HEADER VIRAL PROTEIN/INHIBITOR 03-FEB-12 4DKO TITLE CRYSTAL STRUCTURE OF CLADE A/E 93TH057 HIV-1 GP120 CORE IN COMPLEX TITLE 2 WITH TS-II-224 COMPND MOL_ID: 1; COMPND 2 MOLECULE: 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, TS-II-224, 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 6 13-SEP-23 4DKO 1 REMARK REVDAT 5 19-MAY-21 4DKO 1 SOURCE HETSYN REVDAT 4 29-JUL-20 4DKO 1 COMPND REMARK HETNAM LINK REVDAT 4 2 1 SITE REVDAT 3 20-JUN-12 4DKO 1 JRNL REVDAT 2 09-MAY-12 4DKO 1 SOURCE REVDAT 1 02-MAY-12 4DKO 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. 1.98 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) : 1.98 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 41.94 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.340 REMARK 3 COMPLETENESS FOR RANGE (%) : 93.1 REMARK 3 NUMBER OF REFLECTIONS : 53979 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.205 REMARK 3 R VALUE (WORKING SET) : 0.204 REMARK 3 FREE R VALUE : 0.239 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.990 REMARK 3 FREE R VALUE TEST SET COUNT : 2692 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 41.9507 - 5.2818 0.95 2869 137 0.2227 0.2474 REMARK 3 2 5.2818 - 4.1936 0.97 2838 171 0.1602 0.1798 REMARK 3 3 4.1936 - 3.6638 0.98 2875 124 0.1719 0.1980 REMARK 3 4 3.6638 - 3.3290 0.99 2864 166 0.1874 0.2375 REMARK 3 5 3.3290 - 3.0905 0.99 2885 152 0.1976 0.2189 REMARK 3 6 3.0905 - 2.9083 0.99 2902 151 0.1965 0.2617 REMARK 3 7 2.9083 - 2.7627 1.00 2859 146 0.2117 0.2804 REMARK 3 8 2.7627 - 2.6424 0.99 2900 145 0.2133 0.2462 REMARK 3 9 2.6424 - 2.5407 1.00 2868 152 0.2110 0.2532 REMARK 3 10 2.5407 - 2.4531 1.00 2872 156 0.2230 0.2423 REMARK 3 11 2.4531 - 2.3764 0.99 2873 156 0.2363 0.3038 REMARK 3 12 2.3764 - 2.3085 0.97 2748 173 0.2265 0.2563 REMARK 3 13 2.3085 - 2.2477 0.94 2682 172 0.2263 0.2657 REMARK 3 14 2.2477 - 2.1928 0.92 2636 154 0.2202 0.2632 REMARK 3 15 2.1928 - 2.1430 0.89 2541 123 0.2421 0.2832 REMARK 3 16 2.1430 - 2.0974 0.88 2568 130 0.2495 0.3118 REMARK 3 17 2.0974 - 2.0554 0.85 2453 129 0.2665 0.3048 REMARK 3 18 2.0554 - 2.0167 0.80 2310 95 0.2676 0.3131 REMARK 3 19 2.0167 - 1.9806 0.59 1744 60 0.3099 0.3287 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : FLAT BULK SOLVENT MODEL REMARK 3 SOLVENT RADIUS : 1.20 REMARK 3 SHRINKAGE RADIUS : 0.98 REMARK 3 K_SOL : 0.35 REMARK 3 B_SOL : 33.66 REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.280 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 25.800 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 30.30 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 43.17 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 9.10640 REMARK 3 B22 (A**2) : -3.93880 REMARK 3 B33 (A**2) : -5.16750 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : -4.04780 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 5844 REMARK 3 ANGLE : 0.663 7938 REMARK 3 CHIRALITY : 0.042 922 REMARK 3 PLANARITY : 0.003 980 REMARK 3 DIHEDRAL : 16.168 2224 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): 18.5832 2.3451 39.4091 REMARK 3 T TENSOR REMARK 3 T11: 0.0859 T22: 0.1342 REMARK 3 T33: 0.2001 T12: 0.0025 REMARK 3 T13: 0.0168 T23: -0.0255 REMARK 3 L TENSOR REMARK 3 L11: 1.6394 L22: 2.1795 REMARK 3 L33: 2.2754 L12: -0.3053 REMARK 3 L13: 0.6477 L23: -0.6201 REMARK 3 S TENSOR REMARK 3 S11: -0.0549 S12: 0.0906 S13: 0.1046 REMARK 3 S21: 0.0162 S22: -0.0196 S23: -0.0320 REMARK 3 S31: -0.1577 S32: -0.0644 S33: 0.0569 REMARK 3 TLS GROUP : 2 REMARK 3 SELECTION: ( CHAIN A AND RESID 253:473 ) REMARK 3 ORIGIN FOR THE GROUP (A): 15.0151 -19.7985 40.7922 REMARK 3 T TENSOR REMARK 3 T11: 0.0927 T22: 0.1778 REMARK 3 T33: 0.1670 T12: -0.0019 REMARK 3 T13: 0.0480 T23: -0.0091 REMARK 3 L TENSOR REMARK 3 L11: 1.0526 L22: 1.3118 REMARK 3 L33: 1.9613 L12: -0.1134 REMARK 3 L13: 1.3362 L23: 0.0984 REMARK 3 S TENSOR REMARK 3 S11: 0.0378 S12: -0.0438 S13: -0.0441 REMARK 3 S21: -0.0064 S22: -0.0305 S23: -0.0021 REMARK 3 S31: 0.1828 S32: -0.1193 S33: -0.0202 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): -12.1769 -16.3564 9.2780 REMARK 3 T TENSOR REMARK 3 T11: 0.3132 T22: 0.2337 REMARK 3 T33: 0.2005 T12: -0.0016 REMARK 3 T13: 0.0035 T23: 0.0805 REMARK 3 L TENSOR REMARK 3 L11: 2.8745 L22: 2.1834 REMARK 3 L33: 2.5415 L12: -0.7995 REMARK 3 L13: -0.1731 L23: -0.6636 REMARK 3 S TENSOR REMARK 3 S11: 0.0092 S12: -0.0461 S13: 0.1269 REMARK 3 S21: 0.0003 S22: 0.2119 S23: 0.3085 REMARK 3 S31: -0.1159 S32: -0.5116 S33: -0.1750 REMARK 3 TLS GROUP : 4 REMARK 3 SELECTION: ( CHAIN C AND RESID 253:473 ) REMARK 3 ORIGIN FOR THE GROUP (A): -11.0631 -38.4498 12.6980 REMARK 3 T TENSOR REMARK 3 T11: 0.5087 T22: 0.2807 REMARK 3 T33: 0.3129 T12: -0.1814 REMARK 3 T13: -0.1190 T23: 0.1315 REMARK 3 L TENSOR REMARK 3 L11: 1.4503 L22: 1.7159 REMARK 3 L33: 1.6954 L12: -0.4432 REMARK 3 L13: -0.4117 L23: -0.0841 REMARK 3 S TENSOR REMARK 3 S11: 0.0983 S12: 0.0041 S13: -0.5521 REMARK 3 S21: -0.2470 S22: 0.2108 S23: 0.4610 REMARK 3 S31: 0.7260 S32: -0.4413 S33: -0.0070 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 4DKO 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_1000070449. 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) : 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-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 : 54086 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.981 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 (%) : 94.1 REMARK 200 DATA REDUNDANCY : 3.100 REMARK 200 R MERGE (I) : 0.07800 REMARK 200 R SYM (I) : 0.09900 REMARK 200 FOR THE DATA SET : 11.5000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.00 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.03 REMARK 200 COMPLETENESS FOR SHELL (%) : 74.0 REMARK 200 DATA REDUNDANCY IN SHELL : 1.90 REMARK 200 R MERGE FOR SHELL (I) : 0.48000 REMARK 200 R SYM FOR SHELL (I) : 0.49300 REMARK 200 FOR SHELL : 1.540 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 (%): 54.28 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.69 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 34.45100 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 HOH A 798 O HOH A 816 1.81 REMARK 500 O PHE A 391 O HOH A 672 1.85 REMARK 500 O GLY A 471 O HOH A 698 1.96 REMARK 500 O HOH C 741 O HOH C 744 1.97 REMARK 500 O HOH C 728 O HOH C 730 2.03 REMARK 500 NZ LYS C 59 O HOH C 739 2.04 REMARK 500 O HOH A 815 O HOH A 825 2.04 REMARK 500 O HOH A 799 O HOH A 804 2.04 REMARK 500 O GLN C 490 O HOH C 726 2.08 REMARK 500 ND2 ASN A 289 C2 NAG A 505 2.11 REMARK 500 O HOH C 638 O HOH C 688 2.11 REMARK 500 O ILE A 396 O HOH A 829 2.12 REMARK 500 O HOH C 679 O HOH C 714 2.12 REMARK 500 ND2 ASN C 392 C2 NAG C 510 2.12 REMARK 500 O HOH C 677 O HOH C 740 2.12 REMARK 500 O HOH A 776 O HOH A 833 2.13 REMARK 500 O HOH A 684 O HOH A 764 2.14 REMARK 500 ND2 ASN A 355 C2 NAG A 508 2.14 REMARK 500 ND2 ASN A 448 C2 NAG A 511 2.14 REMARK 500 N GLY C 124 O HOH C 748 2.15 REMARK 500 OE1 GLU A 106 O HOH A 607 2.18 REMARK 500 O HOH A 800 O HOH A 822 2.18 REMARK 500 OE1 GLU C 106 O HOH C 648 2.19 REMARK 500 O HOH C 680 O HOH C 684 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 A 211 106.41 -165.39 REMARK 500 GLN A 258 -56.96 66.47 REMARK 500 GLU A 268 -100.81 -115.72 REMARK 500 ASN A 276 96.47 -163.81 REMARK 500 PRO A 299 160.59 -46.85 REMARK 500 SER A 300 -83.64 -76.06 REMARK 500 PHE A 391 66.81 -106.40 REMARK 500 GLN C 258 -60.09 62.71 REMARK 500 GLU C 268 -98.07 -109.69 REMARK 500 ASN C 276 99.67 -162.23 REMARK 500 SER C 300 -73.34 -63.01 REMARK 500 PHE C 391 62.12 -111.05 REMARK 500 ASN C 474 89.20 -68.05 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 4DKP RELATED DB: PDB REMARK 900 RELATED ID: 4DKQ RELATED DB: PDB REMARK 900 RELATED ID: 4DKR RELATED DB: PDB DBREF 4DKO A 44 492 PDB 4DKO 4DKO 44 492 DBREF 4DKO C 44 492 PDB 4DKO 4DKO 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 4DKO ASN A 241 ASN GLYCOSYLATION SITE MODRES 4DKO ASN A 448 ASN GLYCOSYLATION SITE MODRES 4DKO ASN C 241 ASN GLYCOSYLATION SITE MODRES 4DKO ASN A 234 ASN GLYCOSYLATION SITE MODRES 4DKO ASN C 295 ASN GLYCOSYLATION SITE MODRES 4DKO ASN C 386 ASN GLYCOSYLATION SITE MODRES 4DKO ASN A 355 ASN GLYCOSYLATION SITE MODRES 4DKO ASN A 386 ASN GLYCOSYLATION SITE MODRES 4DKO ASN C 448 ASN GLYCOSYLATION SITE MODRES 4DKO ASN C 276 ASN GLYCOSYLATION SITE MODRES 4DKO ASN C 392 ASN GLYCOSYLATION SITE MODRES 4DKO ASN A 392 ASN GLYCOSYLATION SITE MODRES 4DKO ASN A 262 ASN GLYCOSYLATION SITE MODRES 4DKO ASN C 355 ASN GLYCOSYLATION SITE MODRES 4DKO ASN A 276 ASN GLYCOSYLATION SITE MODRES 4DKO ASN A 295 ASN GLYCOSYLATION SITE MODRES 4DKO ASN A 289 ASN GLYCOSYLATION SITE MODRES 4DKO ASN C 234 ASN GLYCOSYLATION SITE MODRES 4DKO ASN C 334 ASN GLYCOSYLATION SITE MODRES 4DKO ASN A 334 ASN GLYCOSYLATION SITE MODRES 4DKO ASN C 262 ASN GLYCOSYLATION SITE MODRES 4DKO ASN C 289 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 0LM A 513 25 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 15 HET 0LM C 513 25 HETNAM NAG 2-ACETAMIDO-2-DEOXY-BETA-D-GLUCOPYRANOSE HETNAM EPE 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID HETNAM 0LM N-(4-CHLORO-3-FLUOROPHENYL)-N'-(1,2,2,6,6- HETNAM 2 0LM PENTAMETHYLPIPERIDIN-4-YL)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 0LM 2(C18 H25 CL F N3 O2) FORMUL 29 HOH *394(H2 O) HELIX 1 1 GLU A 64 CYS A 74 1 11 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 GLU C 351 1 17 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 VAL A 75 PRO A 76 0 SHEET 2 B 3 PHE A 53 SER A 56 1 N SER A 56 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 GLY A 451 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 LEU A 416 N CYS A 331 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 GLU C 466 PRO C 470 0 SHEET 5 K 5 ILE C 359 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 CYS C 378 O GLU C 381 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 1.44 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 64.723 68.902 94.515 90.00 91.23 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 0.015450 0.000000 0.000332 0.00000 SCALE2 0.000000 0.014513 0.000000 0.00000 SCALE3 0.000000 0.000000 0.010583 0.00000