HEADER PEPTIDE BINDING PROTEIN/INHIBITOR 22-FEB-16 5IC3 TITLE CAL PDZ DOMAIN WITH PEPTIDE AND INHIBITOR COMPND MOL_ID: 1; COMPND 2 MOLECULE: GOLGI-ASSOCIATED PDZ AND COILED-COIL MOTIF-CONTAINING COMPND 3 PROTEIN; COMPND 4 CHAIN: A, B; COMPND 5 FRAGMENT: UNP RESIDUES 284-370; COMPND 6 SYNONYM: CFTR-ASSOCIATED LIGAND,FUSED IN GLIOBLASTOMA,PDZ PROTEIN COMPND 7 INTERACTING SPECIFICALLY WITH TC10,PIST; COMPND 8 ENGINEERED: YES; COMPND 9 MOL_ID: 2; COMPND 10 MOLECULE: HPV18E6 PEPTIDE; COMPND 11 CHAIN: C, D; COMPND 12 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 3 ORGANISM_COMMON: HUMAN; SOURCE 4 ORGANISM_TAXID: 9606; SOURCE 5 GENE: GOPC, CAL, FIG; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: BL21; SOURCE 9 EXPRESSION_SYSTEM_VARIANT: DE3 RIL; SOURCE 10 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 11 EXPRESSION_SYSTEM_PLASMID: PET16; SOURCE 12 MOL_ID: 2; SOURCE 13 SYNTHETIC: YES; SOURCE 14 ORGANISM_SCIENTIFIC: ALPHAPAPILLOMAVIRUS 7; SOURCE 15 ORGANISM_TAXID: 337042 KEYWDS INHIBITOR, COMPLEX, CAL PDZ, PEPTIDE BINDING PROTEIN, PEPTIDE BINDING KEYWDS 2 PROTEIN-INHIBITOR COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR Y.ZHAO,D.R.MADDEN REVDAT 5 16-OCT-24 5IC3 1 REMARK REVDAT 4 27-SEP-23 5IC3 1 REMARK REVDAT 3 25-DEC-19 5IC3 1 REMARK REVDAT 2 13-SEP-17 5IC3 1 REMARK REVDAT 1 09-AUG-17 5IC3 0 JRNL AUTH Y.ZHAO,D.R.MADDEN JRNL TITL CAL PDZ DOMAIN WITH PEPTIDE AND INHIBITOR JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 1.70 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.7_650 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 : NULL REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.70 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 19.29 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 2.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 3 NUMBER OF REFLECTIONS : 17472 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.177 REMARK 3 R VALUE (WORKING SET) : 0.174 REMARK 3 FREE R VALUE : 0.226 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.910 REMARK 3 FREE R VALUE TEST SET COUNT : 858 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 19.2912 - 3.0856 1.00 2842 129 0.1645 0.1998 REMARK 3 2 3.0856 - 2.4507 1.00 2753 172 0.1693 0.2435 REMARK 3 3 2.4507 - 2.1414 1.00 2776 129 0.1716 0.2157 REMARK 3 4 2.1414 - 1.9458 1.00 2767 129 0.1695 0.2357 REMARK 3 5 1.9458 - 1.8064 1.00 2734 171 0.1955 0.2481 REMARK 3 6 1.8064 - 1.7000 1.00 2742 128 0.2489 0.2816 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : NULL REMARK 3 SOLVENT RADIUS : 1.11 REMARK 3 SHRINKAGE RADIUS : 0.90 REMARK 3 K_SOL : 0.42 REMARK 3 B_SOL : 52.15 REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.240 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 22.490 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) : 2.95100 REMARK 3 B22 (A**2) : -1.79670 REMARK 3 B33 (A**2) : -1.15430 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : -2.75440 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 : 0.007 1496 REMARK 3 ANGLE : 1.059 2032 REMARK 3 CHIRALITY : 0.067 233 REMARK 3 PLANARITY : 0.005 272 REMARK 3 DIHEDRAL : 15.708 581 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : NULL 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 5IC3 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 23-FEB-16. REMARK 100 THE DEPOSITION ID IS D_1000215317. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 24-FEB-13 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 7.4 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : NSLS REMARK 200 BEAMLINE : X6A REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9795 REMARK 200 MONOCHROMATOR : SI(111) REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 270 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : XDS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 17472 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.700 REMARK 200 RESOLUTION RANGE LOW (A) : 19.290 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 200 DATA REDUNDANCY : 7.510 REMARK 200 R MERGE (I) : 0.06200 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 23.7800 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.70 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : NULL REMARK 200 COMPLETENESS FOR SHELL (%) : NULL REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : 0.68600 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : NULL 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: 4E34 REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 34.33 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.87 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 35% PEG3350, 100MM NACL, 100MM TRIS REMARK 280 PH7.4, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 291K 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 24.12600 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: DIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 810 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 5120 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -5.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, 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 350 REMARK 350 BIOMOLECULE: 2 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: DIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 650 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 4990 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -2.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: B, D 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 ARG C 1 REMARK 465 LEU C 2 REMARK 465 GLN C 3 REMARK 465 ARG C 4 REMARK 465 ARG D 1 REMARK 465 LEU D 2 REMARK 465 GLN D 3 REMARK 465 ARG D 4 REMARK 465 ARG D 5 REMARK 465 ARG D 6 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 ASP A 287 CB CG OD1 OD2 REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS REMARK 500 REMARK 500 THE FOLLOWING ATOMS THAT ARE RELATED BY CRYSTALLOGRAPHIC REMARK 500 SYMMETRY ARE IN CLOSE CONTACT. AN ATOM LOCATED WITHIN 0.15 REMARK 500 ANGSTROMS OF A SYMMETRY RELATED ATOM IS ASSUMED TO BE ON A REMARK 500 SPECIAL POSITION AND IS, THEREFORE, LISTED IN REMARK 375 REMARK 500 INSTEAD OF REMARK 500. ATOMS WITH NON-BLANK ALTERNATE REMARK 500 LOCATION INDICATORS ARE NOT INCLUDED IN THE CALCULATIONS. REMARK 500 REMARK 500 DISTANCE CUTOFF: REMARK 500 2.2 ANGSTROMS FOR CONTACTS NOT INVOLVING HYDROGEN ATOMS REMARK 500 1.6 ANGSTROMS FOR CONTACTS INVOLVING HYDROGEN ATOMS REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI SSYMOP DISTANCE REMARK 500 O HOH A 551 O HOH B 440 2645 1.70 REMARK 500 O HOH B 447 O HOH B 454 2755 2.02 REMARK 500 REMARK 500 REMARK: NULL REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue PQR A 401 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 4JOR RELATED DB: PDB REMARK 900 4JOR CONTAINS THE SAME PROTEIN COMPLEX WITHOUT THE SMALL MOLECULE REMARK 999 REMARK 999 SEQUENCE REMARK 999 THE NUMBERING OF THE SEQUENCE IS MADE ACCORDING TO THE ISOFROM 2 OF REMARK 999 CAL DBREF 5IC3 A 276 362 UNP Q9HD26 GOPC_HUMAN 284 370 DBREF 5IC3 B 276 362 UNP Q9HD26 GOPC_HUMAN 284 370 DBREF 5IC3 C 1 10 PDB 5IC3 5IC3 1 10 DBREF 5IC3 D 1 10 PDB 5IC3 5IC3 1 10 SEQRES 1 A 87 GLY PRO ILE ARG LYS VAL LEU LEU LEU LYS GLU ASP HIS SEQRES 2 A 87 GLU GLY LEU GLY ILE SER ILE THR GLY GLY LYS GLU HIS SEQRES 3 A 87 GLY VAL PRO ILE LEU ILE SER GLU ILE HIS PRO GLY GLN SEQRES 4 A 87 PRO ALA ASP ARG CYS GLY GLY LEU HIS VAL GLY ASP ALA SEQRES 5 A 87 ILE LEU ALA VAL ASN GLY VAL ASN LEU ARG ASP THR LYS SEQRES 6 A 87 HIS LYS GLU ALA VAL THR ILE LEU SER GLN GLN ARG GLY SEQRES 7 A 87 GLU ILE GLU PHE GLU VAL VAL TYR VAL SEQRES 1 B 87 GLY PRO ILE ARG LYS VAL LEU LEU LEU LYS GLU ASP HIS SEQRES 2 B 87 GLU GLY LEU GLY ILE SER ILE THR GLY GLY LYS GLU HIS SEQRES 3 B 87 GLY VAL PRO ILE LEU ILE SER GLU ILE HIS PRO GLY GLN SEQRES 4 B 87 PRO ALA ASP ARG CYS GLY GLY LEU HIS VAL GLY ASP ALA SEQRES 5 B 87 ILE LEU ALA VAL ASN GLY VAL ASN LEU ARG ASP THR LYS SEQRES 6 B 87 HIS LYS GLU ALA VAL THR ILE LEU SER GLN GLN ARG GLY SEQRES 7 B 87 GLU ILE GLU PHE GLU VAL VAL TYR VAL SEQRES 1 C 10 ARG LEU GLN ARG ARG ARG GLU THR GLN VAL SEQRES 1 D 10 ARG LEU GLN ARG ARG ARG GLU THR GLN VAL HET PQR A 401 12 HETNAM PQR 4-[METHYL(NITROSO)AMINO]BENZENE-1,2-DIOL HETSYN PQR METHYL-3,4-DEPHOSTATIN FORMUL 5 PQR C7 H8 N2 O3 FORMUL 6 HOH *144(H2 O) HELIX 1 AA1 LYS A 299 GLY A 302 5 4 HELIX 2 AA2 GLN A 314 GLY A 320 1 7 HELIX 3 AA3 LYS A 340 GLN A 351 1 12 HELIX 4 AA4 LYS B 299 GLY B 302 5 4 HELIX 5 AA5 GLN B 314 GLY B 320 1 7 HELIX 6 AA6 LYS B 340 GLN B 350 1 11 SHEET 1 AA1 4 ARG A 279 LYS A 285 0 SHEET 2 AA1 4 GLY A 353 TYR A 361 -1 O PHE A 357 N VAL A 281 SHEET 3 AA1 4 ASP A 326 VAL A 331 -1 N ALA A 327 O VAL A 360 SHEET 4 AA1 4 VAL A 334 ASN A 335 -1 O VAL A 334 N VAL A 331 SHEET 1 AA2 6 ARG A 279 LYS A 285 0 SHEET 2 AA2 6 GLY A 353 TYR A 361 -1 O PHE A 357 N VAL A 281 SHEET 3 AA2 6 ASP A 326 VAL A 331 -1 N ALA A 327 O VAL A 360 SHEET 4 AA2 6 VAL A 303 ILE A 310 -1 N ILE A 307 O ASP A 326 SHEET 5 AA2 6 ILE A 293 GLY A 298 -1 N THR A 296 O LEU A 306 SHEET 6 AA2 6 THR C 8 VAL C 10 -1 O VAL C 10 N ILE A 293 SHEET 1 AA3 4 ARG B 279 LEU B 284 0 SHEET 2 AA3 4 GLU B 354 TYR B 361 -1 O PHE B 357 N VAL B 281 SHEET 3 AA3 4 ASP B 326 VAL B 331 -1 N ALA B 327 O VAL B 360 SHEET 4 AA3 4 VAL B 334 ASN B 335 -1 O VAL B 334 N VAL B 331 SHEET 1 AA4 3 VAL B 303 ILE B 310 0 SHEET 2 AA4 3 ILE B 293 GLY B 298 -1 N SER B 294 O SER B 308 SHEET 3 AA4 3 THR D 8 VAL D 10 -1 O VAL D 10 N ILE B 293 LINK SG CYS A 319 C4 PQR A 401 1555 1555 1.82 SITE 1 AC1 4 LEU A 282 LEU A 284 CYS A 319 HOH A 530 CRYST1 32.772 48.252 51.639 90.00 101.47 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 0.030514 0.000000 0.006191 0.00000 SCALE2 0.000000 0.020724 0.000000 0.00000 SCALE3 0.000000 0.000000 0.019760 0.00000