HEADER IMMUNE SYSTEM 15-JAN-10 3LEV TITLE HIV-1 ANTIBODY 2F5 IN COMPLEX WITH EPITOPE SCAFFOLD ES2 COMPND MOL_ID: 1; COMPND 2 MOLECULE: RNA POLYMERASE SIGMA FACTOR; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: UNP RESIDUES 93-271; COMPND 5 ENGINEERED: YES; COMPND 6 MOL_ID: 2; COMPND 7 MOLECULE: 2F5 ANTIBODY LIGHT CHAIN; COMPND 8 CHAIN: L; COMPND 9 ENGINEERED: YES; COMPND 10 MOL_ID: 3; COMPND 11 MOLECULE: 2F5 ANTIBODY HEAVY CHAIN; COMPND 12 CHAIN: H; COMPND 13 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: THERMUS AQUATICUS; SOURCE 3 ORGANISM_TAXID: 271; SOURCE 4 GENE: SIGMA FACTOR SIGA; SOURCE 5 EXPRESSION_SYSTEM: HOMO SAPIENS; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 9606; SOURCE 7 EXPRESSION_SYSTEM_CELL_LINE: HEK293F; SOURCE 8 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 9 EXPRESSION_SYSTEM_PLASMID: CMV-R; SOURCE 10 MOL_ID: 2; SOURCE 11 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 12 ORGANISM_COMMON: HUMAN; SOURCE 13 ORGANISM_TAXID: 9606; SOURCE 14 EXPRESSION_SYSTEM: HOMO SAPIENS; SOURCE 15 EXPRESSION_SYSTEM_COMMON: HUMAN; SOURCE 16 EXPRESSION_SYSTEM_TAXID: 9606; SOURCE 17 EXPRESSION_SYSTEM_CELL_LINE: CB-F7; SOURCE 18 OTHER_DETAILS: HETEROMYELOMA CELL LINE FUSED WITH PERIPHERAL BLOOD SOURCE 19 MONONUCLEAR CELLS; SOURCE 20 MOL_ID: 3; SOURCE 21 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 22 ORGANISM_COMMON: HUMAN; SOURCE 23 ORGANISM_TAXID: 9606; SOURCE 24 EXPRESSION_SYSTEM: HOMO SAPIENS; SOURCE 25 EXPRESSION_SYSTEM_COMMON: HUMAN; SOURCE 26 EXPRESSION_SYSTEM_TAXID: 9606; SOURCE 27 EXPRESSION_SYSTEM_CELL_LINE: CB-F7; SOURCE 28 OTHER_DETAILS: HETEROMYELOMA CELL LINE FUSED WITH PERIPHERAL BLOOD SOURCE 29 MONONUCLEAR CELLS KEYWDS HIV-1, GP41, MONOCLONAL ANTIBODY, 2F5, SCAFFOLD, EPITOPE, TRANSPLANT, KEYWDS 2 GRAFT, SIGMA FACTOR, RE-ELICITATION, IMMUNE SYSTEM, VACCINE DESIGN EXPDTA X-RAY DIFFRACTION AUTHOR G.OFEK,F.J.GUENAGA,W.R.SCHIEF,J.SKINNER,D.BAKER,R.WYATT,P.D.KWONG REVDAT 5 06-SEP-23 3LEV 1 REMARK REVDAT 4 13-OCT-21 3LEV 1 SEQADV REVDAT 3 31-MAR-21 3LEV 1 SOURCE REMARK REVDAT 2 24-NOV-10 3LEV 1 JRNL REVDAT 1 29-SEP-10 3LEV 0 JRNL AUTH G.OFEK,F.J.GUENAGA,W.R.SCHIEF,J.SKINNER,D.BAKER,R.WYATT, JRNL AUTH 2 P.D.KWONG JRNL TITL ELICITATION OF STRUCTURE-SPECIFIC ANTIBODIES BY EPITOPE JRNL TITL 2 SCAFFOLDS. JRNL REF PROC.NATL.ACAD.SCI.USA V. 107 17880 2010 JRNL REFN ISSN 0027-8424 JRNL PMID 20876137 JRNL DOI 10.1073/PNAS.1004728107 REMARK 2 REMARK 2 RESOLUTION. 2.50 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (PHENIX.REFINE) 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 : ML REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.50 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 46.15 REMARK 3 MIN(FOBS/SIGMA_FOBS) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 84.0 REMARK 3 NUMBER OF REFLECTIONS : 22446 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.206 REMARK 3 R VALUE (WORKING SET) : 0.201 REMARK 3 FREE R VALUE : 0.253 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 9.900 REMARK 3 FREE R VALUE TEST SET COUNT : 2222 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT (IN BINS). REMARK 3 BIN RESOLUTION RANGE COMPL. NWORK NFREE RWORK RFREE REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : FLAT BULK SOLVENT MODEL REMARK 3 SOLVENT RADIUS : 1.11 REMARK 3 SHRINKAGE RADIUS : 0.90 REMARK 3 K_SOL : 0.35 REMARK 3 B_SOL : 94.15 REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.300 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : NULL REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 69.40 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 106.8 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 3.09430 REMARK 3 B22 (A**2) : 2.51650 REMARK 3 B33 (A**2) : -9.54410 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 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 : 0.007 5014 REMARK 3 ANGLE : 0.959 6811 REMARK 3 CHIRALITY : 0.053 776 REMARK 3 PLANARITY : 0.005 858 REMARK 3 DIHEDRAL : 15.279 1835 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 9 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: CHAIN A AND RESID 93:158 REMARK 3 ORIGIN FOR THE GROUP (A): 1.9597 -21.6558 10.1007 REMARK 3 T TENSOR REMARK 3 T11: 0.6107 T22: 0.4543 REMARK 3 T33: 1.5092 T12: 0.0942 REMARK 3 T13: -0.0807 T23: -0.4991 REMARK 3 L TENSOR REMARK 3 L11: 2.6155 L22: -0.8977 REMARK 3 L33: 2.0618 L12: 0.9037 REMARK 3 L13: -0.6144 L23: 0.7730 REMARK 3 S TENSOR REMARK 3 S11: -0.1726 S12: -0.5642 S13: 1.9781 REMARK 3 S21: -0.5040 S22: 0.6727 S23: -0.2869 REMARK 3 S31: -0.5038 S32: 0.1366 S33: -0.1239 REMARK 3 TLS GROUP : 2 REMARK 3 SELECTION: CHAIN A AND RESID 159:186 REMARK 3 ORIGIN FOR THE GROUP (A): 8.9658 -12.9282 18.8628 REMARK 3 T TENSOR REMARK 3 T11: 1.1732 T22: 0.6549 REMARK 3 T33: 1.7879 T12: -0.2968 REMARK 3 T13: -0.1902 T23: -0.4077 REMARK 3 L TENSOR REMARK 3 L11: 2.5132 L22: 1.0566 REMARK 3 L33: 1.2104 L12: -0.4264 REMARK 3 L13: 1.0889 L23: 0.0688 REMARK 3 S TENSOR REMARK 3 S11: 0.1969 S12: -0.5534 S13: 1.5225 REMARK 3 S21: -0.3279 S22: -0.0905 S23: -0.2641 REMARK 3 S31: -1.5696 S32: -0.0817 S33: 0.4431 REMARK 3 TLS GROUP : 3 REMARK 3 SELECTION: CHAIN A AND RESID 187:225 REMARK 3 ORIGIN FOR THE GROUP (A): -4.7255 -23.3638 6.5074 REMARK 3 T TENSOR REMARK 3 T11: 0.8535 T22: 0.6437 REMARK 3 T33: 1.9813 T12: -0.0113 REMARK 3 T13: 0.1077 T23: -0.5216 REMARK 3 L TENSOR REMARK 3 L11: 1.8481 L22: 0.8819 REMARK 3 L33: 0.3149 L12: 1.1800 REMARK 3 L13: -0.4039 L23: -0.6609 REMARK 3 S TENSOR REMARK 3 S11: 0.5995 S12: -0.0521 S13: 2.4642 REMARK 3 S21: 0.1490 S22: -0.1197 S23: 0.6737 REMARK 3 S31: 0.3415 S32: 0.1760 S33: -0.2349 REMARK 3 TLS GROUP : 4 REMARK 3 SELECTION: CHAIN A AND RESID 226:271 REMARK 3 ORIGIN FOR THE GROUP (A): -11.9163 -27.8578 12.1719 REMARK 3 T TENSOR REMARK 3 T11: 0.9315 T22: 0.6752 REMARK 3 T33: 1.6170 T12: 0.0427 REMARK 3 T13: 0.3298 T23: -0.1189 REMARK 3 L TENSOR REMARK 3 L11: 0.9375 L22: -1.2182 REMARK 3 L33: 0.0343 L12: -0.0291 REMARK 3 L13: 0.1416 L23: -0.1385 REMARK 3 S TENSOR REMARK 3 S11: 0.0950 S12: -0.5130 S13: 0.6273 REMARK 3 S21: 0.2593 S22: 0.0490 S23: 0.8028 REMARK 3 S31: -0.0440 S32: -0.0733 S33: -0.2110 REMARK 3 TLS GROUP : 5 REMARK 3 SELECTION: CHAIN L AND RESID 1:111 REMARK 3 ORIGIN FOR THE GROUP (A): 16.0368 -39.1503 -15.8130 REMARK 3 T TENSOR REMARK 3 T11: 0.3485 T22: 0.5732 REMARK 3 T33: 0.4699 T12: -0.1275 REMARK 3 T13: -0.0480 T23: 0.0283 REMARK 3 L TENSOR REMARK 3 L11: 1.6838 L22: 1.1373 REMARK 3 L33: 2.9559 L12: 0.4765 REMARK 3 L13: 0.6355 L23: -0.8997 REMARK 3 S TENSOR REMARK 3 S11: -0.2008 S12: 0.4777 S13: 0.2314 REMARK 3 S21: 0.0295 S22: 0.0967 S23: -0.1801 REMARK 3 S31: -0.2397 S32: 0.7424 S33: 0.0942 REMARK 3 TLS GROUP : 6 REMARK 3 SELECTION: CHAIN L AND RESID 112:214 REMARK 3 ORIGIN FOR THE GROUP (A): 9.6012 -45.1336 -51.6364 REMARK 3 T TENSOR REMARK 3 T11: 0.7515 T22: 0.6579 REMARK 3 T33: 0.5462 T12: -0.0805 REMARK 3 T13: 0.1475 T23: -0.0035 REMARK 3 L TENSOR REMARK 3 L11: 2.1336 L22: 4.1954 REMARK 3 L33: 0.9550 L12: -0.1379 REMARK 3 L13: -1.9919 L23: 0.0791 REMARK 3 S TENSOR REMARK 3 S11: 0.0445 S12: 0.2498 S13: -0.0614 REMARK 3 S21: -0.8866 S22: 0.2089 S23: -0.4738 REMARK 3 S31: -0.1180 S32: -0.1452 S33: -0.1905 REMARK 3 TLS GROUP : 7 REMARK 3 SELECTION: CHAIN H AND RESID 1:128 REMARK 3 ORIGIN FOR THE GROUP (A): -4.2902 -45.9963 -14.7003 REMARK 3 T TENSOR REMARK 3 T11: 0.3024 T22: 0.2547 REMARK 3 T33: 0.2974 T12: 0.0389 REMARK 3 T13: 0.0043 T23: 0.0370 REMARK 3 L TENSOR REMARK 3 L11: 1.4008 L22: 0.5379 REMARK 3 L33: 2.4914 L12: -0.3950 REMARK 3 L13: -0.8291 L23: 0.3590 REMARK 3 S TENSOR REMARK 3 S11: -0.0644 S12: -0.0322 S13: 0.0598 REMARK 3 S21: 0.0983 S22: -0.0195 S23: 0.0242 REMARK 3 S31: 0.0956 S32: -0.0593 S33: 0.0585 REMARK 3 TLS GROUP : 8 REMARK 3 SELECTION: CHAIN H AND RESID 129:237 REMARK 3 ORIGIN FOR THE GROUP (A): 4.9096 -57.6120 -43.2639 REMARK 3 T TENSOR REMARK 3 T11: 0.6365 T22: 0.4275 REMARK 3 T33: 0.3999 T12: 0.0835 REMARK 3 T13: 0.0457 T23: 0.0460 REMARK 3 L TENSOR REMARK 3 L11: 0.9257 L22: 1.7703 REMARK 3 L33: 2.1302 L12: 0.4546 REMARK 3 L13: 0.6530 L23: 1.0439 REMARK 3 S TENSOR REMARK 3 S11: -0.1338 S12: -0.1855 S13: -0.1826 REMARK 3 S21: 0.1052 S22: 0.1524 S23: -0.2263 REMARK 3 S31: 0.4965 S32: -0.5660 S33: -0.0358 REMARK 3 TLS GROUP : 9 REMARK 3 SELECTION: CHAIN N REMARK 3 ORIGIN FOR THE GROUP (A): -12.1476 -20.5957 -11.1649 REMARK 3 T TENSOR REMARK 3 T11: 1.1270 T22: 1.2297 REMARK 3 T33: 0.9329 T12: -0.1158 REMARK 3 T13: 0.1657 T23: 0.2285 REMARK 3 L TENSOR REMARK 3 L11: 2.0131 L22: 0.7580 REMARK 3 L33: 1.9590 L12: 1.4431 REMARK 3 L13: -1.3915 L23: -0.4192 REMARK 3 S TENSOR REMARK 3 S11: 0.7882 S12: 0.2738 S13: 0.4819 REMARK 3 S21: 0.0316 S22: -0.2048 S23: -0.2167 REMARK 3 S31: -0.7610 S32: -0.7126 S33: -0.3567 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 3LEV COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 03-FEB-10. REMARK 100 THE DEPOSITION ID IS D_1000057190. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 09-JUN-07 REMARK 200 TEMPERATURE (KELVIN) : 100.0 REMARK 200 PH : 5.50 REMARK 200 NUMBER OF CRYSTALS USED : 2 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) : 1.000 REMARK 200 MONOCHROMATOR : SI(220) 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 : 23675 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.500 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 5.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 88.9 REMARK 200 DATA REDUNDANCY : 8.900 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : 0.09000 REMARK 200 FOR THE DATA SET : 42.9000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.50 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.59 REMARK 200 COMPLETENESS FOR SHELL (%) : 33.1 REMARK 200 DATA REDUNDANCY IN SHELL : 1.90 REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : 0.47000 REMARK 200 FOR SHELL : 1.170 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: PDB ENTRIES 1KU2 AND 1TJI REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 54.79 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.72 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 16% PEG 400, 2.8% PEG 3350, 0.1 M REMARK 280 CH3COONA PH 5.5, 0.02 M ATP, VAPOR DIFFUSION, TEMPERATURE 293K, REMARK 280 PH 5.50 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 29.25300 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 100.00950 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 31.96650 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 100.00950 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 29.25300 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 31.96650 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1, 2, 3 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 APPLY THE FOLLOWING TO CHAINS: A, L, H 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 350 REMARK 350 BIOMOLECULE: 2 REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 APPLY THE FOLLOWING TO CHAINS: 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 350 REMARK 350 BIOMOLECULE: 3 REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 3890 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 20270 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -26.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: L, H 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 ALA A 270 REMARK 465 ARG A 271 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 ALA A 134 -46.82 -168.39 REMARK 500 LEU A 137 178.14 60.19 REMARK 500 ASP A 138 -174.55 -63.02 REMARK 500 ASP A 167 74.94 51.70 REMARK 500 VAL A 171 -71.52 -59.86 REMARK 500 LYS A 177 28.12 -76.98 REMARK 500 LEU A 178 -46.35 -149.09 REMARK 500 SER A 180 79.57 -112.52 REMARK 500 PRO A 182 156.35 -45.10 REMARK 500 TYR A 217 13.34 -144.57 REMARK 500 ARG A 220 -140.92 -98.04 REMARK 500 PHE A 224 -72.89 -46.02 REMARK 500 GLU A 243 84.10 -160.91 REMARK 500 TRP A 257 -25.87 -140.49 REMARK 500 ASP A 268 176.62 63.57 REMARK 500 THR L 30 -119.19 46.47 REMARK 500 ALA L 51 -38.90 75.77 REMARK 500 SER L 76 -74.17 -48.75 REMARK 500 ALA L 84 -175.71 -170.90 REMARK 500 VAL L 110 121.11 -38.71 REMARK 500 LYS L 126 0.42 -67.53 REMARK 500 ASN L 138 94.14 59.07 REMARK 500 TYR L 140 135.73 -174.78 REMARK 500 PRO L 141 -165.71 -76.88 REMARK 500 ALA L 144 142.15 -175.03 REMARK 500 ASN L 152 -10.28 67.46 REMARK 500 LYS L 169 -76.97 -65.86 REMARK 500 SER L 171 52.48 -68.12 REMARK 500 GLU L 187 34.73 -83.44 REMARK 500 LYS L 190 -49.91 -136.82 REMARK 500 ARG L 211 26.12 -71.87 REMARK 500 PRO H 14 150.19 -45.09 REMARK 500 THR H 15 -5.84 67.15 REMARK 500 LEU H 63 39.55 -161.96 REMARK 500 PHE H 100B 74.78 49.61 REMARK 500 ILE H 100F -56.32 -149.71 REMARK 500 ASN H 100L 58.72 -91.03 REMARK 500 ALA H 100M 156.78 179.64 REMARK 500 LEU H 124 72.33 -115.81 REMARK 500 SER H 127 -167.98 -170.31 REMARK 500 ALA H 136 -169.15 -77.05 REMARK 500 ASP H 144 73.06 59.40 REMARK 500 SER H 156 19.74 57.32 REMARK 500 SER H 187 58.58 -108.95 REMARK 500 SER H 188 15.69 -176.43 REMARK 500 SER H 215 30.30 -70.09 REMARK 500 ASP H 217 -58.68 -139.31 REMARK 500 REMARK 500 REMARK: NULL REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE 1PE L 215 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ATP H 219 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL H 220 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 3LES RELATED DB: PDB REMARK 900 2F5 EPITOPE SCAFFOLD ES2 REMARK 900 RELATED ID: 3LEX RELATED DB: PDB REMARK 900 2F5 EPITOPE SCAFFOLD ELICITED ANTI-HIV-1 MONOCLONAL ANTIBODY 11F10 REMARK 900 IN COMPLEX WITH HIV-1 GP41 REMARK 900 RELATED ID: 3LEY RELATED DB: PDB REMARK 900 2F5 EPITOPE SCAFFOLD ELICITED ANTI-HIV-1 MONOCLONAL ANTIBODY 6A7 IN REMARK 900 COMPLEX WITH HIV-1 GP41 REMARK 900 RELATED ID: 1TJI RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF THE BROADLY NEUTRALIZING ANTI-HIV-1 ANTIBODY REMARK 900 2F5 IN COMPLEX WITH A GP41 17MER DBREF 3LEV A 93 271 UNP Q9EZJ8 Q9EZJ8_THEAQ 93 271 DBREF 3LEV L 1 214 PDB 3LEV 3LEV 1 214 DBREF 3LEV H 1 218 PDB 3LEV 3LEV 1 218 SEQADV 3LEV GLU A 105 UNP Q9EZJ8 GLN 105 ENGINEERED MUTATION SEQADV 3LEV LEU A 107 UNP Q9EZJ8 PRO 107 ENGINEERED MUTATION SEQADV 3LEV GLU A 108 UNP Q9EZJ8 LEU 108 ENGINEERED MUTATION SEQADV 3LEV ASP A 110 UNP Q9EZJ8 THR 110 ENGINEERED MUTATION SEQADV 3LEV LYS A 111 UNP Q9EZJ8 LEU 111 ENGINEERED MUTATION SEQADV 3LEV TRP A 112 UNP Q9EZJ8 GLU 112 ENGINEERED MUTATION SEQADV 3LEV ALA A 113 UNP Q9EZJ8 GLU 113 ENGINEERED MUTATION SEQADV 3LEV LEU A 115 UNP Q9EZJ8 ILE 115 ENGINEERED MUTATION SEQADV 3LEV GLY A 116 UNP Q9EZJ8 ASP 116 ENGINEERED MUTATION SEQADV 3LEV ALA A 117 UNP Q9EZJ8 LEU 117 ENGINEERED MUTATION SEQADV 3LEV ALA A 119 UNP Q9EZJ8 ARG 119 ENGINEERED MUTATION SEQADV 3LEV ALA A 155 UNP Q9EZJ8 ARG 155 ENGINEERED MUTATION SEQADV 3LEV GLY A 247 UNP Q9EZJ8 ARG 247 ENGINEERED MUTATION SEQADV 3LEV ALA A 249 UNP Q9EZJ8 LYS 249 ENGINEERED MUTATION SEQRES 1 A 179 SER ASP PRO VAL ARG GLN TYR LEU HIS GLU ILE GLY GLU SEQRES 2 A 179 VAL LEU GLU LEU ASP LYS TRP ALA GLU LEU GLY ALA ALA SEQRES 3 A 179 ALA LYS VAL GLU GLU GLY MET GLU ALA ILE LYS LYS LEU SEQRES 4 A 179 SER GLU ALA THR GLY LEU ASP GLN GLU LEU ILE ARG GLU SEQRES 5 A 179 VAL VAL ARG ALA LYS ILE LEU GLY THR ALA ALA ILE GLN SEQRES 6 A 179 LYS ILE PRO GLY LEU LYS GLU LYS PRO ASP PRO LYS THR SEQRES 7 A 179 VAL GLU GLU VAL ASP GLY LYS LEU LYS SER LEU PRO LYS SEQRES 8 A 179 GLU LEU LYS ARG TYR LEU HIS ILE ALA ARG GLU GLY GLU SEQRES 9 A 179 ALA ALA ARG GLN HIS LEU ILE GLU ALA ASN LEU ARG LEU SEQRES 10 A 179 VAL VAL SER ILE ALA LYS LYS TYR THR GLY ARG GLY LEU SEQRES 11 A 179 SER PHE LEU ASP LEU ILE GLN GLU GLY ASN GLN GLY LEU SEQRES 12 A 179 ILE ARG ALA VAL GLU LYS PHE GLU TYR LYS ARG GLY PHE SEQRES 13 A 179 ALA PHE SER THR TYR ALA THR TRP TRP ILE ARG GLN ALA SEQRES 14 A 179 ILE ASN ARG ALA ILE ALA ASP GLN ALA ARG SEQRES 1 L 214 ALA LEU GLN LEU THR GLN SER PRO SER SER LEU SER ALA SEQRES 2 L 214 SER VAL GLY ASP ARG ILE THR ILE THR CYS ARG ALA SER SEQRES 3 L 214 GLN GLY VAL THR SER ALA LEU ALA TRP TYR ARG GLN LYS SEQRES 4 L 214 PRO GLY SER PRO PRO GLN LEU LEU ILE TYR ASP ALA SER SEQRES 5 L 214 SER LEU GLU SER GLY VAL PRO SER ARG PHE SER GLY SER SEQRES 6 L 214 GLY SER GLY THR GLU PHE THR LEU THR ILE SER THR LEU SEQRES 7 L 214 ARG PRO GLU ASP PHE ALA THR TYR TYR CYS GLN GLN LEU SEQRES 8 L 214 HIS PHE TYR PRO HIS THR PHE GLY GLY GLY THR ARG VAL SEQRES 9 L 214 ASP VAL ARG 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 H 237 ARG ILE THR LEU LYS GLU SER GLY PRO PRO LEU VAL LYS SEQRES 2 H 237 PRO THR GLN THR LEU THR LEU THR CYS SER PHE SER GLY SEQRES 3 H 237 PHE SER LEU SER ASP PHE GLY VAL GLY VAL GLY TRP ILE SEQRES 4 H 237 ARG GLN PRO PRO GLY LYS ALA LEU GLU TRP LEU ALA ILE SEQRES 5 H 237 ILE TYR SER ASP ASP ASP LYS ARG TYR SER PRO SER LEU SEQRES 6 H 237 ASN THR ARG LEU THR ILE THR LYS ASP THR SER LYS ASN SEQRES 7 H 237 GLN VAL VAL LEU VAL MET THR ARG VAL SER PRO VAL ASP SEQRES 8 H 237 THR ALA THR TYR PHE CYS ALA HIS ARG ARG GLY PRO THR SEQRES 9 H 237 THR LEU PHE GLY VAL PRO ILE ALA ARG GLY PRO VAL ASN SEQRES 10 H 237 ALA MET ASP VAL TRP GLY GLN GLY ILE THR VAL THR ILE SEQRES 11 H 237 SER SER THR SER THR LYS GLY PRO SER VAL PHE PRO LEU SEQRES 12 H 237 ALA PRO SER SER LYS SER THR SER GLY GLY THR ALA ALA SEQRES 13 H 237 LEU GLY CYS LEU VAL LYS ASP TYR PHE PRO GLU PRO VAL SEQRES 14 H 237 THR VAL SER TRP ASN SER GLY ALA LEU THR SER GLY VAL SEQRES 15 H 237 HIS THR PHE PRO ALA VAL LEU GLN SER SER GLY LEU TYR SEQRES 16 H 237 SER LEU SER SER VAL VAL THR VAL PRO SER SER SER LEU SEQRES 17 H 237 GLY THR GLN THR TYR ILE CYS ASN VAL ASN HIS LYS PRO SEQRES 18 H 237 SER ASN THR LYS VAL ASP LYS LYS VAL GLU PRO LYS SER SEQRES 19 H 237 CYS ASP LYS HET 1PE L 215 16 HET ATP H 219 62 HET GOL H 220 6 HETNAM 1PE PENTAETHYLENE GLYCOL HETNAM ATP ADENOSINE-5'-TRIPHOSPHATE HETNAM GOL GLYCEROL HETSYN 1PE PEG400 HETSYN GOL GLYCERIN; PROPANE-1,2,3-TRIOL FORMUL 4 1PE C10 H22 O6 FORMUL 5 ATP C10 H16 N5 O13 P3 FORMUL 6 GOL C3 H8 O3 FORMUL 7 HOH *97(H2 O) HELIX 1 1 ASP A 94 GLY A 104 1 11 HELIX 2 2 ASP A 110 GLY A 124 1 15 HELIX 3 3 GLU A 126 LEU A 131 1 6 HELIX 4 4 GLN A 139 GLY A 152 1 14 HELIX 5 5 LYS A 169 SER A 180 1 12 HELIX 6 6 PRO A 182 LEU A 185 5 4 HELIX 7 7 LYS A 186 ASN A 206 1 21 HELIX 8 8 ASN A 206 LYS A 215 1 10 HELIX 9 9 LYS A 216 THR A 218 5 3 HELIX 10 10 SER A 223 PHE A 242 1 20 HELIX 11 11 GLU A 243 GLY A 247 5 5 HELIX 12 12 ALA A 249 ASN A 263 1 15 HELIX 13 13 ARG L 79 PHE L 83 5 5 HELIX 14 14 SER L 121 LYS L 126 1 6 HELIX 15 15 LYS L 183 GLU L 187 1 5 HELIX 16 16 PRO H 61 ASN H 64 5 4 HELIX 17 17 SER H 83 THR H 87 5 5 HELIX 18 18 ARG H 100H ASN H 100L 5 5 HELIX 19 19 SER H 156 ALA H 158 5 3 HELIX 20 20 LYS H 201 ASN H 204 5 4 SHEET 1 A 2 GLU A 108 LEU A 109 0 SHEET 2 A 2 PHE L 93 TYR L 94 -1 O TYR L 94 N GLU A 108 SHEET 1 B 4 LEU L 4 SER L 7 0 SHEET 2 B 4 ILE L 19 ALA L 25 -1 O ARG L 24 N THR L 5 SHEET 3 B 4 GLU L 70 ILE L 75 -1 O PHE L 71 N CYS L 23 SHEET 4 B 4 PHE L 62 SER L 67 -1 N SER L 65 O THR L 72 SHEET 1 C 6 SER L 10 ALA L 13 0 SHEET 2 C 6 THR L 102 VAL L 106 1 O ASP L 105 N LEU L 11 SHEET 3 C 6 THR L 85 GLN L 90 -1 N TYR L 86 O THR L 102 SHEET 4 C 6 LEU L 33 GLN L 38 -1 N TYR L 36 O TYR L 87 SHEET 5 C 6 GLN L 45 TYR L 49 -1 O LEU L 47 N TRP L 35 SHEET 6 C 6 SER L 53 LEU L 54 -1 O SER L 53 N TYR L 49 SHEET 1 D 4 SER L 114 VAL L 115 0 SHEET 2 D 4 THR L 129 PHE L 139 -1 O ASN L 137 N SER L 114 SHEET 3 D 4 TYR L 173 SER L 182 -1 O LEU L 175 N LEU L 136 SHEET 4 D 4 SER L 159 VAL L 163 -1 N SER L 162 O SER L 176 SHEET 1 E 4 ALA L 153 GLN L 155 0 SHEET 2 E 4 LYS L 145 VAL L 150 -1 N TRP L 148 O GLN L 155 SHEET 3 E 4 VAL L 191 THR L 197 -1 O GLU L 195 N GLN L 147 SHEET 4 E 4 VAL L 205 THR L 206 -1 O VAL L 205 N VAL L 196 SHEET 1 F 4 ALA L 153 GLN L 155 0 SHEET 2 F 4 LYS L 145 VAL L 150 -1 N TRP L 148 O GLN L 155 SHEET 3 F 4 VAL L 191 THR L 197 -1 O GLU L 195 N GLN L 147 SHEET 4 F 4 PHE L 209 ASN L 210 -1 O PHE L 209 N TYR L 192 SHEET 1 G 4 THR H 3 SER H 7 0 SHEET 2 G 4 LEU H 18 SER H 25 -1 O SER H 23 N LYS H 5 SHEET 3 G 4 GLN H 77 MET H 82 -1 O VAL H 78 N CYS H 22 SHEET 4 G 4 LEU H 67 ASP H 72 -1 N THR H 70 O VAL H 79 SHEET 1 H 6 LEU H 11 VAL H 12 0 SHEET 2 H 6 ILE H 107 ILE H 111 1 O THR H 110 N VAL H 12 SHEET 3 H 6 ALA H 88 ARG H 95 -1 N TYR H 90 O ILE H 107 SHEET 4 H 6 GLY H 35 GLN H 39 -1 N ILE H 37 O PHE H 91 SHEET 5 H 6 GLU H 46 TYR H 52 -1 O GLU H 46 N ARG H 38 SHEET 6 H 6 LYS H 57 TYR H 59 -1 O ARG H 58 N ILE H 50 SHEET 1 I 4 LEU H 11 VAL H 12 0 SHEET 2 I 4 ILE H 107 ILE H 111 1 O THR H 110 N VAL H 12 SHEET 3 I 4 ALA H 88 ARG H 95 -1 N TYR H 90 O ILE H 107 SHEET 4 I 4 VAL H 102 TRP H 103 -1 O VAL H 102 N HIS H 94 SHEET 1 J 2 THR H 99 LEU H 100A 0 SHEET 2 J 2 VAL H 100D ALA H 100G-1 O ALA H 100G N THR H 99 SHEET 1 K 4 SER H 120 LEU H 124 0 SHEET 2 K 4 LEU H 138 TYR H 145 -1 O LEU H 141 N PHE H 122 SHEET 3 K 4 TYR H 176 VAL H 182 -1 O VAL H 182 N LEU H 138 SHEET 4 K 4 VAL H 163 THR H 165 -1 N HIS H 164 O VAL H 181 SHEET 1 L 4 SER H 120 LEU H 124 0 SHEET 2 L 4 LEU H 138 TYR H 145 -1 O LEU H 141 N PHE H 122 SHEET 3 L 4 TYR H 176 VAL H 182 -1 O VAL H 182 N LEU H 138 SHEET 4 L 4 VAL H 169 LEU H 170 -1 N VAL H 169 O SER H 177 SHEET 1 M 3 THR H 151 TRP H 154 0 SHEET 2 M 3 ILE H 195 HIS H 200 -1 O ASN H 197 N SER H 153 SHEET 3 M 3 THR H 205 LYS H 210 -1 O VAL H 207 N VAL H 198 SSBOND 1 CYS L 23 CYS L 88 1555 1555 2.04 SSBOND 2 CYS L 134 CYS L 194 1555 1555 2.03 SSBOND 3 CYS H 22 CYS H 92 1555 1555 2.05 SSBOND 4 CYS H 140 CYS H 196 1555 1555 2.03 CISPEP 1 SER L 7 PRO L 8 0 -0.61 CISPEP 2 TYR L 94 PRO L 95 0 -6.30 CISPEP 3 TYR L 140 PRO L 141 0 -0.90 CISPEP 4 PHE H 146 PRO H 147 0 -2.62 CISPEP 5 GLU H 148 PRO H 149 0 1.03 SITE 1 AC1 6 SER L 9 PRO L 40 GLY L 41 TYR L 87 SITE 2 AC1 6 GLY L 101 ARG L 103 SITE 1 AC2 12 ARG A 97 LYS A 149 ASP A 175 LYS A 179 SITE 2 AC2 12 LYS A 186 LEU A 189 ARG A 193 SER A 212 SITE 3 AC2 12 PRO H 61 ASN H 64 THR H 65 HOH H 257 SITE 1 AC3 6 ARG H 100H HOH H 283 HOH H 284 HOH H 285 SITE 2 AC3 6 HOH H 286 HOH H 287 CRYST1 58.506 63.933 200.019 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 0.017092 0.000000 0.000000 0.00000 SCALE2 0.000000 0.015641 0.000000 0.00000 SCALE3 0.000000 0.000000 0.005000 0.00000