HEADER VIRAL PROTEIN/INHIBITOR 03-FEB-12 4DKP TITLE CRYSTAL STRUCTURE OF CLADE A/E 93TH057 HIV-1 GP120 CORE IN COMPLEX TITLE 2 WITH AWS-I-50 COMPND MOL_ID: 1; COMPND 2 MOLECULE: CLADE A/E 93TH057 HIV-1 GP120 CORE; COMPND 3 CHAIN: A, C; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HUMAN IMMUNODEFICIENCY VIRUS TYPE 1; SOURCE 3 ORGANISM_COMMON: HIV-1; SOURCE 4 ORGANISM_TAXID: 11686; SOURCE 5 STRAIN: CLADE A/E 93TH057; SOURCE 6 GENE: HIV-1 ENV; SOURCE 7 EXPRESSION_SYSTEM: HOMO SAPIENS; SOURCE 8 EXPRESSION_SYSTEM_COMMON: HUMAN; SOURCE 9 EXPRESSION_SYSTEM_TAXID: 9606; SOURCE 10 EXPRESSION_SYSTEM_CELL_LINE: HEK293F; SOURCE 11 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 12 EXPRESSION_SYSTEM_PLASMID: PVRC8400 KEYWDS HIV-1 GP120, CLADE A/E, CD4 MIMIC, AWS-I-50, VIRAL PROTEIN-INHIBITOR KEYWDS 2 COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR Y.D.KWON,J.M.LALONDE,D.M.JONES,A.W.SUN,J.R.COURTER,T.SOETA, AUTHOR 2 T.KOBAYASHI,A.M.PRINCIOTTO,X.WU,J.MASCOLA,A.SCHON,E.FREIRE, AUTHOR 3 J.SODROSKI,N.MADANI,A.B.SMITH III,P.D.KWONG REVDAT 7 13-SEP-23 4DKP 1 REMARK REVDAT 6 19-MAY-21 4DKP 1 SOURCE HETSYN REVDAT 5 29-JUL-20 4DKP 1 COMPND REMARK HETNAM LINK REVDAT 5 2 1 SITE REVDAT 4 17-JUL-19 4DKP 1 REMARK LINK REVDAT 3 20-JUN-12 4DKP 1 JRNL REVDAT 2 09-MAY-12 4DKP 1 SOURCE REVDAT 1 02-MAY-12 4DKP 0 JRNL AUTH J.M.LALONDE,Y.D.KWON,D.M.JONES,A.W.SUN,J.R.COURTER,T.SOETA, JRNL AUTH 2 T.KOBAYASHI,A.M.PRINCIOTTO,X.WU,A.SCHON,E.FREIRE,P.D.KWONG, JRNL AUTH 3 J.R.MASCOLA,J.SODROSKI,N.MADANI,A.B.SMITH JRNL TITL STRUCTURE-BASED DESIGN, SYNTHESIS, AND CHARACTERIZATION OF JRNL TITL 2 DUAL HOTSPOT SMALL-MOLECULE HIV-1 ENTRY INHIBITORS. JRNL REF J.MED.CHEM. V. 55 4382 2012 JRNL REFN ISSN 0022-2623 JRNL PMID 22497421 JRNL DOI 10.1021/JM300265J REMARK 2 REMARK 2 RESOLUTION. 1.80 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.7.3_928 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) : 1.80 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 33.71 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.340 REMARK 3 COMPLETENESS FOR RANGE (%) : 96.3 REMARK 3 NUMBER OF REFLECTIONS : 74205 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.200 REMARK 3 R VALUE (WORKING SET) : 0.199 REMARK 3 FREE R VALUE : 0.225 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.100 REMARK 3 FREE R VALUE TEST SET COUNT : 3782 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 33.7114 - 5.3865 0.98 2736 159 0.2105 0.2084 REMARK 3 2 5.3865 - 4.2782 0.99 2699 172 0.1664 0.1737 REMARK 3 3 4.2782 - 3.7382 0.99 2725 158 0.1652 0.1964 REMARK 3 4 3.7382 - 3.3967 1.00 2696 146 0.1751 0.1964 REMARK 3 5 3.3967 - 3.1535 1.00 2714 144 0.1871 0.1959 REMARK 3 6 3.1535 - 2.9677 1.00 2736 125 0.1873 0.2207 REMARK 3 7 2.9677 - 2.8191 1.00 2721 131 0.1962 0.2322 REMARK 3 8 2.8191 - 2.6964 1.00 2701 133 0.2039 0.2385 REMARK 3 9 2.6964 - 2.5927 1.00 2728 149 0.2018 0.2438 REMARK 3 10 2.5927 - 2.5032 1.00 2709 150 0.2038 0.2474 REMARK 3 11 2.5032 - 2.4250 1.00 2688 158 0.2147 0.2670 REMARK 3 12 2.4250 - 2.3557 1.00 2704 142 0.2141 0.2857 REMARK 3 13 2.3557 - 2.2937 1.00 2682 140 0.2060 0.2410 REMARK 3 14 2.2937 - 2.2377 1.00 2731 136 0.2040 0.2420 REMARK 3 15 2.2377 - 2.1869 1.00 2739 122 0.2041 0.2607 REMARK 3 16 2.1869 - 2.1404 1.00 2654 133 0.2172 0.2521 REMARK 3 17 2.1404 - 2.0975 1.00 2680 173 0.2058 0.2685 REMARK 3 18 2.0975 - 2.0580 1.00 2695 140 0.2138 0.2592 REMARK 3 19 2.0580 - 2.0212 1.00 2673 159 0.2095 0.2480 REMARK 3 20 2.0212 - 1.9870 1.00 2738 139 0.2240 0.2850 REMARK 3 21 1.9870 - 1.9549 0.99 2618 138 0.2338 0.2978 REMARK 3 22 1.9549 - 1.9248 0.98 2643 173 0.2588 0.2973 REMARK 3 23 1.9248 - 1.8965 0.95 2543 139 0.2660 0.2690 REMARK 3 24 1.8965 - 1.8698 0.91 2465 125 0.2906 0.3041 REMARK 3 25 1.8698 - 1.8446 0.85 2302 119 0.3201 0.3764 REMARK 3 26 1.8446 - 1.8206 0.78 2106 100 0.3586 0.3814 REMARK 3 27 1.8206 - 1.7978 0.60 1597 79 0.3704 0.3197 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 : 0.39 REMARK 3 B_SOL : 45.32 REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.250 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 24.530 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) : 5.19070 REMARK 3 B22 (A**2) : -1.08210 REMARK 3 B33 (A**2) : -4.10860 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : -4.70650 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 : 0.002 5842 REMARK 3 ANGLE : 0.699 7927 REMARK 3 CHIRALITY : 0.085 922 REMARK 3 PLANARITY : 0.003 982 REMARK 3 DIHEDRAL : 13.605 2195 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 4 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: CHAIN A AND (RESID 44:252 OR RESID 474:492) REMARK 3 ORIGIN FOR THE GROUP (A): 18.1654 2.4483 39.4528 REMARK 3 T TENSOR REMARK 3 T11: 0.0925 T22: 0.1244 REMARK 3 T33: 0.1700 T12: 0.0067 REMARK 3 T13: 0.0243 T23: -0.0216 REMARK 3 L TENSOR REMARK 3 L11: 1.7277 L22: 2.2957 REMARK 3 L33: 2.2205 L12: -0.0998 REMARK 3 L13: 0.6526 L23: -0.4202 REMARK 3 S TENSOR REMARK 3 S11: -0.0421 S12: 0.0600 S13: 0.1113 REMARK 3 S21: -0.0331 S22: -0.0293 S23: -0.0253 REMARK 3 S31: -0.1624 S32: -0.1087 S33: 0.0458 REMARK 3 TLS GROUP : 2 REMARK 3 SELECTION: CHAIN A AND RESID 253:473 REMARK 3 ORIGIN FOR THE GROUP (A): 14.7032 -19.7398 40.9047 REMARK 3 T TENSOR REMARK 3 T11: 0.1286 T22: 0.1818 REMARK 3 T33: 0.1664 T12: -0.0083 REMARK 3 T13: 0.0395 T23: -0.0164 REMARK 3 L TENSOR REMARK 3 L11: 1.3864 L22: 1.4449 REMARK 3 L33: 1.6900 L12: -0.1283 REMARK 3 L13: 1.1945 L23: -0.0732 REMARK 3 S TENSOR REMARK 3 S11: 0.0188 S12: -0.0985 S13: -0.0420 REMARK 3 S21: -0.0124 S22: -0.0092 S23: 0.0009 REMARK 3 S31: 0.1953 S32: -0.1822 S33: -0.0263 REMARK 3 TLS GROUP : 3 REMARK 3 SELECTION: CHAIN C AND (RESID 44:252 OR RESID 474:492) REMARK 3 ORIGIN FOR THE GROUP (A): -12.3147 -16.1686 9.3841 REMARK 3 T TENSOR REMARK 3 T11: 0.3233 T22: 0.2265 REMARK 3 T33: 0.2047 T12: 0.0180 REMARK 3 T13: -0.0044 T23: 0.0846 REMARK 3 L TENSOR REMARK 3 L11: 2.9001 L22: 2.5583 REMARK 3 L33: 2.3061 L12: -0.9043 REMARK 3 L13: 0.0204 L23: -0.7017 REMARK 3 S TENSOR REMARK 3 S11: -0.0203 S12: -0.1341 S13: 0.0809 REMARK 3 S21: 0.0604 S22: 0.2575 S23: 0.3208 REMARK 3 S31: -0.2458 S32: -0.4338 S33: -0.1665 REMARK 3 TLS GROUP : 4 REMARK 3 SELECTION: CHAIN C AND RESID 253:473 REMARK 3 ORIGIN FOR THE GROUP (A): -11.3052 -38.3001 12.7953 REMARK 3 T TENSOR REMARK 3 T11: 0.4484 T22: 0.2641 REMARK 3 T33: 0.3544 T12: -0.1314 REMARK 3 T13: -0.0972 T23: 0.1375 REMARK 3 L TENSOR REMARK 3 L11: 1.6379 L22: 2.4852 REMARK 3 L33: 2.3635 L12: -0.7457 REMARK 3 L13: -0.2801 L23: -0.0195 REMARK 3 S TENSOR REMARK 3 S11: 0.0165 S12: -0.1421 S13: -0.5717 REMARK 3 S21: -0.0938 S22: 0.2517 S23: 0.5672 REMARK 3 S31: 0.5248 S32: -0.4632 S33: -0.0744 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 4DKP COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 17-FEB-12. REMARK 100 THE DEPOSITION ID IS D_1000070450. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 01-JAN-11 REMARK 200 TEMPERATURE (KELVIN) : NULL 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-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 : 74276 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.798 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 97.0 REMARK 200 DATA REDUNDANCY : 3.300 REMARK 200 R MERGE (I) : 0.04900 REMARK 200 R SYM (I) : 0.06300 REMARK 200 FOR THE DATA SET : 17.4400 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.80 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.83 REMARK 200 COMPLETENESS FOR SHELL (%) : 72.9 REMARK 200 DATA REDUNDANCY IN SHELL : 1.90 REMARK 200 R MERGE FOR SHELL (I) : 0.50900 REMARK 200 R SYM FOR SHELL (I) : 0.59800 REMARK 200 FOR SHELL : 1.180 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHASES REMARK 200 STARTING MODEL: 3TGT REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 54.06 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.68 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 10% PEG 8000, 5% ISO-PROPANOL, 0.1M REMARK 280 HEPES 7.5 , VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 293K, PH REMARK 280 7.5 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 34.24150 REMARK 290 SMTRY3 2 0.000000 0.000000 -1.000000 0.00000 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1, 2 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: MONOMERIC 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: 2 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: MONOMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 APPLY THE FOLLOWING TO CHAINS: C 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 A 318 REMARK 465 GLY A 319 REMARK 465 SER A 320 REMARK 465 GLY A 321 REMARK 465 SER A 322 REMARK 465 GLY A 323 REMARK 465 GLY A 403 REMARK 465 ASN A 404 REMARK 465 GLU A 405 REMARK 465 THR A 406 REMARK 465 MET A 407 REMARK 465 LYS A 408 REMARK 465 GLY A 409 REMARK 465 CYS A 410 REMARK 465 GLY C 318 REMARK 465 GLY C 319 REMARK 465 SER C 320 REMARK 465 GLY C 321 REMARK 465 SER C 322 REMARK 465 GLY C 323 REMARK 465 GLY C 403 REMARK 465 ASN C 404 REMARK 465 GLU C 405 REMARK 465 THR C 406 REMARK 465 MET C 407 REMARK 465 LYS C 408 REMARK 465 GLY C 409 REMARK 465 CYS C 410 REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS IN SAME ASYMMETRIC UNIT REMARK 500 REMARK 500 THE FOLLOWING ATOMS ARE IN CLOSE CONTACT. REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI DISTANCE REMARK 500 O GLY A 471 O HOH A 659 1.94 REMARK 500 O HOH A 673 O HOH A 771 1.97 REMARK 500 O HOH C 725 O HOH C 749 2.01 REMARK 500 OE1 GLN A 246 O HOH A 681 2.05 REMARK 500 ND2 ASN A 448 C2 NAG A 511 2.07 REMARK 500 ND2 ASN A 461 O HOH A 889 2.07 REMARK 500 ND2 ASN A 355 C2 NAG A 508 2.09 REMARK 500 O HOH A 784 O HOH A 896 2.11 REMARK 500 O LYS A 240 O HOH A 766 2.11 REMARK 500 O HOH A 872 O HOH A 891 2.12 REMARK 500 OE1 GLN A 344 O HOH A 682 2.12 REMARK 500 O6 NAG A 508 O HOH A 874 2.14 REMARK 500 ND2 ASN C 289 C2 NAG C 505 2.15 REMARK 500 O HOH A 781 O HOH A 842 2.15 REMARK 500 OE1 GLN A 432 O HOH A 886 2.15 REMARK 500 NZ LYS A 350 O HOH A 622 2.17 REMARK 500 O HOH A 770 O HOH A 847 2.17 REMARK 500 ND2 ASN A 241 C2 NAG A 502 2.18 REMARK 500 O HOH C 710 O HOH C 744 2.18 REMARK 500 ND2 ASN A 289 C2 NAG A 505 2.18 REMARK 500 OD1 ASP C 477 O HOH C 780 2.19 REMARK 500 ND2 ASN C 448 C2 NAG C 511 2.19 REMARK 500 O PHE A 391 O HOH A 698 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 LEU A 122 75.86 -116.61 REMARK 500 ASP A 211 105.88 -167.56 REMARK 500 GLN A 258 -58.16 65.33 REMARK 500 GLU A 268 -97.01 -110.37 REMARK 500 ASN A 276 97.89 -165.46 REMARK 500 PHE A 391 77.58 -100.07 REMARK 500 ASP C 211 108.13 -162.58 REMARK 500 GLN C 258 -58.91 64.48 REMARK 500 GLU C 268 -101.63 -120.79 REMARK 500 ASN C 276 93.49 -163.44 REMARK 500 PHE C 391 58.32 -115.64 REMARK 500 ASN C 474 91.47 -65.22 REMARK 500 REMARK 500 REMARK: NULL REMARK 610 REMARK 610 MISSING HETEROATOM REMARK 610 THE FOLLOWING RESIDUES HAVE MISSING ATOMS (M=MODEL NUMBER; REMARK 610 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 610 I=INSERTION CODE): REMARK 610 M RES C SSEQI REMARK 610 EPE C 512 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 4DKO RELATED DB: PDB REMARK 900 RELATED ID: 4DKQ RELATED DB: PDB REMARK 900 RELATED ID: 4DKR RELATED DB: PDB DBREF 4DKP A 44 492 PDB 4DKP 4DKP 44 492 DBREF 4DKP C 44 492 PDB 4DKP 4DKP 44 492 SEQRES 1 A 353 VAL TRP LYS ASP ALA ASP THR THR LEU PHE CYS ALA SER SEQRES 2 A 353 ASP ALA LYS ALA HIS GLU THR GLU VAL HIS ASN VAL TRP SEQRES 3 A 353 ALA THR HIS ALA CYS VAL PRO THR ASP PRO ASN PRO GLN SEQRES 4 A 353 GLU ILE HIS LEU GLU ASN VAL THR GLU ASN PHE ASN MET SEQRES 5 A 353 TRP LYS ASN ASN MET VAL GLU GLN MET GLN GLU ASP VAL SEQRES 6 A 353 ILE SER LEU TRP ASP GLN SER LEU GLN PRO CYS VAL LYS SEQRES 7 A 353 LEU THR GLY GLY SER VAL ILE LYS GLN ALA CYS PRO LYS SEQRES 8 A 353 ILE SER PHE ASP PRO ILE PRO ILE HIS TYR CYS THR PRO SEQRES 9 A 353 ALA GLY TYR VAL ILE LEU LYS CYS ASN ASP LYS ASN PHE SEQRES 10 A 353 ASN GLY THR GLY PRO CYS LYS ASN VAL SER SER VAL GLN SEQRES 11 A 353 CYS THR HIS GLY ILE LYS PRO VAL VAL SER THR GLN LEU SEQRES 12 A 353 LEU LEU ASN GLY SER LEU ALA GLU GLU GLU ILE ILE ILE SEQRES 13 A 353 ARG SER GLU ASN LEU THR ASN ASN ALA LYS THR ILE ILE SEQRES 14 A 353 VAL HIS LEU ASN LYS SER VAL GLU ILE ASN CYS THR ARG SEQRES 15 A 353 PRO SER ASN GLY GLY SER GLY SER GLY GLY ASP ILE ARG SEQRES 16 A 353 LYS ALA TYR CYS GLU ILE ASN GLY THR LYS TRP ASN LYS SEQRES 17 A 353 VAL LEU LYS GLN VAL THR GLU LYS LEU LYS GLU HIS PHE SEQRES 18 A 353 ASN ASN LYS THR ILE ILE PHE GLN PRO PRO SER GLY GLY SEQRES 19 A 353 ASP LEU GLU ILE THR MET HIS SER PHE ASN CYS ARG GLY SEQRES 20 A 353 GLU PHE PHE TYR CYS ASN THR THR GLN LEU PHE ASN ASN SEQRES 21 A 353 THR CYS ILE GLY ASN GLU THR MET LYS GLY CYS ASN GLY SEQRES 22 A 353 THR ILE THR LEU PRO CYS LYS ILE LYS GLN ILE ILE ASN SEQRES 23 A 353 MET TRP GLN GLY THR GLY GLN ALA MET TYR ALA PRO PRO SEQRES 24 A 353 ILE ASP GLY LYS ILE ASN CYS VAL SER ASN ILE THR GLY SEQRES 25 A 353 ILE LEU LEU THR ARG ASP GLY GLY ALA ASN ASN THR SER SEQRES 26 A 353 ASN GLU THR PHE ARG PRO GLY GLY GLY ASN ILE LYS ASP SEQRES 27 A 353 ASN TRP ARG SER GLU LEU TYR LYS TYR LYS VAL VAL GLN SEQRES 28 A 353 ILE GLU SEQRES 1 C 353 VAL TRP LYS ASP ALA ASP THR THR LEU PHE CYS ALA SER SEQRES 2 C 353 ASP ALA LYS ALA HIS GLU THR GLU VAL HIS ASN VAL TRP SEQRES 3 C 353 ALA THR HIS ALA CYS VAL PRO THR ASP PRO ASN PRO GLN SEQRES 4 C 353 GLU ILE HIS LEU GLU ASN VAL THR GLU ASN PHE ASN MET SEQRES 5 C 353 TRP LYS ASN ASN MET VAL GLU GLN MET GLN GLU ASP VAL SEQRES 6 C 353 ILE SER LEU TRP ASP GLN SER LEU GLN PRO CYS VAL LYS SEQRES 7 C 353 LEU THR GLY GLY SER VAL ILE LYS GLN ALA CYS PRO LYS SEQRES 8 C 353 ILE SER PHE ASP PRO ILE PRO ILE HIS TYR CYS THR PRO SEQRES 9 C 353 ALA GLY TYR VAL ILE LEU LYS CYS ASN ASP LYS ASN PHE SEQRES 10 C 353 ASN GLY THR GLY PRO CYS LYS ASN VAL SER SER VAL GLN SEQRES 11 C 353 CYS THR HIS GLY ILE LYS PRO VAL VAL SER THR GLN LEU SEQRES 12 C 353 LEU LEU ASN GLY SER LEU ALA GLU GLU GLU ILE ILE ILE SEQRES 13 C 353 ARG SER GLU ASN LEU THR ASN ASN ALA LYS THR ILE ILE SEQRES 14 C 353 VAL HIS LEU ASN LYS SER VAL GLU ILE ASN CYS THR ARG SEQRES 15 C 353 PRO SER ASN GLY GLY SER GLY SER GLY GLY ASP ILE ARG SEQRES 16 C 353 LYS ALA TYR CYS GLU ILE ASN GLY THR LYS TRP ASN LYS SEQRES 17 C 353 VAL LEU LYS GLN VAL THR GLU LYS LEU LYS GLU HIS PHE SEQRES 18 C 353 ASN ASN LYS THR ILE ILE PHE GLN PRO PRO SER GLY GLY SEQRES 19 C 353 ASP LEU GLU ILE THR MET HIS SER PHE ASN CYS ARG GLY SEQRES 20 C 353 GLU PHE PHE TYR CYS ASN THR THR GLN LEU PHE ASN ASN SEQRES 21 C 353 THR CYS ILE GLY ASN GLU THR MET LYS GLY CYS ASN GLY SEQRES 22 C 353 THR ILE THR LEU PRO CYS LYS ILE LYS GLN ILE ILE ASN SEQRES 23 C 353 MET TRP GLN GLY THR GLY GLN ALA MET TYR ALA PRO PRO SEQRES 24 C 353 ILE ASP GLY LYS ILE ASN CYS VAL SER ASN ILE THR GLY SEQRES 25 C 353 ILE LEU LEU THR ARG ASP GLY GLY ALA ASN ASN THR SER SEQRES 26 C 353 ASN GLU THR PHE ARG PRO GLY GLY GLY ASN ILE LYS ASP SEQRES 27 C 353 ASN TRP ARG SER GLU LEU TYR LYS TYR LYS VAL VAL GLN SEQRES 28 C 353 ILE GLU MODRES 4DKP ASN A 355 ASN GLYCOSYLATION SITE MODRES 4DKP ASN C 295 ASN GLYCOSYLATION SITE MODRES 4DKP ASN A 392 ASN GLYCOSYLATION SITE MODRES 4DKP ASN A 234 ASN GLYCOSYLATION SITE MODRES 4DKP ASN C 448 ASN GLYCOSYLATION SITE MODRES 4DKP ASN C 355 ASN GLYCOSYLATION SITE MODRES 4DKP ASN A 448 ASN GLYCOSYLATION SITE MODRES 4DKP ASN A 386 ASN GLYCOSYLATION SITE MODRES 4DKP ASN C 392 ASN GLYCOSYLATION SITE MODRES 4DKP ASN C 386 ASN GLYCOSYLATION SITE MODRES 4DKP ASN A 295 ASN GLYCOSYLATION SITE MODRES 4DKP ASN A 241 ASN GLYCOSYLATION SITE MODRES 4DKP ASN C 234 ASN GLYCOSYLATION SITE MODRES 4DKP ASN A 276 ASN GLYCOSYLATION SITE MODRES 4DKP ASN C 276 ASN GLYCOSYLATION SITE MODRES 4DKP ASN C 262 ASN GLYCOSYLATION SITE MODRES 4DKP ASN C 334 ASN GLYCOSYLATION SITE MODRES 4DKP ASN A 289 ASN GLYCOSYLATION SITE MODRES 4DKP ASN C 289 ASN GLYCOSYLATION SITE MODRES 4DKP ASN A 334 ASN GLYCOSYLATION SITE MODRES 4DKP ASN A 262 ASN GLYCOSYLATION SITE MODRES 4DKP ASN C 241 ASN GLYCOSYLATION SITE HET NAG A 501 14 HET NAG A 502 14 HET NAG A 503 14 HET NAG A 504 14 HET NAG A 505 14 HET NAG A 506 14 HET NAG A 507 14 HET NAG A 508 14 HET NAG A 509 14 HET NAG A 510 14 HET NAG A 511 14 HET EPE A 512 15 HET 0LL A 513 24 HET NAG C 501 14 HET NAG C 502 14 HET NAG C 503 14 HET NAG C 504 14 HET NAG C 505 14 HET NAG C 506 14 HET NAG C 507 14 HET NAG C 508 14 HET NAG C 509 14 HET NAG C 510 14 HET NAG C 511 14 HET EPE C 512 13 HET 0LL C 513 24 HETNAM NAG 2-ACETAMIDO-2-DEOXY-BETA-D-GLUCOPYRANOSE HETNAM EPE 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID HETNAM 0LL N-[(1S,2S)-2-AMINO-2,3-DIHYDRO-1H-INDEN-1-YL]-N'-(4- HETNAM 2 0LL CHLORO-3-FLUOROPHENYL)ETHANEDIAMIDE 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 FORMUL 3 NAG 22(C8 H15 N O6) FORMUL 14 EPE 2(C8 H18 N2 O4 S) FORMUL 15 0LL 2(C17 H15 CL F N3 O2) FORMUL 29 HOH *479(H2 O) HELIX 1 1 GLU A 64 ALA A 73 1 10 HELIX 2 2 ASN A 98 LEU A 116 1 19 HELIX 3 3 GLY A 335 PHE A 353 1 19 HELIX 4 4 ASP A 368 MET A 373 1 6 HELIX 5 5 ILE A 475 TYR A 484 1 10 HELIX 6 6 GLU C 64 ALA C 73 1 10 HELIX 7 7 ASN C 98 LEU C 116 1 19 HELIX 8 8 GLY C 335 PHE C 353 1 19 HELIX 9 9 ASP C 368 MET C 373 1 6 HELIX 10 10 THR C 387 ASN C 392 5 6 HELIX 11 11 ILE C 475 TYR C 484 1 10 SHEET 1 A 5 TRP A 45 ASP A 47 0 SHEET 2 A 5 TYR A 486 ILE A 491 -1 O GLN A 490 N LYS A 46 SHEET 3 A 5 TYR A 223 CYS A 228 -1 N LEU A 226 O LYS A 487 SHEET 4 A 5 VAL A 242 VAL A 245 -1 O SER A 243 N LYS A 227 SHEET 5 A 5 GLU A 83 HIS A 85 -1 N ILE A 84 O SER A 244 SHEET 1 B 3 CYS A 74 PRO A 76 0 SHEET 2 B 3 PHE A 53 SER A 56 1 N CYS A 54 O VAL A 75 SHEET 3 B 3 HIS A 216 CYS A 218 -1 O HIS A 216 N ALA A 55 SHEET 1 C 2 GLU A 91 ASN A 94 0 SHEET 2 C 2 THR A 236 CYS A 239 -1 O GLY A 237 N PHE A 93 SHEET 1 D 4 SER A 199 LYS A 202 0 SHEET 2 D 4 VAL A 120 THR A 123 -1 N LYS A 121 O ILE A 201 SHEET 3 D 4 GLN A 432 MET A 434 -1 O GLN A 432 N LEU A 122 SHEET 4 D 4 ILE A 423 ASN A 425 -1 N ILE A 424 O ALA A 433 SHEET 1 E 5 LEU A 259 LEU A 261 0 SHEET 2 E 5 ILE A 443 ARG A 456 -1 O THR A 450 N LEU A 260 SHEET 3 E 5 ILE A 284 ARG A 298 -1 N VAL A 286 O ILE A 452 SHEET 4 E 5 ASN A 465 PRO A 470 0 SHEET 5 E 5 THR A 358 PHE A 361 1 N ILE A 360 O PHE A 468 SHEET 1 F 7 ILE A 271 ARG A 273 0 SHEET 2 F 7 ILE A 284 ARG A 298 -1 O HIS A 287 N ILE A 271 SHEET 3 F 7 ILE A 443 ARG A 456 -1 O ILE A 452 N VAL A 286 SHEET 4 F 7 LYS A 328 ASN A 334 0 SHEET 5 F 7 THR A 413 ILE A 420 -1 O ILE A 414 N ILE A 333 SHEET 6 F 7 GLU A 381 CYS A 385 -1 N TYR A 384 O LYS A 419 SHEET 7 F 7 HIS A 374 CYS A 378 -1 N CYS A 378 O GLU A 381 SHEET 1 G 5 TRP C 45 ASP C 47 0 SHEET 2 G 5 TYR C 486 ILE C 491 -1 O GLN C 490 N LYS C 46 SHEET 3 G 5 TYR C 223 CYS C 228 -1 N LEU C 226 O LYS C 487 SHEET 4 G 5 VAL C 242 VAL C 245 -1 O SER C 243 N LYS C 227 SHEET 5 G 5 ILE C 84 HIS C 85 -1 N ILE C 84 O SER C 244 SHEET 1 H 3 CYS C 74 PRO C 76 0 SHEET 2 H 3 PHE C 53 SER C 56 1 N SER C 56 O VAL C 75 SHEET 3 H 3 HIS C 216 CYS C 218 -1 O HIS C 216 N ALA C 55 SHEET 1 I 2 GLU C 91 ASN C 94 0 SHEET 2 I 2 THR C 236 CYS C 239 -1 O GLY C 237 N PHE C 93 SHEET 1 J 4 SER C 199 LYS C 202 0 SHEET 2 J 4 VAL C 120 THR C 123 -1 N LYS C 121 O ILE C 201 SHEET 3 J 4 GLY C 431 MET C 434 -1 O GLN C 432 N LEU C 122 SHEET 4 J 4 ILE C 423 ASN C 425 -1 N ILE C 424 O ALA C 433 SHEET 1 K 5 LEU C 259 LEU C 261 0 SHEET 2 K 5 ILE C 443 ARG C 456 -1 O GLY C 451 N LEU C 260 SHEET 3 K 5 ILE C 284 ARG C 298 -1 N ARG C 298 O ILE C 443 SHEET 4 K 5 ASN C 465 PRO C 470 0 SHEET 5 K 5 THR C 358 PHE C 361 1 N ILE C 360 O PHE C 468 SHEET 1 L 7 ILE C 271 ARG C 273 0 SHEET 2 L 7 ILE C 284 ARG C 298 -1 O ILE C 285 N ARG C 273 SHEET 3 L 7 ILE C 443 ARG C 456 -1 O ILE C 443 N ARG C 298 SHEET 4 L 7 LYS C 328 ASN C 334 0 SHEET 5 L 7 THR C 413 ILE C 420 -1 O ILE C 414 N ILE C 333 SHEET 6 L 7 GLU C 381 CYS C 385 -1 N TYR C 384 O LYS C 419 SHEET 7 L 7 HIS C 374 CYS C 378 -1 N HIS C 374 O CYS C 385 SSBOND 1 CYS A 54 CYS A 74 1555 1555 2.03 SSBOND 2 CYS A 119 CYS A 205 1555 1555 2.03 SSBOND 3 CYS A 218 CYS A 247 1555 1555 2.04 SSBOND 4 CYS A 228 CYS A 239 1555 1555 2.04 SSBOND 5 CYS A 296 CYS A 331 1555 1555 2.03 SSBOND 6 CYS A 378 CYS A 445 1555 1555 2.03 SSBOND 7 CYS A 385 CYS A 418 1555 1555 2.03 SSBOND 8 CYS C 54 CYS C 74 1555 1555 2.03 SSBOND 9 CYS C 119 CYS C 205 1555 1555 2.03 SSBOND 10 CYS C 218 CYS C 247 1555 1555 2.03 SSBOND 11 CYS C 228 CYS C 239 1555 1555 2.03 SSBOND 12 CYS C 296 CYS C 331 1555 1555 2.03 SSBOND 13 CYS C 378 CYS C 445 1555 1555 2.03 SSBOND 14 CYS C 385 CYS C 418 1555 1555 2.03 LINK ND2 ASN A 234 C1 NAG A 501 1555 1555 1.44 LINK ND2 ASN A 241 C1 NAG A 502 1555 1555 1.44 LINK ND2 ASN A 262 C1 NAG A 503 1555 1555 1.44 LINK ND2 ASN A 276 C1 NAG A 504 1555 1555 1.44 LINK ND2 ASN A 289 C1 NAG A 505 1555 1555 1.44 LINK ND2 ASN A 295 C1 NAG A 506 1555 1555 1.44 LINK ND2 ASN A 334 C1 NAG A 507 1555 1555 1.44 LINK ND2 ASN A 355 C1 NAG A 508 1555 1555 1.44 LINK ND2 ASN A 386 C1 NAG A 509 1555 1555 1.44 LINK ND2 ASN A 392 C1 NAG A 510 1555 1555 1.44 LINK ND2 ASN A 448 C1 NAG A 511 1555 1555 1.44 LINK ND2 ASN C 234 C1 NAG C 501 1555 1555 1.44 LINK ND2 ASN C 241 C1 NAG C 502 1555 1555 1.45 LINK ND2 ASN C 262 C1 NAG C 503 1555 1555 1.44 LINK ND2 ASN C 276 C1 NAG C 504 1555 1555 1.44 LINK ND2 ASN C 289 C1 NAG C 505 1555 1555 1.44 LINK ND2 ASN C 295 C1 NAG C 506 1555 1555 1.44 LINK ND2 ASN C 334 C1 NAG C 507 1555 1555 1.44 LINK ND2 ASN C 355 C1 NAG C 508 1555 1555 1.44 LINK ND2 ASN C 386 C1 NAG C 509 1555 1555 1.44 LINK ND2 ASN C 392 C1 NAG C 510 1555 1555 1.44 LINK ND2 ASN C 448 C1 NAG C 511 1555 1555 1.44 CRYST1 64.666 68.483 94.747 90.00 91.60 90.00 P 1 21 1 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 0.015464 0.000000 0.000432 0.00000 SCALE2 0.000000 0.014602 0.000000 0.00000 SCALE3 0.000000 0.000000 0.010559 0.00000