HEADER TRANSFERASE 10-JAN-07 2OI3 TITLE NMR STRUCTURE ANALYSIS OF THE HEMATOPOETIC CELL KINASE SH3 DOMAIN TITLE 2 COMPLEXED WITH AN ARTIFICIAL HIGH AFFINITY LIGAND (PD1) COMPND MOL_ID: 1; COMPND 2 MOLECULE: TYROSINE-PROTEIN KINASE HCK; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: SH3 DOMAIN, RESIDUES 60-140; COMPND 5 SYNONYM: P59-HCK/P60-HCK, HEMOPOIETIC CELL KINASE; COMPND 6 EC: 2.7.10.2; COMPND 7 ENGINEERED: YES; COMPND 8 MOL_ID: 2; COMPND 9 MOLECULE: ARTIFICIAL PEPTIDE PD1; COMPND 10 CHAIN: B; COMPND 11 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: HCK; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 511693; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: BL21; SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PGEX6P2; SOURCE 11 MOL_ID: 2; SOURCE 12 SYNTHETIC: YES KEYWDS HUMAN HCK, SH3, SRC-TYPE TYROSINE KINASE, TRANSFERASE EXPDTA SOLUTION NMR MDLTYP MINIMIZED AVERAGE AUTHOR H.SCHMIDT,M.STOLDT,S.HOFFMANN,T.TRAN,D.WILLBOLD REVDAT 4 27-DEC-23 2OI3 1 REMARK REVDAT 3 05-FEB-20 2OI3 1 REMARK SEQADV LINK REVDAT 2 24-FEB-09 2OI3 1 VERSN REVDAT 1 20-FEB-07 2OI3 0 JRNL AUTH H.SCHMIDT,S.HOFFMANN,T.TRAN,M.STOLDT,T.STANGLER,K.WIESEHAN, JRNL AUTH 2 D.WILLBOLD JRNL TITL SOLUTION STRUCTURE OF A HCK SH3 DOMAIN LIGAND COMPLEX JRNL TITL 2 REVEALS NOVEL INTERACTION MODES JRNL REF J.MOL.BIOL. V. 365 1517 2007 JRNL REFN ISSN 0022-2836 JRNL PMID 17141806 JRNL DOI 10.1016/J.JMB.2006.11.013 REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : NMRPIPE 2.3, RADAR 0.9B, AMBER 8.0 REMARK 3 AUTHORS : DELAGLIO (NMRPIPE), HERRMANN (RADAR), CASE (AMBER) REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 2OI3 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 11-JAN-07. REMARK 100 THE DEPOSITION ID IS D_1000041162. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 298 REMARK 210 PH : 6.7 REMARK 210 IONIC STRENGTH : 20MM KPO4, 20MM NACL REMARK 210 PRESSURE : 1 ATM REMARK 210 SAMPLE CONTENTS : 1.3MM HCK-SH3 U-13C, U-15N: REMARK 210 1.3MM PD1, 20MM KPO4, 20MM NACL, REMARK 210 PH 6.7, 93% H2O, 7% D2O REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 3D_13C-SEPARATED_NOESY; 3D_15N REMARK 210 -SEPARATED_NOESY; 3D_13C/15N- REMARK 210 FILTERED/EDITED NOESY; 2D_13C/ REMARK 210 15N-DOUBLE FILTERED NOESY REMARK 210 SPECTROMETER FIELD STRENGTH : 600 MHZ; 800 MHZ REMARK 210 SPECTROMETER MODEL : INOVA REMARK 210 SPECTROMETER MANUFACTURER : VARIAN REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : CARA/NEASY 1.3.1, VNMRJ 1.1D, REMARK 210 CYANA 1.1 REMARK 210 METHOD USED : SIMULATED ANNEALING WITH REMARK 210 GENERALIZED BORN SOLVENT MODEL REMARK 210 AND NMR DISTANCE CONSTRAINTS REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 20 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 1 REMARK 210 CONFORMERS, SELECTION CRITERIA : MINIMIZED AVERAGE STRUCTURE 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 OD2 ASP A 48 HG SER A 64 1.60 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 VAL A 28 CA - CB - CG1 ANGL. DEV. = 10.3 DEGREES REMARK 500 VAL A 78 CA - CB - CG1 ANGL. DEV. = 9.4 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 ALA A 21 -167.68 57.81 REMARK 500 ALA A 36 75.60 27.28 REMARK 500 SER A 56 21.63 -146.22 REMARK 500 SER A 64 106.36 -49.39 REMARK 500 THR A 67 -4.86 -140.32 REMARK 500 PRO B 92 49.71 -76.33 REMARK 500 LEU B 93 154.04 59.61 REMARK 500 REMARK 500 REMARK: NULL REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE NH2 B 100 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 6581 RELATED DB: BMRB REMARK 900 SEQUENCE-SPECIFIC 1H, 13C AND 15N RESONANCE ASSIGNMENTS OF REMARK 900 HEMATOPOIETIC CELL KINASE SH3 DOMAINS IN COMPLEX WITH A SYNTHETIC REMARK 900 PEPTIDE REMARK 900 RELATED ID: 2A4Y RELATED DB: PDB REMARK 900 NMR STRUCTURE ANALYSIS OF THE HEMATOPOETIC CELL KINASE SH3 DOMAIN REMARK 900 COMPLEXED WITH AN ARTIFICIAL HIGH AFFINITY LIGAND (PD1) DBREF 2OI3 A 6 86 UNP P08631 HCK_HUMAN 60 140 DBREF 2OI3 B 87 100 PDB 2OI3 2OI3 87 100 SEQADV 2OI3 GLY A 1 UNP P08631 CLONING ARTIFACT SEQADV 2OI3 PRO A 2 UNP P08631 CLONING ARTIFACT SEQADV 2OI3 LEU A 3 UNP P08631 CLONING ARTIFACT SEQADV 2OI3 GLY A 4 UNP P08631 CLONING ARTIFACT SEQADV 2OI3 SER A 5 UNP P08631 CLONING ARTIFACT SEQRES 1 A 86 GLY PRO LEU GLY SER PRO GLY PRO ASN SER HIS ASN SER SEQRES 2 A 86 ASN THR PRO GLY ILE ARG GLU ALA GLY SER GLU ASP ILE SEQRES 3 A 86 ILE VAL VAL ALA LEU TYR ASP TYR GLU ALA ILE HIS HIS SEQRES 4 A 86 GLU ASP LEU SER PHE GLN LYS GLY ASP GLN MET VAL VAL SEQRES 5 A 86 LEU GLU GLU SER GLY GLU TRP TRP LYS ALA ARG SER LEU SEQRES 6 A 86 ALA THR ARG LYS GLU GLY TYR ILE PRO SER ASN TYR VAL SEQRES 7 A 86 ALA ARG VAL ASP SER LEU GLU THR SEQRES 1 B 14 ACE HIS SER LYS TYR PRO LEU PRO PRO LEU PRO SER LEU SEQRES 2 B 14 NH2 HET ACE B 87 6 HET NH2 B 100 3 HETNAM ACE ACETYL GROUP HETNAM NH2 AMINO GROUP FORMUL 2 ACE C2 H4 O FORMUL 2 NH2 H2 N HELIX 1 1 ASP A 82 LEU A 84 5 3 SHEET 1 A 5 GLU A 70 PRO A 74 0 SHEET 2 A 5 TRP A 59 SER A 64 -1 N ALA A 62 O GLY A 71 SHEET 3 A 5 GLN A 49 GLU A 55 -1 N LEU A 53 O LYS A 61 SHEET 4 A 5 ILE A 26 ALA A 30 -1 N ILE A 26 O VAL A 52 SHEET 5 A 5 VAL A 78 ARG A 80 -1 O ALA A 79 N VAL A 29 LINK C ACE B 87 N HIS B 88 1555 1555 1.33 LINK C LEU B 99 N NH2 B 100 1555 1555 1.33 SITE 1 AC2 2 SER B 98 LEU B 99 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