N TRP L 35 SHEET 6 AA2 6 THR L 53 ARG L 54 -1 O THR L 53 N TYR L 49 SHEET 1 AA3 4 THR L 10 LEU L 13 0 SHEET 2 AA3 4 THR L 102 ILE L 106 1 O GLU L 105 N LEU L 11 SHEET 3 AA3 4 ALA L 84 HIS L 90 -1 N ALA L 84 O VAL L 104 SHEET 4 AA3 4 THR L 97 PHE L 98 -1 O THR L 97 N HIS L 90 SHEET 1 AA4 4 SER L 114 PHE L 118 0 SHEET 2 AA4 4 THR L 129 PHE L 139 -1 O ASN L 137 N SER L 114 SHEET 3 AA4 4 TYR L 173 SER L 182 -1 O LEU L 175 N LEU L 136 SHEET 4 AA4 4 SER L 159 VAL L 163 -1 N SER L 162 O SER L 176 SHEET 1 AA5 4 ALA L 153 LEU L 154 0 SHEET 2 AA5 4 LYS L 145 VAL L 150 -1 N VAL L 150 O ALA L 153 SHEET 3 AA5 4 VAL L 191 THR L 197 -1 O GLU L 195 N GLN L 147 SHEET 4 AA5 4 VAL L 205 ASN L 210 -1 O VAL L 205 N VAL L 196 SHEET 1 AA6 5 ARG G 166 ASP G 167 0 SHEET 2 AA6 5 THR H 100A TRP H 103 -1 O CYS H 100B N ARG G 166 SHEET 3 AA6 5 ALA H 88 ILE H 98 -1 N ILE H 98 O THR H 100A SHEET 4 AA6 5 ALA H 107 VAL H 111 -1 O ALA H 107 N TYR H 90 SHEET 5 AA6 5 LEU H 11 VAL H 12 1 N VAL H 12 O THR H 110 SHEET 1 AA7 6 ARG G 166 ASP G 167 0 SHEET 2 AA7 6 THR H 100A TRP H 103 -1 O CYS H 100B N ARG G 166 SHEET 3 AA7 6 ALA H 88 ILE H 98 -1 N ILE H 98 O THR H 100A SHEET 4 AA7 6 TYR H 34 GLN H 39 -1 N ILE H 37 O TYR H 91 SHEET 5 AA7 6 LEU H 45 TYR H 52 -1 O ILE H 51 N TRP H 35 SHEET 6 AA7 6 THR H 57 TYR H 59 -1 O TYR H 58 N ASN H 50 SHEET 1 AA8 4 GLN H 3 SER H 7 0 SHEET 2 AA8 4 LEU H 18 SER H 25 -1 O SER H 25 N GLN H 3 SHEET 3 AA8 4 GLN H 77 LEU H 82 -1 O LEU H 82 N LEU H 18 SHEET 4 AA8 4 VAL H 67 ASP H 72 -1 N ASP H 72 O GLN H 77 SHEET 1 AA9 4 SER H 120 LEU H 124 0 SHEET 2 AA9 4 THR H 135 TYR H 145 -1 O LEU H 141 N PHE H 122 SHEET 3 AA9 4 TYR H 176 PRO H 185 -1 O LEU H 178 N VAL H 142 SHEET 4 AA9 4 VAL H 163 THR H 165 -1 N HIS H 164 O VAL H 181 SHEET 1 AB1 4 THR H 131 SER H 132 0 SHEET 2 AB1 4 THR H 135 TYR H 145 -1 O THR H 135 N SER H 132 SHEET 3 AB1 4 TYR H 176 PRO H 185 -1 O LEU H 178 N VAL H 142 SHEET 4 AB1 4 VAL H 169 LEU H 170 -1 N VAL H 169 O SER H 177 SHEET 1 AB2 3 THR H 151 TRP H 154 0 SHEET 2 AB2 3 ILE H 195 HIS H 200 -1 O ASN H 197 N SER H 153 SHEET 3 AB2 3 THR H 205 ARG H 210 -1 O VAL H 207 N VAL H 198 SSBOND 1 CYS L 23 CYS L 88 1555 1555 2.21 SSBOND 2 CYS L 134 CYS L 194 1555 1555 2.06 SSBOND 3 CYS H 22 CYS H 92 1555 1555 2.19 SSBOND 4 CYS H 97 CYS H 100B 1555 1555 2.07 SSBOND 5 CYS H 140 CYS H 196 1555 1555 2.04 LINK ND2 ASN L 30 C1 NAG A 1 1555 1555 1.45 LINK O4 NAG A 1 C1 NAG A 2 1555 1555 1.45 LINK O6 NAG A 1 C1 FUC A 4 1555 1555 1.44 LINK O4 NAG A 2 C1 BMA A 3 1555 1555 1.44 CISPEP 1 SER L 7 PRO L 8 0 -11.09 CISPEP 2 TRP L 94 PRO L 95 0 -0.79 CISPEP 3 TYR L 140 PRO L 141 0 1.83 CISPEP 4 PHE H 146 PRO H 147 0 -8.61 CISPEP 5 GLU H 148 PRO H 149 0 -0.93 CRYST1 65.760 72.087 100.833 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 0.015207 0.000000 0.000000 0.00000 SCALE2 0.000000 0.013872 0.000000 0.00000 SCALE3 0.000000 0.000000 0.009917 0.00000