HEADER VIRAL PROTEIN/INHIBITOR 21-APR-13 4KA2 TITLE CRYSTAL STRUCTURE OF CD4-MIMETIC MINIPROTEIN M48U12 IN COMPLEX WITH TITLE 2 HIV-1 YU2 GP120 COMPND MOL_ID: 1; COMPND 2 MOLECULE: HIV-1 YU2 GP120; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES; COMPND 5 MOL_ID: 2; COMPND 6 MOLECULE: M48U12; 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_TAXID: 9606; SOURCE 8 MOL_ID: 2; SOURCE 9 SYNTHETIC: YES; SOURCE 10 OTHER_DETAILS: DERIVED FROM SCYLLATOXIN (A SCORPION TOXIN) BY SOURCE 11 TRANSPLANTING THE GP120-INTERACTIVDERIVED FROM SCYLLATOXIN (A SOURCE 12 SCORPION TOXIN) BY TRANSPLANTING THE GP120-INTERACTIVE REGION OF CD4 SOURCE 13 ONTO THE SCYLLATOXIN SCAFFOLD,E REGION OF CD4 ONTO THE SCYLLATOXIN SOURCE 14 SCAFFOLD, KEYWDS VIRAL PROTEIN-PEPTIDE COMPLEX, HIV-1, GP120, YU2, CD4 MIMIC, M48U12, KEYWDS 2 VIRAL PROTEIN-INHIBITOR COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR P.ACHARYA,P.D.KWONG REVDAT 4 15-NOV-23 4KA2 1 HETSYN LINK ATOM REVDAT 3 29-JUL-20 4KA2 1 COMPND REMARK HETNAM LINK REVDAT 3 2 1 SITE REVDAT 2 10-JUL-13 4KA2 1 JRNL REVDAT 1 19-JUN-13 4KA2 0 JRNL AUTH L.MORELLATO-CASTILLO,P.ACHARYA,O.COMBES,J.MICHIELS, JRNL AUTH 2 A.DESCOURS,O.H.RAMOS,Y.YANG,G.VANHAM,K.K.ARIEN,P.D.KWONG, JRNL AUTH 3 L.MARTIN,P.KESSLER JRNL TITL INTERFACIAL CAVITY FILLING TO OPTIMIZE CD4-MIMETIC JRNL TITL 2 MINIPROTEIN INTERACTIONS WITH HIV-1 SURFACE GLYCOPROTEIN. JRNL REF J.MED.CHEM. V. 56 5033 2013 JRNL REFN ISSN 0022-2623 JRNL PMID 23710622 JRNL DOI 10.1021/JM4002988 REMARK 2 REMARK 2 RESOLUTION. 1.79 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) : 1.79 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 17.48 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.340 REMARK 3 COMPLETENESS FOR RANGE (%) : 81.7 REMARK 3 NUMBER OF REFLECTIONS : NULL REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.170 REMARK 3 R VALUE (WORKING SET) : 0.167 REMARK 3 FREE R VALUE : 0.228 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 6.260 REMARK 3 FREE R VALUE TEST SET COUNT : 1998 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 17.4843 - 4.2987 1.00 2775 185 0.1454 0.1904 REMARK 3 2 4.2987 - 3.4204 1.00 2654 177 0.1415 0.2104 REMARK 3 3 3.4204 - 2.9905 1.00 2652 177 0.1595 0.2069 REMARK 3 4 2.9905 - 2.7182 1.00 2621 174 0.1778 0.2600 REMARK 3 5 2.7182 - 2.5240 1.00 2596 172 0.1813 0.2518 REMARK 3 6 2.5240 - 2.3755 0.99 2582 173 0.1777 0.2356 REMARK 3 7 2.3755 - 2.2568 0.98 2538 169 0.1713 0.2219 REMARK 3 8 2.2568 - 2.1588 0.98 2552 170 0.1797 0.2335 REMARK 3 9 2.1588 - 2.0758 0.94 2419 163 0.1878 0.3060 REMARK 3 10 2.0758 - 2.0043 0.84 2166 144 0.2104 0.2721 REMARK 3 11 2.0043 - 1.9417 0.68 1766 118 0.2377 0.2743 REMARK 3 12 1.9417 - 1.8862 0.50 1276 85 0.2638 0.3187 REMARK 3 13 1.8862 - 1.8366 0.33 852 58 0.2668 0.3614 REMARK 3 14 1.8366 - 1.7919 0.19 484 33 0.2804 0.3218 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) : 0.210 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 26.020 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 26.00 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 : 0.013 3154 REMARK 3 ANGLE : 1.372 4298 REMARK 3 CHIRALITY : 0.082 499 REMARK 3 PLANARITY : 0.007 543 REMARK 3 DIHEDRAL : 14.345 1176 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): 8.5094 -23.6641 -0.8952 REMARK 3 T TENSOR REMARK 3 T11: 0.2183 T22: 0.2152 REMARK 3 T33: 0.1581 T12: -0.0035 REMARK 3 T13: -0.0219 T23: 0.0082 REMARK 3 L TENSOR REMARK 3 L11: 1.3322 L22: 1.2179 REMARK 3 L33: 1.3607 L12: -0.2599 REMARK 3 L13: -0.1693 L23: 0.4199 REMARK 3 S TENSOR REMARK 3 S11: -0.0404 S12: -0.0006 S13: 0.1452 REMARK 3 S21: -0.0368 S22: 0.0441 S23: -0.0405 REMARK 3 S31: -0.0534 S32: 0.0644 S33: -0.0038 REMARK 3 TLS GROUP : 2 REMARK 3 SELECTION: CHAIN R REMARK 3 ORIGIN FOR THE GROUP (A): 20.9574 -31.5077 14.8943 REMARK 3 T TENSOR REMARK 3 T11: 0.5000 T22: 0.8337 REMARK 3 T33: 0.3406 T12: 0.2076 REMARK 3 T13: -0.0765 T23: -0.0468 REMARK 3 L TENSOR REMARK 3 L11: 7.7928 L22: 0.5828 REMARK 3 L33: 7.2588 L12: -1.1992 REMARK 3 L13: 7.0912 L23: -1.4437 REMARK 3 S TENSOR REMARK 3 S11: -0.2671 S12: -0.7161 S13: 0.0472 REMARK 3 S21: 0.4724 S22: 0.2749 S23: -0.5054 REMARK 3 S31: 0.3999 S32: 1.5661 S33: -0.0507 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 4KA2 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 06-MAY-13. REMARK 100 THE DEPOSITION ID IS D_1000079080. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 21-AUG-12 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-BM 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 : CCD REMARK 200 DETECTOR MANUFACTURER : MARMOSAIC 225 MM CCD REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 30289 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.792 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 1.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 92.3 REMARK 200 DATA REDUNDANCY : 5.500 REMARK 200 R MERGE (I) : 0.12800 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 12.4000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.90 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.93 REMARK 200 COMPLETENESS FOR SHELL (%) : 52.0 REMARK 200 DATA REDUNDANCY IN SHELL : 1.90 REMARK 200 R MERGE FOR SHELL (I) : 0.54200 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> FOR SHELL : 1.300 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHENIX REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 46.46 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.30 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 9.0% PEG 4000, 14.0% ISOPROPANOL, 100 REMARK 280 MM SODIUM CITRATE, PH 5.6, VAPOR DIFFUSION, HANGING DROP, REMARK 280 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 39.08400 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 39.08400 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 32.18600 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 81.72050 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 6 -1.000000 0.000000 0.000000 32.18600 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 81.72050 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 39.08400 REMARK 290 SMTRY1 7 -1.000000 0.000000 0.000000 32.18600 REMARK 290 SMTRY2 7 0.000000 1.000000 0.000000 81.72050 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 39.08400 REMARK 290 SMTRY1 8 1.000000 0.000000 0.000000 32.18600 REMARK 290 SMTRY2 8 0.000000 -1.000000 0.000000 81.72050 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 789 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 M48U12 IS PEPTIDE-LIKE, A MEMBER OF REMARK 400 INHIBITOR CLASS. REMARK 400 REMARK 400 GROUP: 1 REMARK 400 NAME: CD4-MIMETIC MINIPROTEIN M48U12 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 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 VAL A 44 CG1 CG2 REMARK 470 LYS A 46 CG CD CE NZ REMARK 470 THR A 396 CB OG1 CG2 REMARK 470 ASN A 463 CG OD1 ND2 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 H PHE R 5 O HOH R 607 1.43 REMARK 500 HD21 ASN A 289 C1 NAG A 505 1.55 REMARK 500 OE1 GLU A 106 O HOH A 708 2.10 REMARK 500 O GLY A 124 O HOH A 747 2.14 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND LENGTHS REMARK 500 REMARK 500 THE STEREOCHEMICAL PARAMETERS OF THE FOLLOWING RESIDUES REMARK 500 HAVE VALUES WHICH DEVIATE FROM EXPECTED VALUES BY MORE REMARK 500 THAN 6*RMSD (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 500 IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT: (10X,I3,1X,2(A3,1X,A1,I4,A1,1X,A4,3X),1X,F6.3) REMARK 500 REMARK 500 EXPECTED VALUES PROTEIN: ENGH AND HUBER, 1999 REMARK 500 EXPECTED VALUES NUCLEIC ACID: CLOWNEY ET AL 1996 REMARK 500 REMARK 500 M RES CSSEQI ATM1 RES CSSEQI ATM2 DEVIATION REMARK 500 MPT R 1 C ASN R 2 N 0.143 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND ANGLES REMARK 500 REMARK 500 THE STEREOCHEMICAL PARAMETERS OF THE FOLLOWING RESIDUES REMARK 500 HAVE VALUES WHICH DEVIATE FROM EXPECTED VALUES BY MORE REMARK 500 THAN 6*RMSD (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 500 IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT: (10X,I3,1X,A3,1X,A1,I4,A1,3(1X,A4,2X),12X,F5.1) REMARK 500 REMARK 500 EXPECTED VALUES PROTEIN: ENGH AND HUBER, 1999 REMARK 500 EXPECTED VALUES NUCLEIC ACID: CLOWNEY ET AL 1996 REMARK 500 REMARK 500 M RES CSSEQI ATM1 ATM2 ATM3 REMARK 500 MPT R 1 O - C - N ANGL. DEV. = -22.6 DEGREES 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 -59.49 68.30 REMARK 500 ASN A 276 102.23 -165.61 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: NON-CIS, NON-TRANS REMARK 500 REMARK 500 THE FOLLOWING PEPTIDE BONDS DEVIATE SIGNIFICANTLY FROM BOTH REMARK 500 CIS AND TRANS CONFORMATION. CIS BONDS, IF ANY, ARE LISTED REMARK 500 ON CISPEP RECORDS. TRANS IS DEFINED AS 180 +/- 30 AND REMARK 500 CIS IS DEFINED AS 0 +/- 30 DEGREES. REMARK 500 MODEL OMEGA REMARK 500 LYS A 232 PHE A 233 -144.35 REMARK 500 REMARK 500 REMARK: NULL 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: 4JZZ RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF CD4-MIMETIC MINIPROTEIN M48U1 IN COMPLEX WITH REMARK 900 HIV-1 YU2 GP120 IN C2221 SPACE GROUP REMARK 900 RELATED ID: 4K0A RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF CD4-MIMETIC MINIPROTEIN M48U7 IN COMPLEX WITH REMARK 900 HIV-1 YU2 GP120 REMARK 900 RELATED ID: 2I5Y RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF CD4M47, A SCORPION-TOXIN MIMIC OF CD4, IN REMARK 900 COMPLEX WITH HIV-1 YU2 GP120 ENVELOPE GLYCOPROTEIN AND ANTI-HIV-1 REMARK 900 ANTIBODY 17B REMARK 900 RELATED ID: 2I60 RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF [PHE23]M47, A SCORPION-TOXIC MIMIC OF CD4, IN REMARK 900 COMPLEX WITH HIV-1 YU2 GP120 ENVELOPE GLYCOPROTEIN AND ANTI-HIV-1 REMARK 900 ANTIBODY 17B DBREF 4KA2 A 20 492 PDB 4KA2 4KA2 20 492 DBREF 4KA2 R 1 28 PDB 4KA2 4KA2 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 U3X CYS ALA CYS SEQRES 3 R 28 VAL NH2 MODRES 4KA2 ASN A 295 ASN GLYCOSYLATION SITE MODRES 4KA2 ASN A 448 ASN GLYCOSYLATION SITE MODRES 4KA2 ASN A 386 ASN GLYCOSYLATION SITE MODRES 4KA2 ASN A 262 ASN GLYCOSYLATION SITE MODRES 4KA2 ASN A 289 ASN GLYCOSYLATION SITE MODRES 4KA2 ASN A 234 ASN GLYCOSYLATION SITE MODRES 4KA2 ASN A 276 ASN GLYCOSYLATION SITE MODRES 4KA2 ASN A 241 ASN GLYCOSYLATION SITE MODRES 4KA2 U3X R 23 PHE HET MPT R 1 9 HET DPR R 21 11 HET U3X R 23 79 HET NH2 R 28 3 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 HETNAM MPT BETA-MERCAPTOPROPIONIC ACID HETNAM DPR D-PROLINE HETNAM U3X 4-[(CYCLOHEXYLMETHYL)AMINO]-L-PHENYLALANINE HETNAM NH2 AMINO GROUP 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 2 MPT C3 H6 O2 S FORMUL 2 DPR C5 H9 N O2 FORMUL 2 U3X C16 H24 N2 O2 FORMUL 2 NH2 H2 N FORMUL 3 NAG 8(C8 H15 N O6) FORMUL 11 HOH *236(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 THR A 392 5 6 HELIX 6 6 MET A 475 TYR A 484 1 10 HELIX 7 7 ASN R 2 SER R 12 1 11 SHEET 1 A 3 CYS A 74 PRO A 76 0 SHEET 2 A 3 PHE A 53 SER A 56 1 N CYS A 54 O VAL A 75 SHEET 3 A 3 HIS A 216 CYS A 218 -1 O CYS A 218 N PHE A 53 SHEET 1 B 4 VAL A 84 LEU A 86 0 SHEET 2 B 4 VAL A 242 VAL A 245 -1 O VAL A 242 N LEU A 86 SHEET 3 B 4 PHE A 223 CYS A 228 -1 N LYS A 227 O SER A 243 SHEET 4 B 4 TYR A 486 LYS A 490 -1 O LYS A 487 N LEU A 226 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 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 GLY A 451 N LEU A 260 SHEET 3 E 5 ILE A 284 ARG A 298 -1 N ILE A 294 O SER A 447 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 GLU A 466 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 SER A 447 N ILE A 294 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 LEU R 16 ALA R 20 0 SHEET 2 G 2 U3X R 23 VAL R 27 -1 O U3X R 23 N ALA R 20 SSBOND 1 CYS A 54 CYS A 74 1555 1555 2.08 SSBOND 2 CYS A 119 CYS A 205 1555 1555 2.04 SSBOND 3 CYS A 218 CYS A 247 1555 1555 2.06 SSBOND 4 CYS A 228 CYS A 239 1555 1555 2.10 SSBOND 5 CYS A 296 CYS A 331 1555 1555 2.06 SSBOND 6 CYS A 378 CYS A 445 1555 1555 2.06 SSBOND 7 CYS A 385 CYS A 418 1555 1555 2.04 SSBOND 8 CYS R 6 CYS R 24 1555 1555 2.11 SSBOND 9 CYS R 10 CYS R 26 1555 1555 2.05 LINK ND2 ASN A 234 C1 NAG A 502 1555 1555 1.45 LINK ND2 ASN A 241 C1 NAG A 503 1555 1555 1.46 LINK ND2 ASN A 262 C1 NAG A 504 1555 1555 1.44 LINK ND2 ASN A 276 C1 NAG A 501 1555 1555 1.46 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 386 C1 NAG 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 1.48 LINK SG MPT R 1 SG CYS R 19 1555 1555 2.19 LINK C ALA R 20 N DPR R 21 1555 1555 1.35 LINK C DPR R 21 N THR R 22 1555 1555 1.33 LINK C THR R 22 N U3X R 23 1555 1555 1.34 LINK C U3X R 23 N CYS R 24 1555 1555 1.38 LINK C VAL R 27 N NH2 R 28 1555 1555 1.36 CRYST1 64.372 163.441 78.168 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 0.015535 0.000000 0.000000 0.00000 SCALE2 0.000000 0.006118 0.000000 0.00000 SCALE3 0.000000 0.000000 0.012793 0.00000