HEADER VIRAL PROTEIN/IMMUNE SYSTEM 19-FEB-13 4JB9 TITLE CRYSTAL STRUCTURE OF ANTIBODY VRC06 IN COMPLEX WITH HIV-1 GP120 CORE COMPND MOL_ID: 1; COMPND 2 MOLECULE: CLADE A/E 93TH057 HIV-1 GP120 CORE; COMPND 3 CHAIN: G; COMPND 4 ENGINEERED: YES; COMPND 5 MOL_ID: 2; COMPND 6 MOLECULE: ANTIBODY VRC06 HEAVY CHAIN; COMPND 7 CHAIN: H; COMPND 8 ENGINEERED: YES; COMPND 9 MOL_ID: 3; COMPND 10 MOLECULE: ANTIBODY VRC06 LIGHT CHAIN; COMPND 11 CHAIN: L; COMPND 12 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_TAXID: 9606; SOURCE 6 EXPRESSION_SYSTEM_CELL_LINE: 293F; SOURCE 7 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 8 EXPRESSION_SYSTEM_PLASMID: PVRC8400; 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_TAXID: 9606; SOURCE 15 EXPRESSION_SYSTEM_CELL_LINE: 293F; SOURCE 16 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 17 EXPRESSION_SYSTEM_PLASMID: PVRC8400; 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_TAXID: 9606; SOURCE 24 EXPRESSION_SYSTEM_CELL_LINE: 293F; SOURCE 25 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 26 EXPRESSION_SYSTEM_PLASMID: PVRC8400 KEYWDS HIV-1, GP120, ANTIBODY, VRC06, GLYCOPROTEIN, IMMUNE SYSTEM, VIRAL KEYWDS 2 PROTEIN-IMMUNE SYSTEM COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR Y.D.KWON,T.ZHOU,S.SRIVATSAN,P.D.KWONG REVDAT 6 25-DEC-24 4JB9 1 REMARK LINK REVDAT 5 20-SEP-23 4JB9 1 HETSYN REVDAT 4 29-JUL-20 4JB9 1 COMPND REMARK HETNAM LINK REVDAT 4 2 1 SITE REVDAT 3 19-OCT-16 4JB9 1 LINK REMARK REVDAT 2 29-MAY-13 4JB9 1 JRNL REVDAT 1 08-MAY-13 4JB9 0 JRNL AUTH I.S.GEORGIEV,N.A.DORIA-ROSE,T.ZHOU,Y.D.KWON,R.P.STAUPE, JRNL AUTH 2 S.MOQUIN,G.Y.CHUANG,M.K.LOUDER,S.D.SCHMIDT,H.R.ALTAE-TRAN, JRNL AUTH 3 R.T.BAILER,K.MCKEE,M.NASON,S.O'DELL,G.OFEK,M.PANCERA, JRNL AUTH 4 S.SRIVATSAN,L.SHAPIRO,M.CONNORS,S.A.MIGUELES,L.MORRIS, JRNL AUTH 5 Y.NISHIMURA,M.A.MARTIN,J.R.MASCOLA,P.D.KWONG JRNL TITL DELINEATING ANTIBODY RECOGNITION IN POLYCLONAL SERA FROM JRNL TITL 2 PATTERNS OF HIV-1 ISOLATE NEUTRALIZATION. JRNL REF SCIENCE V. 340 751 2013 JRNL REFN ISSN 0036-8075 JRNL PMID 23661761 JRNL DOI 10.1126/SCIENCE.1233989 REMARK 2 REMARK 2 RESOLUTION. 2.60 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (PHENIX.REFINE: 1.8.1_1168) 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) : 2.60 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 48.72 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.360 REMARK 3 COMPLETENESS FOR RANGE (%) : 92.0 REMARK 3 NUMBER OF REFLECTIONS : 29132 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.250 REMARK 3 R VALUE (WORKING SET) : 0.248 REMARK 3 FREE R VALUE : 0.287 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.010 REMARK 3 FREE R VALUE TEST SET COUNT : 1454 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 48.7283 - 5.5990 0.99 3128 198 0.2088 0.2413 REMARK 3 2 5.5990 - 4.4450 1.00 3045 157 0.2148 0.2440 REMARK 3 3 4.4450 - 3.8834 1.00 3012 155 0.2383 0.2725 REMARK 3 4 3.8834 - 3.5285 1.00 3008 133 0.2575 0.3311 REMARK 3 5 3.5285 - 3.2756 1.00 2965 159 0.2848 0.3467 REMARK 3 6 3.2756 - 3.0825 1.00 2933 161 0.2988 0.3295 REMARK 3 7 3.0825 - 2.9282 0.97 2851 158 0.3227 0.4027 REMARK 3 8 2.9282 - 2.8007 0.89 2634 121 0.3326 0.3797 REMARK 3 9 2.8007 - 2.6929 0.74 2175 123 0.3263 0.4142 REMARK 3 10 2.6929 - 2.6000 0.61 1832 89 0.3280 0.3862 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 : NULL REMARK 3 B_SOL : NULL REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.410 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 36.980 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 62.00 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 : 0.003 6375 REMARK 3 ANGLE : 0.746 8643 REMARK 3 CHIRALITY : 0.055 975 REMARK 3 PLANARITY : 0.003 1098 REMARK 3 DIHEDRAL : 12.051 2341 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): 12.9798 -0.0493 -48.5033 REMARK 3 T TENSOR REMARK 3 T11: 0.5872 T22: 0.6326 REMARK 3 T33: 0.5994 T12: -0.0429 REMARK 3 T13: 0.2200 T23: 0.0502 REMARK 3 L TENSOR REMARK 3 L11: 4.2449 L22: 7.4457 REMARK 3 L33: 5.2309 L12: 3.3017 REMARK 3 L13: 3.7418 L23: 1.9462 REMARK 3 S TENSOR REMARK 3 S11: 0.1687 S12: -0.1652 S13: 0.1665 REMARK 3 S21: 0.3510 S22: -0.3263 S23: -0.3359 REMARK 3 S31: -0.3803 S32: 0.1363 S33: 0.0688 REMARK 3 TLS GROUP : 2 REMARK 3 SELECTION: CHAIN G AND RESID 254:475 REMARK 3 ORIGIN FOR THE GROUP (A): 15.4493 -23.0224 -50.1785 REMARK 3 T TENSOR REMARK 3 T11: 0.4960 T22: 0.4005 REMARK 3 T33: 0.9386 T12: 0.1283 REMARK 3 T13: 0.1112 T23: 0.0818 REMARK 3 L TENSOR REMARK 3 L11: 5.2192 L22: 6.4008 REMARK 3 L33: 5.6542 L12: 2.2981 REMARK 3 L13: 0.7280 L23: -0.3540 REMARK 3 S TENSOR REMARK 3 S11: 0.1987 S12: 0.0439 S13: -0.7768 REMARK 3 S21: 0.0795 S22: -0.3467 S23: -1.5302 REMARK 3 S31: 0.3990 S32: 0.4768 S33: 0.1003 REMARK 3 TLS GROUP : 3 REMARK 3 SELECTION: CHAIN H AND RESID 1:131 REMARK 3 ORIGIN FOR THE GROUP (A): -4.8396 -28.5772 -26.8718 REMARK 3 T TENSOR REMARK 3 T11: 1.9643 T22: 0.8179 REMARK 3 T33: 0.6914 T12: -0.4811 REMARK 3 T13: -0.0440 T23: -0.0618 REMARK 3 L TENSOR REMARK 3 L11: 2.9723 L22: 2.9843 REMARK 3 L33: 3.9872 L12: 0.9170 REMARK 3 L13: -4.8301 L23: -4.1855 REMARK 3 S TENSOR REMARK 3 S11: 0.9620 S12: -0.6053 S13: 0.3164 REMARK 3 S21: 1.4405 S22: -0.8032 S23: 0.0214 REMARK 3 S31: -1.1672 S32: 0.3862 S33: -0.1446 REMARK 3 TLS GROUP : 4 REMARK 3 SELECTION: CHAIN H AND RESID 132:231 REMARK 3 ORIGIN FOR THE GROUP (A): -21.1051 -41.7500 -2.5053 REMARK 3 T TENSOR REMARK 3 T11: 3.7210 T22: 0.7751 REMARK 3 T33: 0.8607 T12: 0.4219 REMARK 3 T13: 0.2624 T23: -0.0313 REMARK 3 L TENSOR REMARK 3 L11: 1.3027 L22: 1.3680 REMARK 3 L33: 2.1724 L12: -0.3817 REMARK 3 L13: -0.9153 L23: 0.8496 REMARK 3 S TENSOR REMARK 3 S11: 0.0984 S12: 0.7195 S13: 0.7008 REMARK 3 S21: 1.3130 S22: 0.0276 S23: 0.2838 REMARK 3 S31: -4.4796 S32: -1.6786 S33: -0.5189 REMARK 3 TLS GROUP : 5 REMARK 3 SELECTION: CHAIN L AND RESID 1:103 REMARK 3 ORIGIN FOR THE GROUP (A): 4.9223 -18.3756 -9.3242 REMARK 3 T TENSOR REMARK 3 T11: 3.5284 T22: 1.8117 REMARK 3 T33: 1.1076 T12: -1.4474 REMARK 3 T13: -0.0870 T23: -0.0355 REMARK 3 L TENSOR REMARK 3 L11: 0.1982 L22: 0.5827 REMARK 3 L33: 0.9496 L12: -0.2700 REMARK 3 L13: 0.4273 L23: -0.4865 REMARK 3 S TENSOR REMARK 3 S11: 0.9532 S12: -0.5885 S13: 0.3902 REMARK 3 S21: 2.2495 S22: -1.1231 S23: 0.0857 REMARK 3 S31: -0.4353 S32: 0.6120 S33: 0.2345 REMARK 3 TLS GROUP : 6 REMARK 3 SELECTION: CHAIN L AND RESID 104:231 REMARK 3 ORIGIN FOR THE GROUP (A): -8.1357 -47.3898 7.5990 REMARK 3 T TENSOR REMARK 3 T11: 3.0644 T22: 1.2064 REMARK 3 T33: 0.4675 T12: -0.7607 REMARK 3 T13: -0.0733 T23: 0.0685 REMARK 3 L TENSOR REMARK 3 L11: 3.9081 L22: 0.8358 REMARK 3 L33: 0.5278 L12: -0.6976 REMARK 3 L13: -0.4855 L23: 0.5557 REMARK 3 S TENSOR REMARK 3 S11: 0.5104 S12: -0.8447 S13: -0.5087 REMARK 3 S21: 0.5315 S22: -0.1900 S23: -0.0814 REMARK 3 S31: -2.2176 S32: 0.7919 S33: -0.1320 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 4JB9 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 28-FEB-13. REMARK 100 THE DEPOSITION ID IS D_1000077828. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 19-OCT-12 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 8.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : APS REMARK 200 BEAMLINE : 22-ID 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 : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : IMAGE PLATE 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 : 29132 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.600 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 92.2 REMARK 200 DATA REDUNDANCY : 4.600 REMARK 200 R MERGE (I) : 0.09300 REMARK 200 R SYM (I) : 0.10000 REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 13.2000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.60 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.64 REMARK 200 COMPLETENESS FOR SHELL (%) : 57.7 REMARK 200 DATA REDUNDANCY IN SHELL : 2.50 REMARK 200 R MERGE FOR SHELL (I) : 0.37500 REMARK 200 R SYM FOR SHELL (I) : 0.41200 REMARK 200 <I/SIGMA(I)> FOR SHELL : NULL REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: SAD REMARK 200 SOFTWARE USED: PHASES REMARK 200 STARTING MODEL: 3SE8 REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 56.60 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.83 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 10% PEG 4000, 0.2M SODIUM ACETATE, REMARK 280 0.1M TRIS-HCL, PH 8.5, VAPOR DIFFUSION, HANGING DROP, REMARK 280 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 32.12200 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 112.11250 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 34.46200 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 112.11250 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 32.12200 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 34.46200 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: 9520 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 36070 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: 15.0 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 318 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 324 REMARK 465 GLU G 405 REMARK 465 THR G 406 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 THR H 135 REMARK 465 ALA H 136 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 241 C2 NAG G 502 1.40 REMARK 500 ND2 ASN G 276 C2 NAG G 504 1.75 REMARK 500 SG CYS G 395 CB CYS G 410 1.90 REMARK 500 O CYS H 196 O HOH H 309 1.97 REMARK 500 O HOH H 307 O HOH H 312 2.03 REMARK 500 ND2 ASN G 392 C2 NAG G 509 2.03 REMARK 500 CB CYS G 378 SG CYS G 445 2.08 REMARK 500 ND2 ASN G 229 O6 NAG G 502 2.15 REMARK 500 N VAL H 198 O HOH H 308 2.18 REMARK 500 O PHE H 45 O HOH H 301 2.18 REMARK 500 O SER H 153 O HOH H 307 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 LYS G 97 79.19 -119.75 REMARK 500 SER G 115 -68.69 -102.11 REMARK 500 LEU G 116 97.44 -61.74 REMARK 500 GLN G 203 -154.59 -108.69 REMARK 500 PRO G 220 -176.22 -68.55 REMARK 500 ASN G 232 42.11 -92.21 REMARK 500 GLN G 258 -47.81 62.97 REMARK 500 GLU G 268 -72.76 -120.54 REMARK 500 SER G 300 56.34 -98.23 REMARK 500 CYS G 410 20.81 -145.25 REMARK 500 ALA G 460 75.56 -102.22 REMARK 500 ASN G 461 75.92 -66.81 REMARK 500 CYS H 22 91.93 -164.28 REMARK 500 PHE H 39 87.60 -68.15 REMARK 500 TYR H 43 -6.11 -143.47 REMARK 500 PRO H 52A 3.74 -67.32 REMARK 500 LEU H 63 13.04 -143.32 REMARK 500 ASP H 76E -7.31 64.43 REMARK 500 THR H 83 -146.57 -128.17 REMARK 500 SER H 97A -58.74 -154.86 REMARK 500 PHE H 100D 29.15 -148.25 REMARK 500 HIS H 100E 77.95 -105.05 REMARK 500 GLN L 6 62.73 -109.83 REMARK 500 PRO L 15 97.84 -53.49 REMARK 500 CYS L 23 63.56 -101.76 REMARK 500 ARG L 24 81.24 -65.41 REMARK 500 SER L 31 -163.91 -101.17 REMARK 500 LEU L 46 -53.77 -121.29 REMARK 500 ASP L 49 70.21 55.12 REMARK 500 THR L 50 -52.53 59.96 REMARK 500 SER L 51 78.90 -158.15 REMARK 500 LYS L 76 87.33 55.76 REMARK 500 ALA L 83 -149.91 -163.11 REMARK 500 PHE L 90 -125.70 56.08 REMARK 500 ARG L 103 96.49 57.25 REMARK 500 THR L 104 133.79 65.40 REMARK 500 VAL L 105 -103.11 -101.33 REMARK 500 ALA L 106 -9.21 -169.24 REMARK 500 ASN L 133 -139.38 57.17 REMARK 500 PHE L 134 0.00 114.25 REMARK 500 TYR L 135 135.37 -39.28 REMARK 500 GLU L 138 97.41 -67.73 REMARK 500 VAL L 158 -99.24 -111.36 REMARK 500 GLU L 160 70.70 -155.24 REMARK 500 TYR L 168 -165.51 -112.35 REMARK 500 LYS L 185 -55.10 -120.88 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 4J6R RELATED DB: PDB DBREF 4JB9 G 44 492 PDB 4JB9 4JB9 44 492 DBREF 4JB9 H 1 214 PDB 4JB9 4JB9 1 214 DBREF 4JB9 L 1 209 PDB 4JB9 4JB9 1 209 SEQRES 1 G 353 VAL TRP LYS ASP ALA ASP THR THR LEU PHE CYS ALA SER SEQRES 2 G 353 ASP ALA LYS ALA HIS GLU THR GLU VAL HIS ASN VAL TRP SEQRES 3 G 353 ALA THR HIS ALA CYS VAL PRO THR ASP PRO ASN PRO GLN SEQRES 4 G 353 GLU ILE HIS LEU GLU ASN VAL THR GLU ASN PHE ASN MET SEQRES 5 G 353 TRP LYS ASN ASN MET VAL GLU GLN MET GLN GLU ASP VAL SEQRES 6 G 353 ILE SER LEU TRP ASP GLN SER LEU GLN PRO CYS VAL LYS SEQRES 7 G 353 LEU THR GLY GLY SER VAL ILE LYS GLN ALA CYS PRO LYS SEQRES 8 G 353 ILE SER PHE ASP PRO ILE PRO ILE HIS TYR CYS THR PRO SEQRES 9 G 353 ALA GLY TYR VAL ILE LEU LYS CYS ASN ASP LYS ASN PHE SEQRES 10 G 353 ASN GLY THR GLY PRO CYS LYS ASN VAL SER SER VAL GLN SEQRES 11 G 353 CYS THR HIS GLY ILE LYS PRO VAL VAL SER THR GLN LEU SEQRES 12 G 353 LEU LEU ASN GLY SER LEU ALA GLU GLU GLU ILE ILE ILE SEQRES 13 G 353 ARG SER GLU ASN LEU THR ASN ASN ALA LYS THR ILE ILE SEQRES 14 G 353 VAL HIS LEU ASN LYS SER VAL GLU ILE ASN CYS THR ARG SEQRES 15 G 353 PRO SER ASN GLY GLY SER GLY SER GLY GLY ASP ILE ARG SEQRES 16 G 353 LYS ALA TYR CYS GLU ILE ASN GLY THR LYS TRP ASN LYS SEQRES 17 G 353 VAL LEU LYS GLN VAL THR GLU LYS LEU LYS GLU HIS PHE SEQRES 18 G 353 ASN ASN LYS THR ILE ILE PHE GLN PRO PRO SER GLY GLY SEQRES 19 G 353 ASP LEU GLU ILE THR MET HIS HIS PHE ASN CYS ARG GLY SEQRES 20 G 353 GLU PHE PHE TYR CYS ASN THR THR GLN LEU PHE ASN ASN SEQRES 21 G 353 THR CYS ILE GLY ASN GLU THR MET LYS GLY CYS ASN GLY SEQRES 22 G 353 THR ILE THR LEU PRO CYS LYS ILE LYS GLN ILE ILE ASN SEQRES 23 G 353 MET TRP GLN GLY THR GLY GLN ALA MET TYR ALA PRO PRO SEQRES 24 G 353 ILE ASP GLY LYS ILE ASN CYS VAL SER ASN ILE THR GLY SEQRES 25 G 353 ILE LEU LEU THR ARG ASP GLY GLY ALA ASN ASN THR SER SEQRES 26 G 353 ASN GLU THR PHE ARG PRO GLY GLY GLY ASN ILE LYS ASP SEQRES 27 G 353 ASN TRP ARG SER GLU LEU TYR LYS TYR LYS VAL VAL GLN SEQRES 28 G 353 ILE GLU SEQRES 1 H 232 GLU VAL GLN LEU VAL GLU SER GLY PRO VAL MET ARG LYS SEQRES 2 H 232 PRO GLY SER SER MET LYS ILE SER CYS ALA THR SER GLY SEQRES 3 H 232 TYR ASN PHE ARG ASP PHE SER ILE HIS TRP VAL ARG PHE SEQRES 4 H 232 ASN ARG ARG TYR GLY PHE GLU TRP ILE GLY TRP ILE LYS SEQRES 5 H 232 PRO MET TRP GLY ALA VAL ASN TYR ALA ARG GLN LEU GLN SEQRES 6 H 232 GLY ARG VAL SER MET SER ARG LEU PHE SER GLN ASP LEU SEQRES 7 H 232 TYR TYR PRO ASP ARG GLY THR ALA TYR LEU GLU PHE SER SEQRES 8 H 232 GLY LEU THR SER ALA ASP THR ALA ASP TYR PHE CYS VAL SEQRES 9 H 232 ARG ARG GLY SER SER CYS PRO HIS CYS GLY ASP PHE HIS SEQRES 10 H 232 PHE GLU HIS TRP GLY GLN GLY THR ALA VAL VAL VAL SER SEQRES 11 H 232 ALA ALA SER THR LYS GLY PRO SER VAL PHE PRO LEU ALA SEQRES 12 H 232 PRO SER SER LYS SER THR SER GLY GLY THR ALA ALA LEU SEQRES 13 H 232 GLY CYS LEU VAL LYS ASP TYR PHE PRO GLU PRO VAL THR SEQRES 14 H 232 VAL SER TRP ASN SER GLY ALA LEU THR SER GLY VAL HIS SEQRES 15 H 232 THR PHE PRO ALA VAL LEU GLN SER SER GLY LEU TYR SER SEQRES 16 H 232 LEU SER SER VAL VAL THR VAL PRO SER SER SER LEU GLY SEQRES 17 H 232 THR GLN THR TYR ILE CYS ASN VAL ASN HIS LYS PRO SER SEQRES 18 H 232 ASN THR LYS VAL ASP LYS LYS VAL GLU PRO LYS SEQRES 1 L 209 GLU ILE VAL LEU THR GLN SER PRO ALA THR LEU SER LEU SEQRES 2 L 209 SER PRO GLY GLU ARG ALA THR LEU SER CYS ARG ALA SER SEQRES 3 L 209 GLN GLY GLY ASN SER LEU ASN TRP TYR GLN LYS ARG ARG SEQRES 4 L 209 GLY GLN THR PRO ARG LEU LEU ILE TYR ASP THR SER ARG SEQRES 5 L 209 ARG ALA SER ASP ILE PRO GLU LYS PHE VAL GLY SER GLY SEQRES 6 L 209 SER GLY THR ASP PHE SER LEU THR ILE THR LYS VAL GLY SEQRES 7 L 209 PRO GLU ASP PHE ALA VAL TYR TYR CYS GLN GLN PHE GLU SEQRES 8 L 209 PHE PHE GLY LEU GLY THR THR LEU GLU ILE ASN ARG THR SEQRES 9 L 209 VAL ALA ALA PRO SER VAL PHE ILE PHE PRO PRO SER ASP SEQRES 10 L 209 GLU GLN LEU LYS SER GLY THR ALA SER VAL VAL CYS LEU SEQRES 11 L 209 LEU ASN ASN PHE TYR PRO ARG GLU ALA LYS VAL GLN TRP SEQRES 12 L 209 LYS VAL ASP ASN ALA LEU GLN SER GLY ASN SER GLN GLU SEQRES 13 L 209 SER VAL THR GLU GLN ASP SER LYS ASP SER THR TYR SER SEQRES 14 L 209 LEU SER SER THR LEU THR LEU SER LYS ALA ASP TYR GLU SEQRES 15 L 209 LYS HIS LYS VAL TYR ALA CYS GLU VAL THR HIS GLN GLY SEQRES 16 L 209 LEU SER SER PRO VAL THR LYS SER PHE ASN ARG GLY GLU SEQRES 17 L 209 CYS MODRES 4JB9 ASN G 241 ASN GLYCOSYLATION SITE MODRES 4JB9 ASN G 234 ASN GLYCOSYLATION SITE MODRES 4JB9 ASN G 295 ASN GLYCOSYLATION SITE MODRES 4JB9 ASN G 334 ASN GLYCOSYLATION SITE MODRES 4JB9 ASN G 392 ASN GLYCOSYLATION SITE MODRES 4JB9 ASN G 289 ASN GLYCOSYLATION SITE MODRES 4JB9 ASN G 448 ASN GLYCOSYLATION SITE MODRES 4JB9 ASN G 386 ASN GLYCOSYLATION SITE MODRES 4JB9 ASN G 262 ASN GLYCOSYLATION SITE MODRES 4JB9 ASN G 276 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 HETNAM NAG 2-ACETAMIDO-2-DEOXY-BETA-D-GLUCOPYRANOSE 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 FORMUL 4 NAG 10(C8 H15 N O6) FORMUL 14 HOH *40(H2 O) HELIX 1 1 GLU G 64 CYS G 74 1 11 HELIX 2 2 ASN G 98 SER G 115 1 18 HELIX 3 3 GLY G 335 GLU G 351 1 17 HELIX 4 4 HIS G 352 ASN G 354 5 3 HELIX 5 5 ASP G 368 MET G 373 1 6 HELIX 6 6 THR G 388 ASN G 392 5 5 HELIX 7 7 ILE G 475 TYR G 484 1 10 HELIX 8 8 ASN H 28 PHE H 32 5 5 HELIX 9 9 ARG H 61 GLN H 64 5 4 HELIX 10 10 SER L 116 LYS L 121 1 6 HELIX 11 11 LYS L 178 HIS L 184 1 7 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 LEU G 86 -1 N ILE G 84 O SER G 244 SHEET 1 B 3 VAL G 75 PRO G 76 0 SHEET 2 B 3 PHE G 53 SER G 56 1 N SER G 56 O VAL G 75 SHEET 3 B 3 ILE G 215 CYS G 218 -1 O HIS G 216 N ALA G 55 SHEET 1 C 2 GLU G 91 ASN G 92 0 SHEET 2 C 2 PRO G 238 CYS G 239 -1 O CYS G 239 N GLU G 91 SHEET 1 D 3 VAL G 120 LYS G 121 0 SHEET 2 D 3 GLY G 431 MET G 434 -1 O MET G 434 N VAL G 120 SHEET 3 D 3 ILE G 423 MET G 426 -1 N MET G 426 O GLY G 431 SHEET 1 E 5 LEU G 259 LEU G 261 0 SHEET 2 E 5 ILE G 443 ASP G 457 -1 O GLY G 451 N LEU G 260 SHEET 3 E 5 ILE G 284 ARG G 298 -1 N ILE G 284 O LEU G 454 SHEET 4 E 5 ASN 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 ASP G 457 -1 O LEU G 454 N ILE G 284 SHEET 4 F 7 LYS G 328 ASN G 334 0 SHEET 5 F 7 THR G 413 LYS G 421 -1 O ILE G 414 N ILE G 333 SHEET 6 F 7 GLU G 381 CYS G 385 -1 N TYR G 384 O LYS G 419 SHEET 7 F 7 HIS G 374 CYS G 378 -1 N HIS G 374 O CYS G 385 SHEET 1 G 4 GLN H 3 GLU H 6 0 SHEET 2 G 4 SER H 17 SER H 25 -1 O ALA H 23 N VAL H 5 SHEET 3 G 4 GLY H 76G SER H 82A-1 O LEU H 80 N ILE H 20 SHEET 4 G 4 VAL H 67 PHE H 73 -1 N SER H 68 O GLU H 81 SHEET 1 H 6 VAL H 10 ARG H 12 0 SHEET 2 H 6 THR H 107 VAL H 111 1 O ALA H 108 N VAL H 10 SHEET 3 H 6 ALA H 88 ARG H 95 -1 N TYR H 90 O THR H 107 SHEET 4 H 6 ILE H 34 ASN H 40 -1 N VAL H 37 O PHE H 91 SHEET 5 H 6 GLY H 44 LYS H 52 -1 O GLY H 49 N TRP H 36 SHEET 6 H 6 ALA H 56 TYR H 59 -1 O ALA H 56 N LYS H 52 SHEET 1 I 4 VAL H 10 ARG H 12 0 SHEET 2 I 4 THR H 107 VAL H 111 1 O ALA H 108 N VAL H 10 SHEET 3 I 4 ALA H 88 ARG H 95 -1 N TYR H 90 O THR H 107 SHEET 4 I 4 PHE H 100F TRP H 103 -1 O HIS H 102 N ARG H 94 SHEET 1 J 4 SER H 120 LEU H 124 0 SHEET 2 J 4 LEU H 138 TYR H 145 -1 O GLY H 139 N LEU H 124 SHEET 3 J 4 TYR H 176 VAL H 182 -1 O SER H 180 N CYS H 140 SHEET 4 J 4 VAL H 163 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 LEU H 138 TYR H 145 -1 O GLY H 139 N LEU H 124 SHEET 3 K 4 TYR H 176 VAL H 182 -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 2 TYR H 194 CYS H 196 0 SHEET 2 L 2 LYS H 209 VAL H 211 -1 O LYS H 209 N CYS H 196 SHEET 1 M 2 ASN H 199 HIS H 200 0 SHEET 2 M 2 THR H 205 LYS H 206 -1 O THR H 205 N HIS H 200 SHEET 1 N 5 THR L 10 LEU L 13 0 SHEET 2 N 5 THR L 97 ILE L 101 1 O GLU L 100 N LEU L 13 SHEET 3 N 5 VAL L 84 GLN L 89 -1 N TYR L 85 O THR L 97 SHEET 4 N 5 ASN L 33 LYS L 37 -1 N LYS L 37 O VAL L 84 SHEET 5 N 5 ARG L 44 ILE L 47 -1 O ARG L 44 N GLN L 36 SHEET 1 O 4 THR L 10 LEU L 13 0 SHEET 2 O 4 THR L 97 ILE L 101 1 O GLU L 100 N LEU L 13 SHEET 3 O 4 VAL L 84 GLN L 89 -1 N TYR L 85 O THR L 97 SHEET 4 O 4 PHE L 92 PHE L 93 -1 O PHE L 92 N GLN L 89 SHEET 1 P 2 PHE L 61 SER L 66 0 SHEET 2 P 2 ASP L 69 ILE L 74 -1 O THR L 73 N VAL L 62 SHEET 1 Q 4 SER L 109 PHE L 113 0 SHEET 2 Q 4 THR L 124 ASN L 132 -1 O LEU L 130 N PHE L 111 SHEET 3 Q 4 SER L 169 SER L 177 -1 O LEU L 176 N ALA L 125 SHEET 4 Q 4 SER L 154 SER L 157 -1 N GLN L 155 O THR L 173 SHEET 1 R 4 ALA L 148 GLN L 150 0 SHEET 2 R 4 LYS L 140 VAL L 145 -1 N TRP L 143 O GLN L 150 SHEET 3 R 4 VAL L 186 THR L 192 -1 O GLU L 190 N GLN L 142 SHEET 4 R 4 VAL L 200 ASN L 205 -1 O VAL L 200 N VAL L 191 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 2.03 SSBOND 5 CYS G 296 CYS G 331 1555 1555 2.03 SSBOND 6 CYS G 378 CYS G 445 1555 1555 2.03 SSBOND 7 CYS G 385 CYS G 418 1555 1555 2.03 SSBOND 8 CYS G 395 CYS G 410 1555 1555 2.03 SSBOND 9 CYS H 22 CYS H 92 1555 1555 2.03 SSBOND 10 CYS H 98 CYS H 100A 1555 1555 2.03 SSBOND 11 CYS H 140 CYS H 196 1555 1555 2.03 SSBOND 12 CYS L 23 CYS L 87 1555 1555 2.04 LINK ND2 ASN G 234 C1 NAG G 501 1555 1555 1.44 LINK ND2 ASN G 241 C1 NAG G 502 1555 1555 1.45 LINK ND2 ASN G 262 C1 NAG G 503 1555 1555 1.45 LINK ND2 ASN G 276 C1 NAG G 504 1555 1555 1.45 LINK ND2 ASN G 289 C1 NAG G 505 1555 1555 1.44 LINK ND2 ASN G 295 C1 NAG G 506 1555 1555 1.44 LINK ND2 ASN G 334 C1 NAG G 507 1555 1555 1.44 LINK ND2 ASN G 386 C1 NAG G 508 1555 1555 1.45 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 CISPEP 1 PHE H 146 PRO H 147 0 -3.76 CISPEP 2 GLU H 148 PRO H 149 0 -0.46 CISPEP 3 SER L 7 PRO L 8 0 -1.20 CISPEP 4 ARG L 103 THR L 104 0 0.63 CISPEP 5 TYR L 135 PRO L 136 0 2.31 CRYST1 64.244 68.924 224.225 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 0.015566 0.000000 0.000000 0.00000 SCALE2 0.000000 0.014509 0.000000 0.00000 SCALE3 0.000000 0.000000 0.004460 0.00000