PDB Short entry for 1K9Q HEADER STRUCTURAL PROTEIN 30-OCT-01 1K9Q TITLE YAP65 WW DOMAIN COMPLEXED TO N-(N-OCTYL)-GPPPY-NH2 COMPND MOL_ID: 1; COMPND 2 MOLECULE: 65 KDA YES-ASSOCIATED PROTEIN; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: WILD TYPE WW DOMAIN; COMPND 5 SYNONYM: YAP65; COMPND 6 ENGINEERED: YES; COMPND 7 MOL_ID: 2; COMPND 8 MOLECULE: WW DOMAIN BINDING PROTEIN-1; COMPND 9 CHAIN: B; COMPND 10 FRAGMENT: RESIDUES 149-153; COMPND 11 SYNONYM: WBP-1; COMPND 12 ENGINEERED: YES; COMPND 13 MUTATION: YES SOURCE MOL_ID: 1; SOURCE 2 SYNTHETIC: YES; SOURCE 3 OTHER_DETAILS: THIS SEQUENCE WAS SYNTHETICALLY OBTAINED, BY SOURCE 4 SEMIAUTOMATED SPOT SYNTHESIS IN A CELLULOSE SUPPORT.; SOURCE 5 MOL_ID: 2; SOURCE 6 SYNTHETIC: YES; SOURCE 7 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 8 ORGANISM_TAXID: 9606; SOURCE 9 OTHER_DETAILS: THIS SEQUENCE WAS SYNTHETICALLY OBTAINED BY SPOT SOURCE 10 SYNTHESIS IN A CELLULOSE SUPPORT. KEYWDS WW DOMAIN, YAP65, BETA-SHEET PROTEINS, LIGANDS, PROLINE-RICH KEYWDS 2 PEPTIDES, STRUCTURAL PROTEIN EXPDTA SOLUTION NMR NUMMDL 20 AUTHOR J.R.PIRES,F.TAHA-NEJAD,F.TOEPERT,T.AST,U.HOFFMULLER,J.SCHNEIDER- AUTHOR 2 MERGENER,R.KUHNE,M.J.MACIAS,H.OSCHKINAT REVDAT 5 10-NOV-21 1K9Q 1 REMARK SEQADV LINK REVDAT 4 24-FEB-09 1K9Q 1 VERSN REVDAT 3 30-SEP-03 1K9Q 1 DBREF REVDAT 2 04-DEC-02 1K9Q 1 REMARK REVDAT 1 28-DEC-01 1K9Q 0 JRNL AUTH J.R.PIRES,F.TAHA-NEJAD,F.TOEPERT,T.AST,U.HOFFMULLER, JRNL AUTH 2 J.SCHNEIDER-MERGENER,R.KUHNE,M.J.MACIAS,H.OSCHKINAT JRNL TITL SOLUTION STRUCTURES OF THE YAP65 WW DOMAIN AND THE VARIANT JRNL TITL 2 L30 K IN COMPLEX WITH THE PEPTIDES GTPPPPYTVG, JRNL TITL 3 N-(N-OCTYL)-GPPPY AND PLPPY AND THE APPLICATION OF PEPTIDE JRNL TITL 4 LIBRARIES REVEAL A MINIMAL BINDING EPITOPE. JRNL REF J.MOL.BIOL. V. 314 1147 2001 JRNL REFN ISSN 0022-2836 JRNL PMID 11743730 JRNL DOI 10.1006/JMBI.2000.5199 REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : XWINNMR 2.6, X-PLOR 3.1 REMARK 3 AUTHORS : BRUKER (XWINNMR), BRUNGER, A.T. (X-PLOR) REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: 2000K, 200 RUNS, FORCE CONSTANTS FOR REMARK 3 NOE 50KCAL MOL-1 RAD-2, 422 RESTRAINTS REMARK 4 REMARK 4 1K9Q COMPLIES WITH FORMAT V. 3.15, 01-DEC-08 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 01-NOV-01. REMARK 100 THE DEPOSITION ID IS D_1000014736. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 288; 288 REMARK 210 PH : 6; 6 REMARK 210 IONIC STRENGTH : 100MM NACL; 100MM NACL REMARK 210 PRESSURE : 1 ATM; 1 ATM REMARK 210 SAMPLE CONTENTS : PHOSPHATE BUFFER 10MM, NACL REMARK 210 100MM, DTT 0.1MM, EDTA 0.1MM, PH REMARK 210 6, WW DOMAIN 1.2MM, LIGAND 2.4MM; REMARK 210 PHOSPHATE BUFFER 10MM, NACL REMARK 210 100MM, DTT 0.1MM, EDTA 0.1MM, PH REMARK 210 6, WW DOMAIN 1.2MM, LIGAND 2.4MM REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 2D NOESY REMARK 210 SPECTROMETER FIELD STRENGTH : 600 MHZ; 750 MHZ REMARK 210 SPECTROMETER MODEL : DRX; DMX REMARK 210 SPECTROMETER MANUFACTURER : BRUKER REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : ANSIG 3.3 REMARK 210 METHOD USED : SIMULATED ANNELING REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 200 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 20 REMARK 210 CONFORMERS, SELECTION CRITERIA : STRUCTURES WITH THE LOWEST REMARK 210 ENERGY REMARK 210 REMARK 210 BEST REPRESENTATIVE CONFORMER IN THIS ENSEMBLE : 1 REMARK 210 REMARK 210 REMARK: NULL REMARK 215 REMARK 215 NMR STUDY REMARK 215 THE COORDINATES IN THIS ENTRY WERE GENERATED FROM SOLUTION REMARK 215 NMR DATA. PROTEIN DATA BANK CONVENTIONS REQUIRE THAT REMARK 215 CRYST1 AND SCALE RECORDS BE INCLUDED, BUT THE VALUES ON REMARK 215 THESE RECORDS ARE MEANINGLESS. 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, B 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 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS 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 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 1 ILE A 7 71.34 -167.65 REMARK 500 1 PRO A 12 -159.13 -71.88 REMARK 500 1 ALA A 20 149.16 -172.73 REMARK 500 1 SER A 23 -154.70 -176.11 REMARK 500 1 SER A 24 74.58 -66.68 REMARK 500 1 ARG A 27 74.27 -63.97 REMARK 500 1 GLN A 35 72.02 54.94 REMARK 500 1 TRP A 39 -160.83 -63.70 REMARK 500 1 ASP A 41 -59.90 -177.54 REMARK 500 2 GLU A 6 99.21 54.35 REMARK 500 2 LEU A 13 176.96 54.64 REMARK 500 2 SER A 23 -85.68 178.56 REMARK 500 2 SER A 24 -80.52 -128.30 REMARK 500 2 ARG A 27 72.41 -64.93 REMARK 500 2 GLN A 35 75.30 53.93 REMARK 500 2 TRP A 39 -66.99 -109.36 REMARK 500 3 GLU A 6 -72.89 -79.19 REMARK 500 3 PRO A 12 -159.59 -73.62 REMARK 500 3 SER A 23 59.98 -176.82 REMARK 500 3 SER A 24 90.01 48.09 REMARK 500 3 ARG A 27 73.57 -65.16 REMARK 500 3 TRP A 39 -149.63 -63.54 REMARK 500 3 ASP A 41 -60.13 -175.99 REMARK 500 4 ILE A 7 108.45 -52.84 REMARK 500 4 ASP A 9 77.63 -113.84 REMARK 500 4 ASP A 10 -60.99 -174.39 REMARK 500 4 PRO A 12 -87.89 -71.62 REMARK 500 4 ALA A 20 145.63 -170.21 REMARK 500 4 SER A 23 -151.70 -176.43 REMARK 500 4 SER A 24 74.77 -66.55 REMARK 500 4 ARG A 27 74.10 -63.98 REMARK 500 4 TRP A 39 -64.95 -100.38 REMARK 500 4 ARG A 43 78.78 -101.52 REMARK 500 5 ASP A 9 41.64 -91.06 REMARK 500 5 ASP A 10 83.65 -173.40 REMARK 500 5 LEU A 13 -179.30 53.56 REMARK 500 5 ALA A 20 145.66 -171.19 REMARK 500 5 SER A 23 -153.65 -178.08 REMARK 500 5 ARG A 27 75.41 -65.67 REMARK 500 5 GLN A 35 71.07 54.06 REMARK 500 5 TRP A 39 -61.33 -106.62 REMARK 500 6 GLU A 6 172.16 -53.67 REMARK 500 6 ASP A 10 74.62 -67.39 REMARK 500 6 VAL A 11 99.06 54.16 REMARK 500 6 PRO A 12 -158.38 -71.69 REMARK 500 6 LEU A 13 177.02 -51.44 REMARK 500 6 SER A 23 -153.07 -177.89 REMARK 500 6 SER A 24 -70.17 -53.73 REMARK 500 6 ARG A 27 69.08 -65.72 REMARK 500 6 GLN A 35 78.66 51.98 REMARK 500 REMARK 500 THIS ENTRY HAS 168 RAMACHANDRAN OUTLIERS. 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 OCT B 2 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1JMQ RELATED DB: PDB REMARK 900 1JMQ CONTAINS YAP65 (L30K MUTANT) WW DOMAIN IN COMPLEXED WITH REMARK 900 GTPPPPYTVG PEPTIDE REMARK 900 RELATED ID: 1E0M RELATED DB: PDB REMARK 900 1E0M CONTAINS PROTOTYPE WW DOMAIN REMARK 900 RELATED ID: 1EG3 RELATED DB: PDB REMARK 900 1EG3 CONTAINS DYSTROPHIN WW DOMAIN FRAGMENT REMARK 900 RELATED ID: 1EG4 RELATED DB: PDB REMARK 900 1EG4 CONTAINS DYSTROPHIN WW DOMAIN FRAGMENT IN COMPLEXED WITH BETA- REMARK 900 DYSTROGLYCAN PEPTIDE REMARK 900 RELATED ID: 1I5H RELATED DB: PDB REMARK 900 1I5H CONTAINS RNEDD4 WWIII DOMAIN-RENAC BP2 PEPTIDE COMPLEX REMARK 900 RELATED ID: 1K9R RELATED DB: PDB REMARK 900 1K9R CONTAINS YAP65 WW DOMAIN COMPLEXED WITH ACETYL-PLPPY DBREF 1K9Q A 5 44 UNP P46937 YAP1_HUMAN 165 204 DBREF 1K9Q B 3 7 GB 4205084 AAD10950 149 153 SEQADV 1K9Q GLY B 3 GB 4205084 PRO 149 ENGINEERED MUTATION SEQADV 1K9Q NH2 B 8 GB 4205084 AMIDATION SEQRES 1 A 40 PHE GLU ILE PRO ASP ASP VAL PRO LEU PRO ALA GLY TRP SEQRES 2 A 40 GLU MET ALA LYS THR SER SER GLY GLN ARG TYR PHE LEU SEQRES 3 A 40 ASN HIS ILE ASP GLN THR THR THR TRP GLN ASP PRO ARG SEQRES 4 A 40 LYS SEQRES 1 B 6 GLY PRO PRO PRO TYR NH2 HET NH2 B 8 3 HET OCT B 2 25 HETNAM NH2 AMINO GROUP HETNAM OCT N-OCTANE FORMUL 2 NH2 H2 N FORMUL 3 OCT C8 H18 SHEET 1 A 3 TRP A 17 LYS A 21 0 SHEET 2 A 3 ARG A 27 ASN A 31 -1 O TYR A 28 N ALA A 20 SHEET 3 A 3 THR A 36 THR A 38 -1 O THR A 38 N PHE A 29 LINK C1 OCT B 2 N GLY B 3 1555 1555 1.49 LINK C TYR B 7 N NH2 B 8 1555 1555 1.30 SITE 1 AC1 1 GLY B 3 CRYST1 1.000 1.000 1.000 90.00 90.00 90.00 P 1 1 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 1.000000 0.000000 0.000000 0.00000 SCALE2 0.000000 1.000000 0.000000 0.00000 SCALE3 0.000000 0.000000 1.000000 0.00000