HEADER VIRAL PROTEIN/IMMUNE SYSTEM 19-MAR-13 4JPV TITLE CRYSTAL STRUCTURE OF BROADLY AND POTENTLY NEUTRALIZING ANTIBODY TITLE 2 3BNC117 IN COMPLEX WITH HIV-1 GP120 COMPND MOL_ID: 1; COMPND 2 MOLECULE: HIV-1 CLADE A STRAIN 93TH057 GP120 WITH LOOP D AND LOOPD V5 COMPND 3 REPLACED FROM HIV STRAIN 3415V1; COMPND 4 CHAIN: G; COMPND 5 ENGINEERED: YES; COMPND 6 MOL_ID: 2; COMPND 7 MOLECULE: HEAVY CHAIN OF ANTIBODY 3BNC117; COMPND 8 CHAIN: H; COMPND 9 ENGINEERED: YES; COMPND 10 MOL_ID: 3; COMPND 11 MOLECULE: LIGHT CHAIN OF ANTIBODY 3BNC117; 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: HOMO SAPIENS; SOURCE 5 EXPRESSION_SYSTEM_COMMON: HUMAN; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 9606; SOURCE 7 EXPRESSION_SYSTEM_CELL_LINE: HEK293F; SOURCE 8 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 9 MOL_ID: 2; SOURCE 10 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 11 ORGANISM_COMMON: HUMAN; SOURCE 12 ORGANISM_TAXID: 9606; SOURCE 13 EXPRESSION_SYSTEM: HOMO SAPIENS; SOURCE 14 EXPRESSION_SYSTEM_COMMON: HUMAN; SOURCE 15 EXPRESSION_SYSTEM_TAXID: 9606; SOURCE 16 EXPRESSION_SYSTEM_CELL_LINE: HEK293F; SOURCE 17 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 18 MOL_ID: 3; SOURCE 19 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 20 ORGANISM_COMMON: HUMAN; SOURCE 21 ORGANISM_TAXID: 9606; SOURCE 22 EXPRESSION_SYSTEM: HOMO SAPIENS; SOURCE 23 EXPRESSION_SYSTEM_COMMON: HUMAN; SOURCE 24 EXPRESSION_SYSTEM_TAXID: 9606; SOURCE 25 EXPRESSION_SYSTEM_CELL_LINE: HEK293F; SOURCE 26 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID KEYWDS HIV, GP120, CD4-BINDING SITE, 3BNC117, NEUTRALIZATION, VACCINE, KEYWDS 2 ANTIBODY, ENVELOPE PROTEIN, VIRAL PROTEIN-IMMUNE SYSTEM COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR T.ZHOU,S.MOQUIN,P.D.KWONG REVDAT 4 20-SEP-23 4JPV 1 REMARK REVDAT 3 02-JUN-21 4JPV 1 SOURCE HETSYN REVDAT 2 29-JUL-20 4JPV 1 COMPND REMARK HETNAM LINK REVDAT 2 2 1 SITE REVDAT 1 17-APR-13 4JPV 0 JRNL AUTH F.KLEIN,R.DISKIN,J.F.SCHEID,C.GAEBLER,H.MOUQUET, JRNL AUTH 2 I.S.GEORGIEV,M.PANCERA,T.ZHOU,R.B.INCESU,B.Z.FU, JRNL AUTH 3 P.N.GNANAPRAGASAM,T.Y.OLIVEIRA,M.S.SEAMAN,P.D.KWONG, JRNL AUTH 4 P.J.BJORKMAN,M.C.NUSSENZWEIG JRNL TITL SOMATIC MUTATIONS OF THE IMMUNOGLOBULIN FRAMEWORK ARE JRNL TITL 2 GENERALLY REQUIRED FOR BROAD AND POTENT HIV-1 JRNL TITL 3 NEUTRALIZATION. JRNL REF CELL(CAMBRIDGE,MASS.) V. 153 126 2013 JRNL REFN ISSN 0092-8674 JRNL PMID 23540694 JRNL DOI 10.1016/J.CELL.2013.03.018 REMARK 2 REMARK 2 RESOLUTION. 2.83 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (PHENIX.REFINE: DEV_998) 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) : 2.83 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 48.97 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.350 REMARK 3 COMPLETENESS FOR RANGE (%) : 97.9 REMARK 3 NUMBER OF REFLECTIONS : 26952 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.203 REMARK 3 R VALUE (WORKING SET) : 0.199 REMARK 3 FREE R VALUE : 0.259 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.090 REMARK 3 FREE R VALUE TEST SET COUNT : 1371 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 48.9733 - 6.0869 1.00 2793 146 0.2188 0.2826 REMARK 3 2 6.0869 - 4.8328 0.98 2610 142 0.1853 0.2341 REMARK 3 3 4.8328 - 4.2222 0.99 2576 157 0.1574 0.2317 REMARK 3 4 4.2222 - 3.8364 0.99 2574 136 0.1716 0.2337 REMARK 3 5 3.8364 - 3.5615 0.99 2571 136 0.1822 0.2344 REMARK 3 6 3.5615 - 3.3516 1.00 2569 144 0.2078 0.2655 REMARK 3 7 3.3516 - 3.1837 1.00 2562 134 0.2175 0.2716 REMARK 3 8 3.1837 - 3.0452 1.00 2570 129 0.2255 0.3028 REMARK 3 9 3.0452 - 2.9280 0.98 2528 124 0.2586 0.2859 REMARK 3 10 2.9280 - 2.8269 0.87 2228 123 0.3307 0.4231 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : FLAT BULK SOLVENT MODEL REMARK 3 SOLVENT RADIUS : 1.10 REMARK 3 SHRINKAGE RADIUS : 0.86 REMARK 3 K_SOL : 0.35 REMARK 3 B_SOL : 64.81 REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.400 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 28.090 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) : -9.46300 REMARK 3 B22 (A**2) : -6.70080 REMARK 3 B33 (A**2) : 16.16380 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 : 0.004 6306 REMARK 3 ANGLE : 0.876 8555 REMARK 3 CHIRALITY : 0.059 963 REMARK 3 PLANARITY : 0.005 1084 REMARK 3 DIHEDRAL : 13.248 2320 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 6 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: CHAIN G AND (RESID 44:253 OR RESID 476:492) REMARK 3 ORIGIN FOR THE GROUP (A): -19.0943 3.3739 -6.1982 REMARK 3 T TENSOR REMARK 3 T11: 0.3846 T22: 0.3574 REMARK 3 T33: 0.9685 T12: 0.0450 REMARK 3 T13: 0.0398 T23: 0.0035 REMARK 3 L TENSOR REMARK 3 L11: 3.1960 L22: 4.0115 REMARK 3 L33: 2.9915 L12: 1.5329 REMARK 3 L13: 1.3265 L23: 1.8391 REMARK 3 S TENSOR REMARK 3 S11: 0.1260 S12: 0.0584 S13: -0.2150 REMARK 3 S21: 0.0802 S22: -0.1460 S23: 0.3427 REMARK 3 S31: 0.2966 S32: -0.2178 S33: 0.0265 REMARK 3 TLS GROUP : 2 REMARK 3 SELECTION: CHAIN G AND RESID 254:475 REMARK 3 ORIGIN FOR THE GROUP (A): 3.3976 -1.1781 -6.2006 REMARK 3 T TENSOR REMARK 3 T11: 0.4418 T22: 0.3664 REMARK 3 T33: 0.9935 T12: 0.0587 REMARK 3 T13: 0.0463 T23: 0.0216 REMARK 3 L TENSOR REMARK 3 L11: 2.7958 L22: 2.6084 REMARK 3 L33: 3.6291 L12: 0.3440 REMARK 3 L13: -0.0754 L23: 1.1360 REMARK 3 S TENSOR REMARK 3 S11: -0.0186 S12: 0.1066 S13: -0.6856 REMARK 3 S21: 0.1120 S22: -0.0120 S23: -0.1933 REMARK 3 S31: 0.4160 S32: 0.3410 S33: 0.0168 REMARK 3 TLS GROUP : 3 REMARK 3 SELECTION: CHAIN H AND RESID 1:113 REMARK 3 ORIGIN FOR THE GROUP (A): 9.0983 15.3018 -27.8491 REMARK 3 T TENSOR REMARK 3 T11: 0.3869 T22: 0.5090 REMARK 3 T33: 0.4415 T12: -0.0386 REMARK 3 T13: -0.0378 T23: -0.0399 REMARK 3 L TENSOR REMARK 3 L11: 9.2907 L22: 6.2802 REMARK 3 L33: 6.1967 L12: 1.2425 REMARK 3 L13: -1.3199 L23: -2.4987 REMARK 3 S TENSOR REMARK 3 S11: 0.1704 S12: 0.5826 S13: 0.5133 REMARK 3 S21: -0.1980 S22: -0.0273 S23: 0.4892 REMARK 3 S31: -0.2090 S32: 0.2578 S33: -0.1242 REMARK 3 TLS GROUP : 4 REMARK 3 SELECTION: CHAIN H AND RESID 114:217 REMARK 3 ORIGIN FOR THE GROUP (A): 26.5559 29.3566 -55.0503 REMARK 3 T TENSOR REMARK 3 T11: 0.9454 T22: 1.3180 REMARK 3 T33: 0.8446 T12: 0.3629 REMARK 3 T13: 0.2891 T23: 0.2377 REMARK 3 L TENSOR REMARK 3 L11: 3.6121 L22: 3.3880 REMARK 3 L33: 4.7091 L12: 0.3379 REMARK 3 L13: 0.7163 L23: -2.0988 REMARK 3 S TENSOR REMARK 3 S11: 0.2310 S12: -0.1438 S13: 0.3578 REMARK 3 S21: -0.3761 S22: 0.1478 S23: -0.1122 REMARK 3 S31: -0.7869 S32: -1.2802 S33: -0.3611 REMARK 3 TLS GROUP : 5 REMARK 3 SELECTION: CHAIN L AND RESID 1:108 REMARK 3 ORIGIN FOR THE GROUP (A): -1.9179 7.8003 -47.6586 REMARK 3 T TENSOR REMARK 3 T11: 0.7606 T22: 1.4393 REMARK 3 T33: 0.8175 T12: -0.1432 REMARK 3 T13: -0.2258 T23: -0.0170 REMARK 3 L TENSOR REMARK 3 L11: 3.8221 L22: 4.1783 REMARK 3 L33: 7.1436 L12: -0.9516 REMARK 3 L13: 0.3782 L23: -0.3524 REMARK 3 S TENSOR REMARK 3 S11: -0.3389 S12: 2.0822 S13: 0.1166 REMARK 3 S21: -1.0292 S22: 0.0342 S23: 0.5609 REMARK 3 S31: 0.3821 S32: -0.4557 S33: 0.2349 REMARK 3 TLS GROUP : 6 REMARK 3 SELECTION: CHAIN L AND RESID 109:213 REMARK 3 ORIGIN FOR THE GROUP (A): 28.8578 15.8760 -65.1678 REMARK 3 T TENSOR REMARK 3 T11: 1.0952 T22: 1.3635 REMARK 3 T33: 0.8012 T12: -0.1342 REMARK 3 T13: 0.2252 T23: 0.0835 REMARK 3 L TENSOR REMARK 3 L11: 5.8716 L22: 3.8069 REMARK 3 L33: 2.8038 L12: 2.3235 REMARK 3 L13: 0.7428 L23: 0.2667 REMARK 3 S TENSOR REMARK 3 S11: -0.5798 S12: 0.6931 S13: -0.8154 REMARK 3 S21: -0.9635 S22: 0.5483 S23: -0.3832 REMARK 3 S31: 0.1493 S32: -0.2494 S33: 0.0271 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 4JPV COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 26-MAR-13. REMARK 100 THE DEPOSITION ID IS D_1000078353. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 05-DEC-11 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 7.5 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 REMARK 200 MONOCHROMATOR : APS 22-BM REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : NULL REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 27017 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.800 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 2.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 98.4 REMARK 200 DATA REDUNDANCY : 4.100 REMARK 200 R MERGE (I) : 0.10500 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 14.1000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.80 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.85 REMARK 200 COMPLETENESS FOR SHELL (%) : 87.1 REMARK 200 DATA REDUNDANCY IN SHELL : 3.20 REMARK 200 R MERGE FOR SHELL (I) : 0.51000 REMARK 200 R SYM FOR SHELL (I) : 0.62000 REMARK 200 FOR SHELL : 2.100 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: 3SE9 REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 61.53 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.20 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1 M HEPES, 11% PEG 8000, 7% ETHYLENE REMARK 280 GLYCOL , PH 7.5, 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 34.31350 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 115.81650 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 34.94350 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 115.81650 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 34.31350 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 34.94350 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: 9820 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 36180 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: 40.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: G, 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 G 319 REMARK 465 SER G 320 REMARK 465 GLY G 321 REMARK 465 SER G 322 REMARK 465 GLY G 323 REMARK 465 GLY G 403 REMARK 465 ASN G 404 REMARK 465 GLU G 405 REMARK 465 THR G 406 REMARK 465 MET G 407 REMARK 465 SER H 128 REMARK 465 LYS H 129 REMARK 465 SER H 130 REMARK 465 THR H 131 REMARK 465 SER H 132 REMARK 465 GLY H 133 REMARK 465 GLY H 134 REMARK 465 LYS H 214 REMARK 465 SER H 215 REMARK 465 CYS H 216 REMARK 465 GLU L 213 REMARK 465 CYS L 214 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 ND2 ASN G 448 C2 NAG G 510 2.05 REMARK 500 OD2 ASP L 105 OH TYR L 173 2.15 REMARK 500 O PRO G 417 O HOH G 640 2.17 REMARK 500 O LEU H 4 O HOH H 311 2.18 REMARK 500 ND2 ASN G 392 C2 NAG G 509 2.19 REMARK 500 O SER L 7 N SER L 9 2.19 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 G 211 102.17 -163.38 REMARK 500 GLN G 258 -60.32 63.64 REMARK 500 GLU G 267 29.50 -72.25 REMARK 500 GLU G 268 119.08 62.58 REMARK 500 THR G 274 -65.98 -143.32 REMARK 500 GLU G 275 -56.04 118.62 REMARK 500 ASN G 354 52.23 38.96 REMARK 500 ASN G 463 -62.16 61.37 REMARK 500 VAL H 2 -94.48 51.29 REMARK 500 GLN H 3 120.33 70.10 REMARK 500 SER H 25 -84.23 -136.92 REMARK 500 VAL H 67 132.24 56.78 REMARK 500 ASP H 85 37.34 -77.75 REMARK 500 THR H 87 108.71 -59.24 REMARK 500 SER H 113 -128.55 -70.37 REMARK 500 ALA H 114 95.24 58.76 REMARK 500 ASP H 144 77.51 60.10 REMARK 500 SER H 153 -167.98 -125.12 REMARK 500 PRO L 8 -28.15 15.38 REMARK 500 SER L 9 -8.19 66.22 REMARK 500 SER L 10 119.10 -166.83 REMARK 500 ARG L 66 57.41 -111.41 REMARK 500 TYR L 91 -129.45 52.55 REMARK 500 THR L 109 56.04 -103.53 REMARK 500 ASN L 138 91.75 57.55 REMARK 500 LYS L 169 -63.41 -94.01 REMARK 500 ARG L 211 95.38 -63.25 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 3NGB RELATED DB: PDB REMARK 900 RELATED ID: 3SE8 RELATED DB: PDB REMARK 900 RELATED ID: 3SE9 RELATED DB: PDB REMARK 900 RELATED ID: 4JPW RELATED DB: PDB REMARK 900 RELATED ID: 4GW4 RELATED DB: PDB DBREF 4JPV G 44 492 PDB 4JPV 4JPV 44 492 DBREF 4JPV H 1 216 PDB 4JPV 4JPV 1 216 DBREF 4JPV L 1 214 PDB 4JPV 4JPV 1 214 SEQRES 1 G 352 VAL TRP LYS ASP ALA ASP THR THR LEU PHE CYS ALA SER SEQRES 2 G 352 ASP ALA LYS ALA HIS GLU THR GLU VAL HIS ASN VAL TRP SEQRES 3 G 352 ALA THR HIS ALA CYS VAL PRO THR ASP PRO ASN PRO GLN SEQRES 4 G 352 GLU ILE HIS LEU GLU ASN VAL THR GLU ASN PHE ASN MET SEQRES 5 G 352 TRP LYS ASN ASN MET VAL GLU GLN MET GLN GLU ASP VAL SEQRES 6 G 352 ILE SER LEU TRP ASP GLN SER LEU GLN PRO CYS VAL LYS SEQRES 7 G 352 LEU THR GLY GLY SER VAL ILE LYS GLN ALA CYS PRO LYS SEQRES 8 G 352 ILE SER PHE ASP PRO ILE PRO ILE HIS TYR CYS THR PRO SEQRES 9 G 352 ALA GLY TYR VAL ILE LEU LYS CYS ASN ASP LYS ASN PHE SEQRES 10 G 352 ASN GLY THR GLY PRO CYS LYS ASN VAL SER SER VAL GLN SEQRES 11 G 352 CYS THR HIS GLY ILE LYS PRO VAL VAL SER THR GLN LEU SEQRES 12 G 352 LEU LEU ASN GLY SER LEU ALA GLU GLU GLU ILE ILE ILE SEQRES 13 G 352 ARG THR GLU ASN ILE THR ASP ASN ALA LYS THR ILE ILE SEQRES 14 G 352 VAL HIS LEU ASN LYS SER VAL GLU ILE ASN CYS THR ARG SEQRES 15 G 352 PRO SER ASN GLY GLY SER GLY SER GLY GLY ASP ILE ARG SEQRES 16 G 352 LYS ALA TYR CYS GLU ILE ASN GLY THR LYS TRP ASN LYS SEQRES 17 G 352 VAL LEU LYS GLN VAL THR GLU LYS LEU LYS GLU HIS PHE SEQRES 18 G 352 ASN ASN LYS THR ILE ILE PHE GLN PRO PRO SER GLY GLY SEQRES 19 G 352 ASP LEU GLU ILE THR MET HIS HIS PHE ASN CYS ARG GLY SEQRES 20 G 352 GLU PHE PHE TYR CYS ASN THR THR GLN LEU PHE ASN ASN SEQRES 21 G 352 THR CYS ILE GLY ASN GLU THR MET LYS GLY CYS ASN GLY SEQRES 22 G 352 THR ILE THR LEU PRO CYS LYS ILE LYS GLN ILE ILE ASN SEQRES 23 G 352 MET TRP GLN GLY THR GLY GLN ALA MET TYR ALA PRO PRO SEQRES 24 G 352 ILE ASP GLY LYS ILE ASN CYS VAL SER ASN ILE THR GLY SEQRES 25 G 352 ILE LEU LEU THR ARG ASP GLY GLY GLU ASN ASN SER THR SEQRES 26 G 352 GLU ILE PHE ARG PRO GLY GLY GLY ASN ILE LYS ASP ASN SEQRES 27 G 352 TRP ARG SER GLU LEU TYR LYS TYR LYS VAL VAL GLN ILE SEQRES 28 G 352 GLU SEQRES 1 H 226 GLN VAL GLN LEU LEU GLN SER GLY ALA ALA VAL THR LYS SEQRES 2 H 226 PRO GLY ALA SER VAL ARG VAL SER CYS GLU ALA SER GLY SEQRES 3 H 226 TYR ASN ILE ARG ASP TYR PHE ILE HIS TRP TRP ARG GLN SEQRES 4 H 226 ALA PRO GLY GLN GLY LEU GLN TRP VAL GLY TRP ILE ASN SEQRES 5 H 226 PRO LYS THR GLY GLN PRO ASN ASN PRO ARG GLN PHE GLN SEQRES 6 H 226 GLY ARG VAL SER LEU THR ARG HIS ALA SER TRP ASP PHE SEQRES 7 H 226 ASP THR TYR SER PHE TYR MET ASP LEU LYS ALA LEU ARG SEQRES 8 H 226 SER ASP ASP THR ALA VAL TYR PHE CYS ALA ARG GLN ARG SEQRES 9 H 226 SER ASP TYR TRP ASP PHE ASP VAL TRP GLY SER GLY THR SEQRES 10 H 226 GLN VAL THR VAL SER SER ALA SER THR LYS GLY PRO SER SEQRES 11 H 226 VAL PHE PRO LEU ALA PRO SER SER LYS SER THR SER GLY SEQRES 12 H 226 GLY THR ALA ALA LEU GLY CYS LEU VAL LYS ASP TYR PHE SEQRES 13 H 226 PRO GLU PRO VAL THR VAL SER TRP ASN SER GLY ALA LEU SEQRES 14 H 226 THR SER GLY VAL HIS THR PHE PRO ALA VAL LEU GLN SER SEQRES 15 H 226 SER GLY LEU TYR SER LEU SER SER VAL VAL THR VAL PRO SEQRES 16 H 226 SER SER SER LEU GLY THR GLN THR TYR ILE CYS ASN VAL SEQRES 17 H 226 ASN HIS LYS PRO SER ASN THR LYS VAL ASP LYS LYS VAL SEQRES 18 H 226 GLU PRO LYS SER CYS SEQRES 1 L 206 ASP ILE GLN MET THR GLN SER PRO SER SER LEU SER ALA SEQRES 2 L 206 SER VAL GLY ASP THR VAL THR ILE THR CYS GLN ALA ASN SEQRES 3 L 206 GLY TYR LEU ASN TRP TYR GLN GLN ARG ARG GLY LYS ALA SEQRES 4 L 206 PRO LYS LEU LEU ILE TYR ASP GLY SER LYS LEU GLU ARG SEQRES 5 L 206 GLY VAL PRO SER ARG PHE SER GLY ARG ARG TRP GLY GLN SEQRES 6 L 206 GLU TYR ASN LEU THR ILE ASN ASN LEU GLN PRO GLU ASP SEQRES 7 L 206 ILE ALA THR TYR PHE CYS GLN VAL TYR GLU PHE VAL VAL SEQRES 8 L 206 PRO GLY THR ARG LEU ASP LEU LYS ARG THR VAL ALA ALA SEQRES 9 L 206 PRO SER VAL PHE ILE PHE PRO PRO SER ASP GLU GLN LEU SEQRES 10 L 206 LYS SER GLY THR ALA SER VAL VAL CYS LEU LEU ASN ASN SEQRES 11 L 206 PHE TYR PRO ARG GLU ALA LYS VAL GLN TRP LYS VAL ASP SEQRES 12 L 206 ASN ALA LEU GLN SER GLY ASN SER GLN GLU SER VAL THR SEQRES 13 L 206 GLU GLN ASP SER LYS ASP SER THR TYR SER LEU SER SER SEQRES 14 L 206 THR LEU THR LEU SER LYS ALA ASP TYR GLU LYS HIS LYS SEQRES 15 L 206 VAL TYR ALA CYS GLU VAL THR HIS GLN GLY LEU SER SER SEQRES 16 L 206 PRO VAL THR LYS SER PHE ASN ARG GLY GLU CYS MODRES 4JPV ASN G 295 ASN GLYCOSYLATION SITE MODRES 4JPV ASN G 234 ASN GLYCOSYLATION SITE MODRES 4JPV ASN G 448 ASN GLYCOSYLATION SITE MODRES 4JPV ASN G 386 ASN GLYCOSYLATION SITE MODRES 4JPV ASN G 276 ASN GLYCOSYLATION SITE MODRES 4JPV ASN G 334 ASN GLYCOSYLATION SITE MODRES 4JPV ASN G 241 ASN GLYCOSYLATION SITE MODRES 4JPV ASN G 392 ASN GLYCOSYLATION SITE MODRES 4JPV ASN G 262 ASN GLYCOSYLATION SITE MODRES 4JPV ASN G 289 ASN GLYCOSYLATION SITE MODRES 4JPV ASN L 72 ASN GLYCOSYLATION SITE HET NAG G 501 14 HET NAG G 502 14 HET NAG G 503 14 HET NAG G 504 14 HET NAG G 505 14 HET NAG G 506 14 HET NAG G 507 14 HET NAG G 508 14 HET NAG G 509 14 HET NAG G 510 14 HET EPE G 511 15 HET EDO G 512 4 HET EDO G 513 4 HET EDO G 514 4 HET NAG L 301 14 HET EDO L 302 4 HETNAM NAG 2-ACETAMIDO-2-DEOXY-BETA-D-GLUCOPYRANOSE HETNAM EPE 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID HETNAM EDO 1,2-ETHANEDIOL 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 EPE HEPES HETSYN EDO ETHYLENE GLYCOL FORMUL 4 NAG 11(C8 H15 N O6) FORMUL 14 EPE C8 H18 N2 O4 S FORMUL 15 EDO 4(C2 H6 O2) FORMUL 20 HOH *81(H2 O) HELIX 1 1 GLU G 64 ALA G 73 1 10 HELIX 2 2 TRP G 96 ASN G 98 5 3 HELIX 3 3 ASN G 99 LEU G 116 1 18 HELIX 4 4 GLY G 335 PHE G 353 1 19 HELIX 5 5 ASP G 368 MET G 373 1 6 HELIX 6 6 THR G 387 PHE G 391 5 5 HELIX 7 7 ASN G 392 ILE G 396 5 5 HELIX 8 8 ILE G 475 TYR G 484 1 10 HELIX 9 9 ASN H 28 TYR H 32 5 5 HELIX 10 10 ARG H 83 THR H 87 5 5 HELIX 11 11 PRO H 185 LEU H 189 5 5 HELIX 12 12 LYS H 201 ASN H 204 5 4 HELIX 13 13 GLN L 79 ILE 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 SHEET 1 A 5 TRP G 45 ASP G 47 0 SHEET 2 A 5 TYR G 486 ILE G 491 -1 O GLN G 490 N LYS G 46 SHEET 3 A 5 TYR G 223 CYS G 228 -1 N LEU G 226 O LYS G 487 SHEET 4 A 5 VAL G 242 VAL G 245 -1 O SER G 243 N LYS G 227 SHEET 5 A 5 ILE G 84 HIS G 85 -1 N ILE G 84 O SER G 244 SHEET 1 B 3 CYS G 74 PRO G 76 0 SHEET 2 B 3 PHE G 53 SER G 56 1 N CYS G 54 O VAL G 75 SHEET 3 B 3 HIS G 216 CYS G 218 -1 O CYS G 218 N PHE G 53 SHEET 1 C 2 GLU G 91 ASN G 94 0 SHEET 2 C 2 THR G 236 CYS G 239 -1 O GLY G 237 N PHE G 93 SHEET 1 D 4 SER G 199 LYS G 202 0 SHEET 2 D 4 VAL G 120 THR G 123 -1 N LYS G 121 O ILE G 201 SHEET 3 D 4 GLN G 432 MET G 434 -1 O MET G 434 N VAL G 120 SHEET 4 D 4 ILE G 423 ASN G 425 -1 N ILE G 424 O ALA G 433 SHEET 1 E 5 LEU G 259 LEU G 261 0 SHEET 2 E 5 ILE G 443 ARG G 456 -1 O GLY G 451 N LEU G 260 SHEET 3 E 5 ILE G 284 ARG G 298 -1 N VAL G 286 O ILE G 452 SHEET 4 E 5 THR G 465 PRO G 470 0 SHEET 5 E 5 THR G 358 PHE G 361 1 N ILE G 360 O PHE G 468 SHEET 1 F 7 ILE G 271 ARG G 273 0 SHEET 2 F 7 ILE G 284 ARG G 298 -1 O ILE G 285 N ARG G 273 SHEET 3 F 7 ILE G 443 ARG G 456 -1 O ILE G 452 N VAL G 286 SHEET 4 F 7 LYS G 328 ASN G 334 0 SHEET 5 F 7 THR G 413 ILE G 420 -1 O LEU G 416 N CYS G 331 SHEET 6 F 7 GLU G 381 CYS G 385 -1 N TYR G 384 O LYS G 419 SHEET 7 F 7 PHE G 376 CYS G 378 -1 N CYS G 378 O GLU G 381 SHEET 1 G 4 VAL H 2 GLN H 6 0 SHEET 2 G 4 VAL H 18 GLY H 26 -1 O GLU H 23 N LEU H 5 SHEET 3 G 4 TYR H 76 LEU H 82 -1 O PHE H 78 N CYS H 22 SHEET 4 G 4 LEU H 69 ALA H 71B-1 N HIS H 71A O SER H 77 SHEET 1 H 6 ALA H 10 THR H 12 0 SHEET 2 H 6 THR H 107 VAL H 111 1 O GLN H 108 N ALA H 10 SHEET 3 H 6 ALA H 88 GLN H 95 -1 N TYR H 90 O THR H 107 SHEET 4 H 6 PHE H 33 GLN H 39 -1 N TRP H 37 O PHE H 91 SHEET 5 H 6 LEU H 45 ILE H 51 -1 O GLY H 49 N TRP H 36 SHEET 6 H 6 PRO H 57 ASN H 58 -1 O ASN H 58 N TRP H 50 SHEET 1 I 4 ALA H 10 THR H 12 0 SHEET 2 I 4 THR H 107 VAL H 111 1 O GLN H 108 N ALA H 10 SHEET 3 I 4 ALA H 88 GLN H 95 -1 N TYR H 90 O THR H 107 SHEET 4 I 4 PHE H 100B TRP H 103 -1 O VAL H 102 N ARG H 94 SHEET 1 J 4 SER H 120 LEU H 124 0 SHEET 2 J 4 ALA H 136 TYR H 145 -1 O LEU H 141 N PHE H 122 SHEET 3 J 4 TYR H 176 VAL H 184 -1 O SER H 180 N CYS H 140 SHEET 4 J 4 HIS H 164 THR H 165 -1 N HIS H 164 O VAL H 181 SHEET 1 K 4 SER H 120 LEU H 124 0 SHEET 2 K 4 ALA H 136 TYR H 145 -1 O LEU H 141 N PHE H 122 SHEET 3 K 4 TYR H 176 VAL H 184 -1 O SER H 180 N CYS H 140 SHEET 4 K 4 VAL H 169 LEU H 170 -1 N VAL H 169 O SER H 177 SHEET 1 L 3 THR H 151 TRP H 154 0 SHEET 2 L 3 TYR H 194 HIS H 200 -1 O ASN H 197 N SER H 153 SHEET 3 L 3 THR H 205 VAL H 211 -1 O VAL H 207 N VAL H 198 SHEET 1 M 2 SER L 10 SER L 12 0 SHEET 2 M 2 ARG L 103 ASP L 105 1 O ARG L 103 N LEU L 11 SHEET 1 N 3 VAL L 19 GLN L 24 0 SHEET 2 N 3 GLU L 70 ILE L 75 -1 O TYR L 71 N CYS L 23 SHEET 3 N 3 PHE L 62 TRP L 67 -1 N SER L 63 O THR L 74 SHEET 1 O 5 LYS L 53 LEU L 54 0 SHEET 2 O 5 LYS L 45 TYR L 49 -1 N TYR L 49 O LYS L 53 SHEET 3 O 5 LEU L 33 GLN L 38 -1 N TRP L 35 O LEU L 47 SHEET 4 O 5 THR L 85 VAL L 90 -1 O PHE L 87 N TYR L 36 SHEET 5 O 5 PHE L 97 VAL L 98 -1 O PHE L 97 N VAL L 90 SHEET 1 P 4 PHE L 116 PHE L 118 0 SHEET 2 P 4 THR L 129 PHE L 139 -1 O LEU L 135 N PHE L 116 SHEET 3 P 4 TYR L 173 SER L 182 -1 O LEU L 179 N VAL L 132 SHEET 4 P 4 SER L 159 VAL L 163 -1 N GLN L 160 O THR L 178 SHEET 1 Q 4 LEU L 154 GLN L 155 0 SHEET 2 Q 4 ALA L 144 VAL L 150 -1 N TRP L 148 O GLN L 155 SHEET 3 Q 4 VAL L 191 HIS L 198 -1 O ALA L 193 N LYS L 149 SHEET 4 Q 4 VAL L 205 ASN L 210 -1 O LYS L 207 N CYS L 194 SSBOND 1 CYS G 54 CYS G 74 1555 1555 2.04 SSBOND 2 CYS G 119 CYS G 205 1555 1555 2.03 SSBOND 3 CYS G 218 CYS G 247 1555 1555 2.04 SSBOND 4 CYS G 228 CYS G 239 1555 1555 2.04 SSBOND 5 CYS G 296 CYS G 331 1555 1555 2.04 SSBOND 6 CYS G 378 CYS G 445 1555 1555 2.04 SSBOND 7 CYS G 385 CYS G 418 1555 1555 2.04 SSBOND 8 CYS G 395 CYS G 410 1555 1555 2.03 SSBOND 9 CYS H 22 CYS H 92 1555 1555 2.04 SSBOND 10 CYS H 140 CYS H 196 1555 1555 2.03 SSBOND 11 CYS L 23 CYS L 88 1555 1555 2.03 SSBOND 12 CYS L 134 CYS L 194 1555 1555 2.03 LINK ND2 ASN G 234 C1 NAG G 501 1555 1555 1.43 LINK ND2 ASN G 241 C1 NAG G 502 1555 1555 1.44 LINK ND2 ASN G 262 C1 NAG G 503 1555 1555 1.44 LINK ND2 ASN G 276 C1 NAG G 504 1555 1555 1.44 LINK ND2 ASN G 289 C1 NAG G 505 1555 1555 1.44 LINK ND2 ASN G 295 C1 NAG G 506 1555 1555 1.43 LINK ND2 ASN G 334 C1 NAG G 507 1555 1555 1.44 LINK ND2 ASN G 386 C1 NAG G 508 1555 1555 1.44 LINK ND2 ASN G 392 C1 NAG G 509 1555 1555 1.44 LINK ND2 ASN G 448 C1 NAG G 510 1555 1555 1.44 LINK ND2 ASN L 72 C1 NAG L 301 1555 1555 1.44 CISPEP 1 GLU G 268 GLU G 269 0 13.91 CISPEP 2 PHE H 146 PRO H 147 0 -3.89 CISPEP 3 GLU H 148 PRO H 149 0 -4.13 CISPEP 4 TYR L 140 PRO L 141 0 1.01 CRYST1 68.627 69.887 231.633 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 0.014572 0.000000 0.000000 0.00000 SCALE2 0.000000 0.014309 0.000000 0.00000 SCALE3 0.000000 0.000000 0.004317 0.00000