HEADER VIRAL PROTEIN/INHIBITOR 03-APR-13 4JZZ TITLE CRYSTAL STRUCTURE OF CD4-MIMETIC MINIPROTEIN M48U1 IN COMPLEX WITH TITLE 2 HIV-1 YU2 GP120 IN C2221 SPACE GROUP COMPND MOL_ID: 1; COMPND 2 MOLECULE: HIV-1 YU2 GP120 GLYCOPROTEIN; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES; COMPND 5 MOL_ID: 2; COMPND 6 MOLECULE: CD4-MIMETIC MINIPROTEIN M48U1; COMPND 7 CHAIN: R; COMPND 8 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HUMAN IMMUNODEFICIENCY VIRUS 1; SOURCE 3 ORGANISM_TAXID: 11676; SOURCE 4 STRAIN: YU2; SOURCE 5 GENE: GP120; SOURCE 6 EXPRESSION_SYSTEM: HOMO SAPIENS; SOURCE 7 EXPRESSION_SYSTEM_COMMON: HUMAN; SOURCE 8 EXPRESSION_SYSTEM_TAXID: 9606; SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PVRC8400; SOURCE 11 MOL_ID: 2; SOURCE 12 SYNTHETIC: YES; SOURCE 13 OTHER_DETAILS: DERIVED FROM SCYLLATOXIN (A SCORPION TOXIN) BY SOURCE 14 TRANSPLANTING THE GP120-INTERACTIVDERIVED FROM SCYLLATOXIN (A SOURCE 15 SCORPION TOXIN) BY TRANSPLANTING THE GP120-INTERACTIVE REGION OF CD4 SOURCE 16 ONTO THE SCYLLATOXIN SCAFFOLD,E REGION OF CD4 ONTO THE SCYLLATOXIN SOURCE 17 SCAFFOLD, KEYWDS HIV-1 ATTACHMENT PROTEIN GP120, HIV-1 ENVELOPE, VIRAL PROTEIN- KEYWDS 2 INHIBITOR COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR P.ACHARYA,P.D.KWONG REVDAT 3 29-JUL-20 4JZZ 1 CAVEAT COMPND REMARK HETNAM REVDAT 3 2 1 LINK SITE REVDAT 2 10-JUL-13 4JZZ 1 JRNL REVDAT 1 12-JUN-13 4JZZ 0 JRNL AUTH P.ACHARYA,T.S.LUONGO,M.K.LOUDER,K.MCKEE,Y.YANG,Y.DO KWON, JRNL AUTH 2 J.R.MASCOLA,P.KESSLER,L.MARTIN,P.D.KWONG JRNL TITL STRUCTURAL BASIS FOR HIGHLY EFFECTIVE HIV-1 NEUTRALIZATION JRNL TITL 2 BY CD4-MIMETIC MINIPROTEINS REVEALED BY 1.5 A COCRYSTAL JRNL TITL 3 STRUCTURE OF GP120 AND M48U1. JRNL REF STRUCTURE V. 21 1018 2013 JRNL REFN ISSN 0969-2126 JRNL PMID 23707685 JRNL DOI 10.1016/J.STR.2013.04.015 REMARK 2 REMARK 2 RESOLUTION. 1.49 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (PHENIX.REFINE: 1.8.2_1309) 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) : 1.49 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 35.26 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.330 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.1 REMARK 3 NUMBER OF REFLECTIONS : 67985 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.168 REMARK 3 R VALUE (WORKING SET) : 0.167 REMARK 3 FREE R VALUE : 0.189 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.070 REMARK 3 FREE R VALUE TEST SET COUNT : 3446 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 35.2691 - 4.3577 0.99 2735 160 0.1695 0.2010 REMARK 3 2 4.3577 - 3.4598 1.00 2653 163 0.1441 0.1710 REMARK 3 3 3.4598 - 3.0227 1.00 2661 131 0.1604 0.1650 REMARK 3 4 3.0227 - 2.7465 1.00 2641 128 0.1650 0.1817 REMARK 3 5 2.7465 - 2.5497 1.00 2618 151 0.1694 0.2005 REMARK 3 6 2.5497 - 2.3994 1.00 2621 126 0.1662 0.2021 REMARK 3 7 2.3994 - 2.2793 1.00 2608 141 0.1596 0.1539 REMARK 3 8 2.2793 - 2.1800 1.00 2603 138 0.1588 0.1853 REMARK 3 9 2.1800 - 2.0961 1.00 2607 140 0.1600 0.1726 REMARK 3 10 2.0961 - 2.0238 1.00 2590 133 0.1576 0.1940 REMARK 3 11 2.0238 - 1.9605 1.00 2609 117 0.1634 0.1801 REMARK 3 12 1.9605 - 1.9045 1.00 2606 135 0.1744 0.1976 REMARK 3 13 1.9045 - 1.8544 1.00 2570 148 0.1758 0.2128 REMARK 3 14 1.8544 - 1.8091 1.00 2582 132 0.1727 0.1986 REMARK 3 15 1.8091 - 1.7680 1.00 2573 150 0.1722 0.2113 REMARK 3 16 1.7680 - 1.7304 1.00 2584 139 0.1857 0.2106 REMARK 3 17 1.7304 - 1.6958 1.00 2564 134 0.1903 0.1987 REMARK 3 18 1.6958 - 1.6638 0.99 2542 142 0.1902 0.2037 REMARK 3 19 1.6638 - 1.6340 1.00 2589 149 0.1945 0.2323 REMARK 3 20 1.6340 - 1.6064 0.99 2568 131 0.1970 0.2314 REMARK 3 21 1.6064 - 1.5804 0.99 2542 132 0.2040 0.2226 REMARK 3 22 1.5804 - 1.5561 0.99 2536 126 0.2225 0.2598 REMARK 3 23 1.5561 - 1.5332 0.98 2512 136 0.2350 0.2390 REMARK 3 24 1.5332 - 1.5116 0.97 2517 127 0.2466 0.2555 REMARK 3 25 1.5116 - 1.4912 0.90 2308 137 0.2693 0.2524 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) : 0.140 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 19.060 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 21.55 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 21.55 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 : 0.006 3234 REMARK 3 ANGLE : 1.191 4403 REMARK 3 CHIRALITY : 0.064 508 REMARK 3 PLANARITY : 0.005 552 REMARK 3 DIHEDRAL : 13.243 1247 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 2 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: CHAIN A REMARK 3 ORIGIN FOR THE GROUP (A): -23.9526 23.7048 0.9540 REMARK 3 T TENSOR REMARK 3 T11: 0.1337 T22: 0.1255 REMARK 3 T33: 0.0992 T12: 0.0137 REMARK 3 T13: 0.0238 T23: 0.0169 REMARK 3 L TENSOR REMARK 3 L11: 1.1596 L22: 1.2786 REMARK 3 L33: 1.3126 L12: 0.0713 REMARK 3 L13: 0.0447 L23: 0.3669 REMARK 3 S TENSOR REMARK 3 S11: -0.0736 S12: -0.0346 S13: -0.1268 REMARK 3 S21: 0.0373 S22: 0.0449 S23: -0.0100 REMARK 3 S31: 0.0689 S32: 0.0867 S33: 0.0256 REMARK 3 TLS GROUP : 2 REMARK 3 SELECTION: CHAIN R REMARK 3 ORIGIN FOR THE GROUP (A): -11.0387 31.8623 -14.6824 REMARK 3 T TENSOR REMARK 3 T11: 0.4322 T22: 0.6146 REMARK 3 T33: 0.2444 T12: -0.1332 REMARK 3 T13: 0.1060 T23: -0.0113 REMARK 3 L TENSOR REMARK 3 L11: 5.9126 L22: 1.6070 REMARK 3 L33: 2.7942 L12: -0.6204 REMARK 3 L13: -4.0487 L23: 0.2425 REMARK 3 S TENSOR REMARK 3 S11: -0.1221 S12: 0.6934 S13: 0.1011 REMARK 3 S21: -0.7975 S22: 0.1159 S23: -0.4732 REMARK 3 S31: -0.1806 S32: 1.0156 S33: 0.0075 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 4JZZ COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 11-APR-13. REMARK 100 THE DEPOSITION ID IS D_1000078717. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 19-JUN-10 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 5.6 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) : 1.0000 REMARK 200 MONOCHROMATOR : SI(111) 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 : 68096 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.490 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 (%) : 93.0 REMARK 200 DATA REDUNDANCY : 7.600 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : 0.11700 REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 20.5000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.49 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.52 REMARK 200 COMPLETENESS FOR SHELL (%) : 93.0 REMARK 200 DATA REDUNDANCY IN SHELL : 3.50 REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : 0.58500 REMARK 200 <I/SIGMA(I)> 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: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 47.36 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.34 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 9.0% PEG 4000, 14.0% ISOPROPANOL, 100 REMARK 280 MM SODIUM CITRATE, PH 5.6, VAPOR DIFFUSION, TEMPERATURE 298K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: C 2 2 21 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,-Y,Z+1/2 REMARK 290 3555 -X,Y,-Z+1/2 REMARK 290 4555 X,-Y,-Z REMARK 290 5555 X+1/2,Y+1/2,Z REMARK 290 6555 -X+1/2,-Y+1/2,Z+1/2 REMARK 290 7555 -X+1/2,Y+1/2,-Z+1/2 REMARK 290 8555 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 0.00000 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 39.01550 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 39.01550 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 5 1.000000 0.000000 0.000000 32.54350 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 82.35950 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 6 -1.000000 0.000000 0.000000 32.54350 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 82.35950 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 39.01550 REMARK 290 SMTRY1 7 -1.000000 0.000000 0.000000 32.54350 REMARK 290 SMTRY2 7 0.000000 1.000000 0.000000 82.35950 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 39.01550 REMARK 290 SMTRY1 8 1.000000 0.000000 0.000000 32.54350 REMARK 290 SMTRY2 8 0.000000 -1.000000 0.000000 82.35950 REMARK 290 SMTRY3 8 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: DIMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, R 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 375 REMARK 375 SPECIAL POSITION REMARK 375 THE FOLLOWING ATOMS ARE FOUND TO BE WITHIN 0.15 ANGSTROMS REMARK 375 OF A SYMMETRY RELATED ATOM AND ARE ASSUMED TO BE ON SPECIAL REMARK 375 POSITIONS. REMARK 375 REMARK 375 ATOM RES CSSEQI REMARK 375 HOH A 874 LIES ON A SPECIAL POSITION. REMARK 400 REMARK 400 COMPOUND REMARK 400 THE CD4-MIMETIC MINIPROTEINS INHIBIT HIV-1 ENTRY AND ARE DERIVED REMARK 400 FROM SCYLLATOXIN (A SCORPION TOXIN) BY TRANSPLANTING THE GP120- REMARK 400 INTERACTIVE REGION OF CD4 ONTO THE SCYLLATOXIN SCAFFOLD, FOLLOWED REMARK 400 BY MANY ROUNDS OF ITERATIVE OPTIMIZATION REMARK 400 REMARK 400 THE CD4-MIMETIC MINIPROTEIN M48U1 IS PEPTIDE-LIKE, A MEMBER OF REMARK 400 INHIBITOR CLASS. REMARK 400 REMARK 400 GROUP: 1 REMARK 400 NAME: CD4-MIMETIC MINIPROTEIN M48U1 REMARK 400 CHAIN: R REMARK 400 COMPONENT_1: PEPTIDE LIKE POLYMER REMARK 400 DESCRIPTION: NULL 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 MET A 20 REMARK 465 PRO A 21 REMARK 465 MET A 22 REMARK 465 GLY A 23 REMARK 465 SER A 24 REMARK 465 LEU A 25 REMARK 465 GLN A 26 REMARK 465 PRO A 27 REMARK 465 LEU A 28 REMARK 465 ALA A 29 REMARK 465 THR A 30 REMARK 465 LEU A 31 REMARK 465 TYR A 32 REMARK 465 LEU A 33 REMARK 465 LEU A 34 REMARK 465 GLY A 35 REMARK 465 MET A 36 REMARK 465 LEU A 37 REMARK 465 VAL A 38 REMARK 465 ALA A 39 REMARK 465 SER A 40 REMARK 465 VAL A 41 REMARK 465 LEU A 42 REMARK 465 ALA A 43 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 324 REMARK 465 ARG A 405 REMARK 465 LYS A 406 REMARK 465 LEU A 407 REMARK 465 ASN A 408 REMARK 465 ASN A 409 REMARK 465 THR A 410 REMARK 465 LYS A 460 REMARK 465 ASP A 461 REMARK 465 THR A 462 REMARK 470 REMARK 470 MISSING ATOM REMARK 470 THE FOLLOWING RESIDUES HAVE MISSING ATOMS (M=MODEL NUMBER; REMARK 470 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 470 I=INSERTION CODE): REMARK 470 M RES CSSEQI ATOMS REMARK 470 THR A 396 CB OG1 CG2 REMARK 470 ASN A 463 CG OD1 ND2 REMARK 480 REMARK 480 ZERO OCCUPANCY ATOM REMARK 480 THE FOLLOWING RESIDUES HAVE ATOMS MODELED WITH ZERO REMARK 480 OCCUPANCY. THE LOCATION AND PROPERTIES OF THESE ATOMS REMARK 480 MAY NOT BE RELIABLE. (M=MODEL NUMBER; RES=RESIDUE NAME; REMARK 480 C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 480 M RES C SSEQI ATOMS REMARK 480 LYS A 59 CA CB CG CD CE NZ 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 946 O HOH A 959 1.84 REMARK 500 OE1 GLU A 102 O HOH A 916 1.85 REMARK 500 O HOH A 882 O HOH A 946 1.87 REMARK 500 O2 IPA A 519 O HOH A 952 1.95 REMARK 500 O HOH A 901 O HOH A 952 1.98 REMARK 500 O HOH A 924 O HOH A 931 1.99 REMARK 500 O HOH A 900 O HOH A 935 2.01 REMARK 500 O HOH A 842 O HOH A 896 2.02 REMARK 500 O HOH A 897 O HOH A 899 2.03 REMARK 500 OE1 GLN R 7 O HOH R 109 2.05 REMARK 500 O VAL R 27 O HOH R 116 2.06 REMARK 500 OE1 GLU A 429 O HOH A 910 2.09 REMARK 500 NZ LYS R 11 O HOH R 113 2.12 REMARK 500 NZ LYS A 85 O HOH A 915 2.14 REMARK 500 O HOH A 921 O HOH A 922 2.16 REMARK 500 O HOH A 794 O HOH A 819 2.18 REMARK 500 ND2 ASN A 234 C2 NAG A 502 2.19 REMARK 500 OD1 ASP A 325 O HOH A 919 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 GLN A 258 -59.33 71.27 REMARK 500 GLU A 268 -97.65 -110.39 REMARK 500 ASN A 276 98.95 -167.16 REMARK 500 REMARK 500 REMARK: NULL REMARK 620 REMARK 620 METAL COORDINATION REMARK 620 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 620 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 NA A 516 NA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 PRO A 253 O REMARK 620 2 HOH A 604 O 78.8 REMARK 620 N 1 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 NA A 514 NA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 SER A 256 OG REMARK 620 2 HOH A 852 O 115.8 REMARK 620 N 1 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 NA A 509 NA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 VAL A 372 O REMARK 620 2 HOH A 713 O 94.4 REMARK 620 N 1 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 NA A 517 NA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASN A 377 O REMARK 620 2 NAG A 504 O7 102.5 REMARK 620 3 HOH A 604 O 117.3 139.6 REMARK 620 4 HOH A 621 O 71.3 112.9 76.1 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 NA A 515 NA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HOH A 713 O REMARK 620 2 HOH A 784 O 98.4 REMARK 620 N 1 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 4JZW RELATED DB: PDB REMARK 900 'CRYSTAL STRUCTURE OF CD4-MIMETIC MINIPROTEIN M48U1 IN COMPLEX WITH REMARK 900 HIV-1 YU2 GP120 IN P212121 SPACE GROUP REMARK 900 RELATED ID: 4K0A RELATED DB: PDB DBREF 4JZZ A 20 492 PDB 4JZZ 4JZZ 20 492 DBREF 4JZZ R 1 28 PDB 4JZZ 4JZZ 1 28 SEQRES 1 A 376 MET PRO MET GLY SER LEU GLN PRO LEU ALA THR LEU TYR SEQRES 2 A 376 LEU LEU GLY MET LEU VAL ALA SER VAL LEU ALA VAL TRP SEQRES 3 A 376 LYS GLU ALA THR THR THR LEU PHE CYS ALA SER ASP ALA SEQRES 4 A 376 LYS ALA TYR ASP THR GLU VAL HIS ASN VAL TRP ALA THR SEQRES 5 A 376 HIS ALA CYS VAL PRO THR ASP PRO ASN PRO GLN GLU VAL SEQRES 6 A 376 LYS LEU GLU ASN VAL THR GLU ASN PHE ASN MET TRP LYS SEQRES 7 A 376 ASN ASN MET VAL GLU GLN MET HIS GLU ASP ILE ILE SER SEQRES 8 A 376 LEU TRP ASP GLN SER LEU LYS PRO CYS VAL LYS LEU THR SEQRES 9 A 376 GLY GLY SER VAL ILE THR GLN ALA CYS PRO LYS VAL SER SEQRES 10 A 376 PHE GLU PRO ILE PRO ILE HIS TYR CYS ALA PRO ALA GLY SEQRES 11 A 376 PHE ALA ILE LEU LYS CYS ASN ASP LYS LYS PHE ASN GLY SEQRES 12 A 376 THR GLY PRO CYS THR ASN VAL SER THR VAL GLN CYS THR SEQRES 13 A 376 HIS GLY ILE ARG PRO VAL VAL SER THR GLN LEU LEU LEU SEQRES 14 A 376 ASN GLY SER LEU ALA GLU GLU GLU ILE VAL ILE ARG SER SEQRES 15 A 376 GLU ASN PHE THR ASN ASN ALA LYS THR ILE ILE VAL GLN SEQRES 16 A 376 LEU ASN GLU SER VAL VAL ILE ASN CYS THR ARG PRO ASN SEQRES 17 A 376 ASN GLY GLY SER GLY SER GLY GLY ASP ILE ARG GLN ALA SEQRES 18 A 376 HIS CYS ASN LEU SER LYS THR GLN TRP GLU ASN THR LEU SEQRES 19 A 376 GLU GLN ILE ALA ILE LYS LEU LYS GLU GLN PHE GLY ASN SEQRES 20 A 376 ASN LYS THR ILE ILE PHE ASN PRO SER SER GLY GLY ASP SEQRES 21 A 376 PRO GLU ILE VAL THR HIS SER PHE ASN CYS GLY GLY GLU SEQRES 22 A 376 PHE PHE TYR CYS ASN SER THR GLN LEU PHE THR TRP ASN SEQRES 23 A 376 ASP THR ARG LYS LEU ASN ASN THR GLY ARG ASN ILE THR SEQRES 24 A 376 LEU PRO CYS ARG ILE LYS GLN ILE ILE ASN MET TRP GLN SEQRES 25 A 376 GLU VAL GLY LYS ALA MET TYR ALA PRO PRO ILE ARG GLY SEQRES 26 A 376 GLN ILE ARG CYS SER SER ASN ILE THR GLY LEU LEU LEU SEQRES 27 A 376 THR ARG ASP GLY GLY LYS ASP THR ASN GLY THR GLU ILE SEQRES 28 A 376 PHE ARG PRO GLY GLY GLY ASP MET ARG ASP ASN TRP ARG SEQRES 29 A 376 SER GLU LEU TYR LYS TYR LYS VAL VAL LYS ILE GLU SEQRES 1 R 28 MPT ASN LEU HIS PHE CYS GLN LEU ARG CYS LYS SER LEU SEQRES 2 R 28 GLY LEU LEU GLY ARG CYS ALA DPR THR U2X CYS ALA CYS SEQRES 3 R 28 VAL NH2 MODRES 4JZZ ASN A 262 ASN GLYCOSYLATION SITE MODRES 4JZZ ASN A 386 ASN GLYCOSYLATION SITE MODRES 4JZZ ASN A 295 ASN GLYCOSYLATION SITE MODRES 4JZZ ASN A 234 ASN GLYCOSYLATION SITE MODRES 4JZZ ASN A 448 ASN GLYCOSYLATION SITE MODRES 4JZZ ASN A 276 ASN GLYCOSYLATION SITE MODRES 4JZZ ASN A 289 ASN GLYCOSYLATION SITE MODRES 4JZZ ASN A 241 ASN GLYCOSYLATION SITE MODRES 4JZZ U2X R 23 TYR O-(CYCLOHEXYLMETHYL)-L-TYROSINE HET MPT R 1 5 HET DPR R 21 7 HET U2X R 23 35 HET NH2 R 28 1 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 28 HET NAG A 508 14 HET NA A 509 1 HET IPA A 510 4 HET IPA A 511 4 HET IPA A 512 4 HET IPA A 513 4 HET NA A 514 1 HET NA A 515 1 HET NA A 516 1 HET NA A 517 1 HET NA A 518 1 HET IPA A 519 4 HET FLC A 520 13 HETNAM MPT BETA-MERCAPTOPROPIONIC ACID HETNAM DPR D-PROLINE HETNAM U2X O-(CYCLOHEXYLMETHYL)-L-TYROSINE HETNAM NH2 AMINO GROUP HETNAM NAG 2-ACETAMIDO-2-DEOXY-BETA-D-GLUCOPYRANOSE HETNAM NA SODIUM ION HETNAM IPA ISOPROPYL ALCOHOL HETNAM FLC CITRATE ANION HETSYN IPA 2-PROPANOL FORMUL 2 MPT C3 H6 O2 S FORMUL 2 DPR C5 H9 N O2 FORMUL 2 U2X C16 H23 N O3 FORMUL 2 NH2 H2 N FORMUL 3 NAG 8(C8 H15 N O6) FORMUL 11 NA 6(NA 1+) FORMUL 12 IPA 5(C3 H8 O) FORMUL 22 FLC C6 H5 O7 3- FORMUL 23 HOH *377(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 LYS A 335 GLY A 354 1 20 HELIX 4 4 ASP A 368 THR A 373 1 6 HELIX 5 5 SER A 387 PHE A 391 5 5 HELIX 6 6 ASP A 474 TYR A 484 1 11 HELIX 7 7 ASN R 2 LYS R 11 1 10 HELIX 8 8 SER R 12 GLY R 14 5 3 SHEET 1 A 5 LYS A 46 GLU A 47 0 SHEET 2 A 5 TYR A 486 LYS A 490 -1 O LYS A 490 N LYS A 46 SHEET 3 A 5 PHE 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 LYS A 85 -1 N VAL A 84 O THR 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 CYS A 218 N PHE A 53 SHEET 1 C 2 GLU A 91 ASN A 94 0 SHEET 2 C 2 THR A 236 CYS A 239 -1 O CYS A 239 N GLU A 91 SHEET 1 D 4 SER A 199 THR 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 LYS A 432 MET A 434 -1 O LYS 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 CYS A 296 O CYS A 445 SHEET 4 E 5 THR 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 VAL A 271 ARG A 273 0 SHEET 2 F 7 ILE A 284 ARG A 298 -1 O GLN A 287 N VAL A 271 SHEET 3 F 7 ILE A 443 ARG A 456 -1 O CYS A 445 N CYS A 296 SHEET 4 F 7 GLN A 328 SER A 334 0 SHEET 5 F 7 ASN A 413 LYS A 421 -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 ARG A 419 SHEET 7 F 7 HIS A 374 CYS A 378 -1 N HIS A 374 O CYS A 385 SHEET 1 G 2 GLY R 17 ALA R 20 0 SHEET 2 G 2 U2X R 23 CYS R 26 -1 O U2X R 23 N ALA R 20 SSBOND 1 CYS A 54 CYS A 74 1555 1555 2.06 SSBOND 2 CYS A 119 CYS A 205 1555 1555 2.04 SSBOND 3 CYS A 218 CYS A 247 1555 1555 2.05 SSBOND 4 CYS A 228 CYS A 239 1555 1555 2.05 SSBOND 5 CYS A 296 CYS A 331 1555 1555 2.05 SSBOND 6 CYS A 378 CYS A 445 1555 1555 2.05 SSBOND 7 CYS A 385 CYS A 418 1555 1555 2.04 SSBOND 8 MPT R 1 CYS R 19 1555 1555 2.11 SSBOND 9 CYS R 6 CYS R 24 1555 1555 2.06 SSBOND 10 CYS R 10 CYS R 26 1555 1555 2.04 LINK ND2 ASN A 234 C1 NAG A 502 1555 1555 1.44 LINK ND2 ASN A 241 C1 NAG A 503 1555 1555 1.45 LINK ND2 ASN A 262 C1 NAG A 504 1555 1555 1.44 LINK ND2 ASN A 276 C1 NAG A 501 1555 1555 1.45 LINK ND2 ASN A 289 C1 NAG A 505 1555 1555 1.45 LINK ND2 ASN A 295 C1 NAG A 506 1555 1555 1.44 LINK ND2 ASN A 386 C1 BNAG A 507 1555 1555 1.44 LINK ND2 ASN A 386 C1 ANAG A 507 1555 1555 1.44 LINK ND2 ASN A 448 C1 NAG A 508 1555 1555 1.44 LINK C MPT R 1 N ASN R 2 1555 1555 1.38 LINK SG MPT R 1 SG CYS R 19 1555 1555 2.11 LINK C ALA R 20 N DPR R 21 1555 1555 1.32 LINK C DPR R 21 N THR R 22 1555 1555 1.32 LINK C THR R 22 N U2X R 23 1555 1555 1.34 LINK C U2X R 23 N CYS R 24 1555 1555 1.31 LINK C VAL R 27 N NH2 R 28 1555 1555 1.43 LINK O PRO A 253 NA NA A 516 1555 1555 2.72 LINK OG SER A 256 NA NA A 514 1555 1555 2.75 LINK O VAL A 372 NA NA A 509 1555 1555 2.80 LINK O ASN A 377 NA NA A 517 1555 1555 2.93 LINK O7 NAG A 504 NA NA A 517 1555 1555 2.83 LINK NA NA A 509 O HOH A 713 1555 1555 2.83 LINK NA NA A 514 O HOH A 852 1555 1555 2.74 LINK NA NA A 515 O HOH A 713 1555 1555 2.60 LINK NA NA A 515 O HOH A 784 1555 1555 2.81 LINK NA NA A 516 O HOH A 604 1555 1555 2.87 LINK NA NA A 517 O HOH A 604 1555 1555 2.82 LINK NA NA A 517 O HOH A 621 1555 1555 2.81 LINK NA NA A 518 O HOH A 875 1555 1555 2.21 CRYST1 65.087 164.719 78.031 90.00 90.00 90.00 C 2 2 21 8 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 0.015364 0.000000 0.000000 0.00000 SCALE2 0.000000 0.006071 0.000000 0.00000 SCALE3 0.000000 0.000000 0.012815 0.00000