HEADER IMMUNE SYSTEM 15-JAN-10 3LEY TITLE 2F5 EPITOPE SCAFFOLD ELICITED ANTI-HIV-1 MONOCLONAL ANTIBODY 6A7 IN TITLE 2 COMPLEX WITH HIV-1 GP41 COMPND MOL_ID: 1; COMPND 2 MOLECULE: 6A7 ANTIBODY HEAVY CHAIN; COMPND 3 CHAIN: H; COMPND 4 MOL_ID: 2; COMPND 5 MOLECULE: 6A7 ANTIBODY LIGHT CHAIN; COMPND 6 CHAIN: L; COMPND 7 MOL_ID: 3; COMPND 8 MOLECULE: ENVELOPE GLYCOPROTEIN GP41; COMPND 9 CHAIN: P; COMPND 10 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: MUS MUSCULUS; SOURCE 3 ORGANISM_COMMON: MOUSE; SOURCE 4 ORGANISM_TAXID: 10090; SOURCE 5 STRAIN: BALB/C; SOURCE 6 CELL_LINE: MYELOMA CELL LINE FO; SOURCE 7 CELL: HYBRIDOMA; SOURCE 8 MOL_ID: 2; SOURCE 9 ORGANISM_SCIENTIFIC: MUS MUSCULUS; SOURCE 10 ORGANISM_COMMON: MOUSE; SOURCE 11 ORGANISM_TAXID: 10090; SOURCE 12 STRAIN: BALB/C; SOURCE 13 CELL_LINE: MYELOMA CELL LINE FO; SOURCE 14 CELL: HYBRIDOMA; SOURCE 15 MOL_ID: 3; SOURCE 16 SYNTHETIC: YES; SOURCE 17 ORGANISM_SCIENTIFIC: HUMAN IMMUNODEFICIENCY VIRUS 1; SOURCE 18 ORGANISM_TAXID: 11676; SOURCE 19 OTHER_DETAILS: HIV-1 GP41 PEPTIDE KEYWDS HIV-1, GP-41, MONOCLONAL ANTIBODY, 2F5, SCAFFOLD, EPITOPE, KEYWDS 2 TRANSPLANT, GRAFT, RE-ELCITATION, ENVELOPE PROTEIN, IMMUNE SYSTEM, KEYWDS 3 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 2 24-NOV-10 3LEY 1 JRNL REVDAT 1 29-SEP-10 3LEY 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. 1.99 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (PHENIX.REFINE) REMARK 3 AUTHORS : PAUL ADAMS,PAVEL AFONINE,VICENT CHEN,IAN REMARK 3 : DAVIS,KRESHNA GOPAL,RALF GROSSE- REMARK 3 : KUNSTLEVE,LI-WEI HUNG,ROBERT IMMORMINO, REMARK 3 : TOM IOERGER,AIRLIE MCCOY,ERIK MCKEE,NIGEL REMARK 3 : MORIARTY,REETAL PAI,RANDY READ,JANE REMARK 3 : RICHARDSON,DAVID RICHARDSON,TOD ROMO,JIM REMARK 3 : SACCHETTINI,NICHOLAS SAUTER,JACOB SMITH, REMARK 3 : LAURENT STORONI,TOM TERWILLIGER,PETER REMARK 3 : ZWART REMARK 3 REMARK 3 REFINEMENT TARGET : ML REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.99 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 27.10 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 0.050 REMARK 3 COMPLETENESS FOR RANGE (%) : 92.0 REMARK 3 NUMBER OF REFLECTIONS : 25977 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.180 REMARK 3 R VALUE (WORKING SET) : 0.177 REMARK 3 FREE R VALUE : 0.215 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 7.380 REMARK 3 FREE R VALUE TEST SET COUNT : 1916 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 27.0980 - 4.7840 0.96 1852 149 0.1730 0.1800 REMARK 3 2 4.7840 - 3.8010 0.98 1838 147 0.1380 0.1560 REMARK 3 3 3.8010 - 3.3210 0.98 1825 146 0.1540 0.2190 REMARK 3 4 3.3210 - 3.0180 0.98 1819 147 0.1710 0.1900 REMARK 3 5 3.0180 - 2.8020 0.98 1839 147 0.1970 0.2460 REMARK 3 6 2.8020 - 2.6370 0.96 1801 141 0.2020 0.2530 REMARK 3 7 2.6370 - 2.5050 0.95 1771 134 0.2050 0.2530 REMARK 3 8 2.5050 - 2.3960 0.95 1769 146 0.2010 0.2930 REMARK 3 9 2.3960 - 2.3040 0.95 1773 145 0.1970 0.2480 REMARK 3 10 2.3040 - 2.2240 0.93 1721 133 0.2030 0.3140 REMARK 3 11 2.2240 - 2.1550 0.92 1703 142 0.2040 0.2570 REMARK 3 12 2.1550 - 2.0930 0.90 1678 127 0.1960 0.2690 REMARK 3 13 2.0930 - 2.0380 0.84 1547 123 0.1990 0.2580 REMARK 3 14 2.0380 - 1.9880 0.60 1125 89 0.2230 0.3110 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 : 0.32 REMARK 3 B_SOL : 50.67 REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 1.200 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : NULL REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 29.30 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 41.75 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 7.70800 REMARK 3 B22 (A**2) : 0.71100 REMARK 3 B33 (A**2) : -8.41900 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : 5.83400 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 : 0.004 3491 REMARK 3 ANGLE : 0.768 4756 REMARK 3 CHIRALITY : 0.051 542 REMARK 3 PLANARITY : 0.003 598 REMARK 3 DIHEDRAL : 15.031 1215 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 9 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: CHAIN H AND RESID 1:32 REMARK 3 ORIGIN FOR THE GROUP (A): 6.8970 -21.0727 3.8943 REMARK 3 T TENSOR REMARK 3 T11: 0.3340 T22: 0.3294 REMARK 3 T33: 0.2085 T12: 0.0663 REMARK 3 T13: -0.0174 T23: -0.0628 REMARK 3 L TENSOR REMARK 3 L11: 1.4640 L22: 0.9435 REMARK 3 L33: 2.1133 L12: -0.5831 REMARK 3 L13: -2.0358 L23: 0.0680 REMARK 3 S TENSOR REMARK 3 S11: -0.1758 S12: 0.2695 S13: -0.1441 REMARK 3 S21: 0.4536 S22: 0.0109 S23: 0.1885 REMARK 3 S31: -0.2362 S32: -0.5715 S33: 0.2159 REMARK 3 TLS GROUP : 2 REMARK 3 SELECTION: CHAIN H AND RESID 33:121 REMARK 3 ORIGIN FOR THE GROUP (A): 14.1935 -19.9172 6.3434 REMARK 3 T TENSOR REMARK 3 T11: 0.1866 T22: 0.2225 REMARK 3 T33: 0.1603 T12: 0.0757 REMARK 3 T13: -0.0194 T23: -0.0281 REMARK 3 L TENSOR REMARK 3 L11: 1.7552 L22: 1.7150 REMARK 3 L33: 2.4446 L12: 0.1544 REMARK 3 L13: -1.3752 L23: 0.8551 REMARK 3 S TENSOR REMARK 3 S11: -0.0877 S12: 0.1760 S13: -0.1769 REMARK 3 S21: -0.0211 S22: -0.0457 S23: -0.0455 REMARK 3 S31: -0.0318 S32: 0.1306 S33: 0.1253 REMARK 3 TLS GROUP : 3 REMARK 3 SELECTION: CHAIN H AND RESID 122:139 REMARK 3 ORIGIN FOR THE GROUP (A): -10.8774 -15.9718 38.8010 REMARK 3 T TENSOR REMARK 3 T11: 0.3545 T22: 0.2664 REMARK 3 T33: 0.3382 T12: -0.0338 REMARK 3 T13: 0.0687 T23: -0.0010 REMARK 3 L TENSOR REMARK 3 L11: 2.9695 L22: 2.0270 REMARK 3 L33: 3.6864 L12: -1.7733 REMARK 3 L13: -1.8650 L23: 1.9544 REMARK 3 S TENSOR REMARK 3 S11: 0.1121 S12: -0.1916 S13: 0.4271 REMARK 3 S21: -0.2699 S22: 0.0730 S23: -0.0795 REMARK 3 S31: -0.2044 S32: -0.0988 S33: -0.0859 REMARK 3 TLS GROUP : 4 REMARK 3 SELECTION: CHAIN H AND RESID 140:220 REMARK 3 ORIGIN FOR THE GROUP (A): -7.6121 -18.1842 30.5780 REMARK 3 T TENSOR REMARK 3 T11: 0.1588 T22: 0.2591 REMARK 3 T33: 0.1592 T12: -0.0017 REMARK 3 T13: -0.0393 T23: 0.0351 REMARK 3 L TENSOR REMARK 3 L11: 1.7010 L22: 1.9502 REMARK 3 L33: 3.8170 L12: 0.2218 REMARK 3 L13: -0.5834 L23: 0.1116 REMARK 3 S TENSOR REMARK 3 S11: -0.0771 S12: 0.0758 S13: -0.0143 REMARK 3 S21: -0.0552 S22: 0.0877 S23: 0.1727 REMARK 3 S31: 0.2411 S32: -0.5177 S33: -0.0159 REMARK 3 TLS GROUP : 5 REMARK 3 SELECTION: CHAIN L AND RESID 1:82 REMARK 3 ORIGIN FOR THE GROUP (A): 18.6894 2.1866 12.3026 REMARK 3 T TENSOR REMARK 3 T11: 0.5041 T22: 0.2124 REMARK 3 T33: 0.2759 T12: -0.0474 REMARK 3 T13: 0.1617 T23: -0.0085 REMARK 3 L TENSOR REMARK 3 L11: 2.6799 L22: 1.0933 REMARK 3 L33: 2.4630 L12: 0.1339 REMARK 3 L13: -1.0719 L23: 0.9517 REMARK 3 S TENSOR REMARK 3 S11: 0.4534 S12: -0.0570 S13: 0.4009 REMARK 3 S21: -0.2256 S22: -0.0362 S23: 0.0137 REMARK 3 S31: -0.5937 S32: 0.0266 S33: -0.4147 REMARK 3 TLS GROUP : 6 REMARK 3 SELECTION: CHAIN L AND RESID 83:141 REMARK 3 ORIGIN FOR THE GROUP (A): 7.3563 -8.4860 27.3458 REMARK 3 T TENSOR REMARK 3 T11: 0.2345 T22: 0.1466 REMARK 3 T33: 0.1799 T12: 0.0040 REMARK 3 T13: -0.0061 T23: -0.0469 REMARK 3 L TENSOR REMARK 3 L11: 1.6452 L22: 0.6355 REMARK 3 L33: 3.3416 L12: 0.1500 REMARK 3 L13: -1.7461 L23: -0.3906 REMARK 3 S TENSOR REMARK 3 S11: 0.2205 S12: -0.0276 S13: 0.2115 REMARK 3 S21: -0.0766 S22: 0.0793 S23: 0.0819 REMARK 3 S31: -0.2631 S32: 0.1191 S33: -0.2693 REMARK 3 TLS GROUP : 7 REMARK 3 SELECTION: CHAIN L AND RESID 142:188 REMARK 3 ORIGIN FOR THE GROUP (A): 4.5769 -11.7083 40.1609 REMARK 3 T TENSOR REMARK 3 T11: 0.1353 T22: 0.2736 REMARK 3 T33: 0.1914 T12: 0.0298 REMARK 3 T13: -0.0410 T23: -0.0191 REMARK 3 L TENSOR REMARK 3 L11: 1.6940 L22: 1.5019 REMARK 3 L33: 2.2713 L12: 0.0180 REMARK 3 L13: -1.8577 L23: 1.7493 REMARK 3 S TENSOR REMARK 3 S11: 0.0569 S12: -0.4196 S13: 0.1974 REMARK 3 S21: -0.0329 S22: 0.1219 S23: -0.0296 REMARK 3 S31: 0.0404 S32: 0.4519 S33: -0.1763 REMARK 3 TLS GROUP : 8 REMARK 3 SELECTION: CHAIN L AND RESID 189:219 REMARK 3 ORIGIN FOR THE GROUP (A): -1.8486 -16.5386 51.3723 REMARK 3 T TENSOR REMARK 3 T11: 0.3182 T22: 0.4012 REMARK 3 T33: 0.1814 T12: 0.0516 REMARK 3 T13: 0.0070 T23: -0.0142 REMARK 3 L TENSOR REMARK 3 L11: 0.6578 L22: 0.1273 REMARK 3 L33: 1.9841 L12: -0.8061 REMARK 3 L13: -0.7898 L23: 0.4765 REMARK 3 S TENSOR REMARK 3 S11: -0.1801 S12: -0.4046 S13: 0.0398 REMARK 3 S21: 0.2527 S22: 0.2906 S23: -0.0284 REMARK 3 S31: 0.1878 S32: 0.7346 S33: -0.0704 REMARK 3 TLS GROUP : 9 REMARK 3 SELECTION: CHAIN P AND RESID 659:668 REMARK 3 ORIGIN FOR THE GROUP (A): 18.6053 -4.4647 -4.9447 REMARK 3 T TENSOR REMARK 3 T11: 0.5462 T22: 0.5343 REMARK 3 T33: 0.3300 T12: 0.0721 REMARK 3 T13: 0.0455 T23: 0.0628 REMARK 3 L TENSOR REMARK 3 L11: 0.4364 L22: -0.0066 REMARK 3 L33: 0.1656 L12: -0.0973 REMARK 3 L13: 0.1441 L23: -0.1112 REMARK 3 S TENSOR REMARK 3 S11: -0.1500 S12: 0.3061 S13: 0.1169 REMARK 3 S21: -0.4850 S22: 0.4830 S23: 0.4176 REMARK 3 S31: -0.4887 S32: -0.4830 S33: -0.3300 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 3LEY COMPLIES WITH FORMAT V. 3.20, 01-DEC-08 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 03-FEB-10. REMARK 100 THE RCSB ID CODE IS RCSB057193. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 02-APR-09 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 4.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : APS REMARK 200 BEAMLINE : 22-BM 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 : MAR SCANNER 300 MM PLATE REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 26922 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.980 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 (%) : 96.7 REMARK 200 DATA REDUNDANCY : NULL REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : 0.08100 REMARK 200 FOR THE DATA SET : 31.5000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.98 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.05 REMARK 200 COMPLETENESS FOR SHELL (%) : 86.9 REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : 0.34200 REMARK 200 FOR SHELL : 5.200 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: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 42.27 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.13 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 31.5 % PEG 1000, 0.2 M ZN(CH3COO)2, REMARK 280 0.1 M CH3COONA PH 4.5, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE REMARK 280 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 1 21 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,Y+1/2,-Z REMARK 290 REMARK 290 WHERE NNN -> OPERATOR NUMBER REMARK 290 MMM -> TRANSLATION VECTOR REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY TRANSFORMATIONS REMARK 290 THE FOLLOWING TRANSFORMATIONS OPERATE ON THE ATOM/HETATM REMARK 290 RECORDS IN THIS ENTRY TO PRODUCE CRYSTALLOGRAPHICALLY REMARK 290 RELATED MOLECULES. REMARK 290 SMTRY1 1 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 1 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 1 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 2 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 2 0.000000 1.000000 0.000000 40.08000 REMARK 290 SMTRY3 2 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: 4990 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 19650 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -29.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: P, 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 ASP H 129 REMARK 465 THR H 130 REMARK 465 THR H 131 REMARK 465 LYS H 217 REMARK 465 THR L 205 REMARK 465 SER L 206 REMARK 465 THR L 207 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 SER H 15 -17.93 80.30 REMARK 500 TYR H 27 136.39 -171.19 REMARK 500 TYR H 33 171.64 82.08 REMARK 500 ASN H 43 -0.87 91.58 REMARK 500 SER H 155 18.60 56.92 REMARK 500 VAL L 56 -53.48 72.47 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 ZN H 222 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASN L 143 ND2 REMARK 620 2 HOH L 268 O 77.9 REMARK 620 3 HOH H 244 O 144.6 91.6 REMARK 620 4 HIS H 163 NE2 90.1 82.6 122.4 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN H 223 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP H 1 OD2 REMARK 620 2 HOH H 288 O 91.9 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 ZN H 222 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ZN H 223 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ZN L 233 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 3LES RELATED DB: PDB REMARK 900 2F5 EPITOPE SCAFFOLD ES2 REMARK 900 RELATED ID: 3LEV RELATED DB: PDB REMARK 900 HIV-1 ANTIBODY 2F5 IN COMPLEX WITH EPITOPE SCAFFOLD ES2 REMARK 900 RELATED ID: 3LEX RELATED DB: PDB REMARK 900 2F5 EPITOPE SCAFFOLD ELICITED ANTI-HIV-1 MONOCLONAL REMARK 900 ANTIBODY 11F10 IN COMPLEX WITH HIV-1 GP41 REMARK 900 RELATED ID: 1TJI RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF THE BROADLY NEUTRALIZING ANTI-HIV-1 REMARK 900 ANTIBODY 2F5 IN COMPLEX WITH A GP41 17MER DBREF 3LEY H 1 217 PDB 3LEY 3LEY 1 221 DBREF 3LEY L 1 219 PDB 3LEY 3LEY 1 219 DBREF 3LEY P 660 668 UNP Q9IJQ0 Q9IJQ0_9HIV1 100 108 SEQRES 1 H 221 ASP VAL GLN LEU GLN GLU SER GLY PRO GLY LEU VAL LYS SEQRES 2 H 221 PRO SER GLN SER LEU SER LEU THR CYS THR VAL THR GLY SEQRES 3 H 221 TYR LEU ILE THR THR ASP TYR ALA TRP ASN TRP ILE ARG SEQRES 4 H 221 GLN PHE PRO GLY ASN LYS LEU GLU TRP MET GLY TYR ILE SEQRES 5 H 221 SER TYR SER GLY PHE THR SER TYR ASN PRO SER LEU LYS SEQRES 6 H 221 SER GLN ILE SER ILE THR ARG ASP THR SER LYS ASN GLN SEQRES 7 H 221 PHE PHE LEU GLN LEU ASN SER VAL THR THR GLU ASP THR SEQRES 8 H 221 ALA THR TYR TYR CYS ALA PHE GLY ASN TYR LEU PRO ALA SEQRES 9 H 221 TYR TRP GLY GLN GLY THR LEU VAL THR VAL SER ALA ALA SEQRES 10 H 221 LYS THR THR ALA PRO SER VAL TYR PRO LEU ALA PRO VAL SEQRES 11 H 221 CYS GLY ASP THR THR GLY SER SER VAL THR LEU GLY CYS SEQRES 12 H 221 LEU VAL LYS GLY TYR PHE PRO GLU PRO VAL THR LEU THR SEQRES 13 H 221 TRP ASN SER GLY SER LEU SER SER GLY VAL HIS THR PHE SEQRES 14 H 221 PRO ALA VAL LEU GLN SER ASP LEU TYR THR LEU SER SER SEQRES 15 H 221 SER VAL THR VAL THR SER SER THR TRP PRO SER GLN SER SEQRES 16 H 221 ILE THR CYS ASN VAL ALA HIS PRO ALA SER SER THR LYS SEQRES 17 H 221 VAL ASP LYS LYS ILE GLU PRO ARG GLY PRO THR ILE LYS SEQRES 1 L 219 ASP VAL VAL MET THR GLN THR PRO LEU SER LEU SER VAL SEQRES 2 L 219 THR LEU GLY GLN PRO ALA SER ILE SER CYS LYS SER SER SEQRES 3 L 219 GLN SER LEU LEU ASP SER ASP GLY LYS THR TYR LEU ASN SEQRES 4 L 219 TRP LEU LEU GLN ARG PRO GLY GLN SER PRO LYS ARG LEU SEQRES 5 L 219 ILE TYR LEU VAL SER LYS LEU ALA SER GLY VAL PRO ASP SEQRES 6 L 219 ARG PHE THR GLY SER GLY SER GLY THR ASP PHE THR LEU SEQRES 7 L 219 LYS ILE ASN ARG VAL GLU ALA GLU ASP LEU GLY ILE TYR SEQRES 8 L 219 TYR CYS TRP GLN GLY THR HIS PHE PRO TRP THR PHE GLY SEQRES 9 L 219 GLY GLY THR LYS LEU GLU ILE LYS ARG ALA ASP ALA ALA SEQRES 10 L 219 PRO THR VAL SER ILE PHE PRO PRO SER SER GLU GLN LEU SEQRES 11 L 219 THR SER GLY GLY ALA SER VAL VAL CYS PHE LEU ASN ASN SEQRES 12 L 219 PHE TYR PRO LYS ASP ILE ASN VAL LYS TRP LYS ILE ASP SEQRES 13 L 219 GLY SER GLU ARG GLN ASN GLY VAL LEU ASN SER TRP THR SEQRES 14 L 219 ASP GLN ASP SER LYS ASP SER THR TYR SER MET SER SER SEQRES 15 L 219 THR LEU THR LEU THR LYS ASP GLU TYR GLU ARG HIS ASN SEQRES 16 L 219 SER TYR THR CYS GLU ALA THR HIS LYS THR SER THR SER SEQRES 17 L 219 PRO ILE VAL LYS SER PHE ASN ARG ASN GLU CYS SEQRES 1 P 9 LEU LEU GLU LEU ASP LYS TRP ALA NH2 HET NH2 P 668 1 HET ZN H 222 1 HET ZN H 223 1 HET ZN L 233 1 HETNAM NH2 AMINO GROUP HETNAM ZN ZINC ION FORMUL 3 NH2 H2 N FORMUL 4 ZN 3(ZN 2+) FORMUL 7 HOH *331(H2 O) HELIX 1 4 GLU L 84 LEU L 88 5 5 HELIX 2 5 SER L 126 SER L 132 1 7 HELIX 3 6 LYS L 188 GLU L 192 1 5 HELIX 4 7 ASN L 217 CYS L 219 5 3 SHEET 1 A 4 GLN H 3 SER H 7 0 SHEET 2 A 4 LEU H 18 THR H 25 -1 O THR H 23 N GLN H 5 SHEET 1 B 6 LEU H 11 VAL H 12 0 SHEET 1 C 4 LEU H 11 VAL H 12 0 SHEET 1 F 4 MET L 4 THR L 7 0 SHEET 2 F 4 ALA L 19 SER L 25 -1 O SER L 22 N THR L 7 SHEET 3 F 4 ASP L 75 ILE L 80 -1 O ILE L 80 N ALA L 19 SHEET 4 F 4 PHE L 67 SER L 72 -1 N THR L 68 O LYS L 79 SHEET 1 G 6 SER L 10 THR L 14 0 SHEET 2 G 6 THR L 107 LYS L 112 1 O LYS L 108 N LEU L 11 SHEET 3 G 6 GLY L 89 GLN L 95 -1 N GLY L 89 O LEU L 109 SHEET 4 G 6 LEU L 38 GLN L 43 -1 N GLN L 43 O ILE L 90 SHEET 5 G 6 LYS L 50 TYR L 54 -1 O LYS L 50 N LEU L 42 SHEET 6 G 6 LYS L 58 LEU L 59 -1 O LYS L 58 N TYR L 54 SHEET 1 H 4 SER L 10 THR L 14 0 SHEET 2 H 4 THR L 107 LYS L 112 1 O LYS L 108 N LEU L 11 SHEET 3 H 4 GLY L 89 GLN L 95 -1 N GLY L 89 O LEU L 109 SHEET 4 H 4 THR L 102 PHE L 103 -1 O THR L 102 N GLN L 95 SHEET 1 I 4 THR L 119 PHE L 123 0 SHEET 2 I 4 GLY L 134 PHE L 144 -1 O PHE L 140 N SER L 121 SHEET 3 I 4 TYR L 178 THR L 187 -1 O LEU L 186 N ALA L 135 SHEET 4 I 4 VAL L 164 TRP L 168 -1 N SER L 167 O SER L 181 SHEET 1 J 4 SER L 158 GLU L 159 0 SHEET 2 J 4 ILE L 149 ILE L 155 -1 N ILE L 155 O SER L 158 SHEET 3 J 4 SER L 196 HIS L 203 -1 O THR L 202 N ASN L 150 SHEET 4 J 4 ILE L 210 ASN L 215 -1 O PHE L 214 N TYR L 197 SSBOND 1 CYS H 22 CYS H 92 1555 1555 2.06 SSBOND 2 CYS H 139 CYS H 194 1555 1555 2.03 SSBOND 3 CYS L 23 CYS L 93 1555 1555 2.04 SSBOND 4 CYS L 139 CYS L 199 1555 1555 2.03 LINK ND2 ASN L 143 ZN ZN H 222 1555 1555 2.32 LINK NE2 HIS L 194 ZN ZN L 233 1555 1555 2.54 LINK OD2 ASP H 1 ZN ZN H 223 1555 1555 2.59 LINK ZN ZN H 223 O HOH H 288 1555 1555 2.43 LINK ZN ZN H 222 O HOH L 268 1555 1555 2.48 LINK ZN ZN H 222 O HOH H 244 1555 1555 2.51 LINK NE2 HIS H 163 ZN ZN H 222 1555 1555 2.21 CISPEP 1 ASN H 96 TYR H 97 0 1.79 CISPEP 2 PHE H 145 PRO H 146 0 -1.85 CISPEP 3 GLU H 147 PRO H 148 0 -3.77 CISPEP 4 TRP H 187 PRO H 188 0 7.76 CISPEP 5 THR L 7 PRO L 8 0 -4.16 CISPEP 6 PHE L 99 PRO L 100 0 3.28 CISPEP 7 TYR L 145 PRO L 146 0 0.32 SITE 1 AC1 4 HIS H 163 HOH H 244 ASN L 143 HOH L 268 SITE 1 AC2 5 ASP H 1 HOH H 275 HOH H 288 HIS L 98 SITE 2 AC2 5 HOH L 321 SITE 1 AC3 3 GLU L 190 HIS L 194 HOH L 290 CRYST1 36.249 80.160 72.139 90.00 97.07 90.00 P 1 21 1 2 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 0.027587 0.000000 0.003421 0.00000 SCALE2 0.000000 0.012475 0.000000 0.00000 SCALE3 0.000000 0.000000 0.013968 0.00000