HEADER PROTEIN BINDING/INHIBITOR 22-JUL-19 6PW8 TITLE HYDROCARBON-STAPLED PAXILLIN PEPTIDE BOUND TO THE FOCAL ADHESION TITLE 2 TARGETING (FAT) DOMAIN OF THE FOCAL ADHESION KINASE (FAK) COMPND MOL_ID: 1; COMPND 2 MOLECULE: FOCAL ADHESION KINASE 1; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: FOCAL ADHESION TARGETING DOMAIN (UNP RESIDUES 749-874); COMPND 5 SYNONYM: FADK 1, FOCAL ADHESION KINASE-RELATED NONKINASE, FRNK, COMPND 6 PROTEIN PHOSPHATASE 1 REGULATORY SUBUNIT 71, PPP1R71, PROTEIN- COMPND 7 TYROSINE KINASE 2, P125FAK, PP125FAK; COMPND 8 EC: 2.7.10.2; COMPND 9 ENGINEERED: YES; COMPND 10 MOL_ID: 2; COMPND 11 MOLECULE: SP3; COMPND 12 CHAIN: B; COMPND 13 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: PTK2, FAK, FAK1; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 MOL_ID: 2; SOURCE 9 SYNTHETIC: YES; SOURCE 10 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 11 ORGANISM_COMMON: HUMAN; SOURCE 12 ORGANISM_TAXID: 9606 KEYWDS INHIBITOR, STAPLED PEPTIDE, TYROSINE KINASE, PROTEIN BINDING- KEYWDS 2 INHIBITOR COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR D.G.THIFAULT,P.FROMME,J.M.MARTIN-GARCIA REVDAT 3 15-NOV-23 6PW8 1 LINK ATOM REVDAT 2 11-OCT-23 6PW8 1 LINK REVDAT 1 22-JUL-20 6PW8 0 JRNL AUTH D.G.THIFAULT,P.FROMME,J.M.MARTIN-GARCIA JRNL TITL STAPLED PEPTIDE LIGAND BOUND TO THE FOCAL ADHESION TARGETING JRNL TITL 2 (FAT) DOMAIN OF THE FOCAL ADHESION KINASE (FAK) JRNL REF TO BE PUBLISHED JRNL REFN REMARK 1 REMARK 1 REFERENCE 1 REMARK 1 AUTH P.V.AFONINE,R.W.GROSSE-KUNSTLEVE,N.ECHOLS,J.J.HEADD, REMARK 1 AUTH 2 N.W.MORIARTY,M.MUSTYAKIMOV,T.C.TERWILLIGER,A.URZHUMTSEV, REMARK 1 AUTH 3 P.H.ZWART,P.D.ADAMS REMARK 1 TITL TOWARDS AUTOMATED CRYSTALLOGRAPHIC STRUCTURE REFINEMENT WITH REMARK 1 TITL 2 PHENIX.REFINE. REMARK 1 REF ACTA CRYSTALLOGR.,SECT.D V. 68 352 2012 REMARK 1 REFN ESSN 1399-0047 REMARK 1 PMID 22505256 REMARK 1 DOI 10.1107/S0907444912001308 REMARK 1 REFERENCE 2 REMARK 1 AUTH P.D.ADAMS,P.V.AFONINE,G.BUNKOCZI,V.B.CHEN,I.W.DAVIS, REMARK 1 AUTH 2 N.ECHOLS,J.J.HEADD,L.W.HUNG,G.J.KAPRAL,R.W.GROSSE-KUNSTLEVE, REMARK 1 AUTH 3 A.J.MCCOY,N.W.MORIARTY,R.OEFFNER,R.J.READ,D.C.RICHARDSON, REMARK 1 AUTH 4 J.S.RICHARDSON,T.C.TERWILLIGER,P.H.ZWART REMARK 1 TITL PHENIX: A COMPREHENSIVE PYTHON-BASED SYSTEM FOR REMARK 1 TITL 2 MACROMOLECULAR STRUCTURE SOLUTION. REMARK 1 REF ACTA CRYSTALLOGR.,SECT.D V. 66 213 2010 REMARK 1 REFN ESSN 1399-0047 REMARK 1 PMID 20124702 REMARK 1 DOI 10.1107/S0907444909052925 REMARK 2 REMARK 2 RESOLUTION. 1.95 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.14_3260 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 : CDL V1.2 REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.95 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 37.66 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.350 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.7 REMARK 3 NUMBER OF REFLECTIONS : 10289 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.219 REMARK 3 R VALUE (WORKING SET) : 0.217 REMARK 3 FREE R VALUE : 0.250 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.050 REMARK 3 FREE R VALUE TEST SET COUNT : 520 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 37.6600 - 3.1000 1.00 2542 139 0.2075 0.2188 REMARK 3 2 3.1000 - 2.4600 1.00 2434 127 0.2377 0.2930 REMARK 3 3 2.4600 - 2.1500 1.00 2418 111 0.2131 0.3067 REMARK 3 4 2.1500 - 1.9500 1.00 2375 143 0.2315 0.3112 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) : 0.237 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 29.020 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 33.57 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 38.06 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 : 0.010 1106 REMARK 3 ANGLE : 1.124 1494 REMARK 3 CHIRALITY : 0.057 183 REMARK 3 PLANARITY : 0.008 189 REMARK 3 DIHEDRAL : 22.751 433 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 6PW8 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 23-JUL-19. REMARK 100 THE DEPOSITION ID IS D_1000243112. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 21-APR-19 REMARK 200 TEMPERATURE (KELVIN) : 293 REMARK 200 PH : NULL REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : APS REMARK 200 BEAMLINE : 23-ID-D REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.02 REMARK 200 MONOCHROMATOR : SI(111) REMARK 200 OPTICS : K-B PAIR BIMORPH MIRRORS REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS3 6M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : AIMLESS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 10290 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.950 REMARK 200 RESOLUTION RANGE LOW (A) : 47.490 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.7 REMARK 200 DATA REDUNDANCY : 2.000 REMARK 200 R MERGE (I) : 0.11400 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 12.8000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.95 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.02 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.5 REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : 1.85900 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: PHASER REMARK 200 STARTING MODEL: PDB ENTRY 1K05 REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 42.85 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.15 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.02 M ZINC CHLORIDE, 20% PEG3350, REMARK 280 VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 21 21 21 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X+1/2,-Y,Z+1/2 REMARK 290 3555 -X,Y+1/2,-Z+1/2 REMARK 290 4555 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 23.74450 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 26.70950 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 26.54700 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 26.70950 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 23.74450 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 26.54700 REMARK 290 SMTRY3 4 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 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 1660 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 7560 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -36.0 KCAL/MOL 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 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 ZN A1101 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 GLU A 937 OE1 REMARK 620 2 GLU A 956 OE2 121.4 REMARK 620 3 HIS A 980 ND1 104.8 41.8 REMARK 620 4 HOH A1216 O 112.6 90.6 60.1 REMARK 620 N 1 2 3 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue ZN A 1101 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue CL A 1102 DBREF 6PW8 A 922 1047 UNP Q05397 FAK1_HUMAN 749 874 DBREF 6PW8 B 0 14 PDB 6PW8 6PW8 0 14 SEQRES 1 A 126 ASP LYS VAL TYR GLU ASN VAL THR GLY LEU VAL LYS ALA SEQRES 2 A 126 VAL ILE GLU MET SER SER LYS ILE GLN PRO ALA PRO PRO SEQRES 3 A 126 GLU GLU TYR VAL PRO MET VAL LYS GLU VAL GLY LEU ALA SEQRES 4 A 126 LEU ARG THR LEU LEU ALA THR VAL ASP GLU THR ILE PRO SEQRES 5 A 126 LEU LEU PRO ALA SER THR HIS ARG GLU ILE GLU MET ALA SEQRES 6 A 126 GLN LYS LEU LEU ASN SER ASP LEU GLY GLU LEU ILE ASN SEQRES 7 A 126 LYS MET LYS LEU ALA GLN GLN TYR VAL MET THR SER LEU SEQRES 8 A 126 GLN GLN GLU TYR LYS LYS GLN MET LEU THR ALA ALA HIS SEQRES 9 A 126 ALA LEU ALA VAL ASP ALA LYS ASN LEU LEU ASP VAL ILE SEQRES 10 A 126 ASP GLN ALA ARG LEU LYS MET LEU GLY SEQRES 1 B 15 ACE ASN LEU 2JN GLU LEU ASP ARG LEU LEU UZA GLU LEU SEQRES 2 B 15 ASN NH2 HET ACE B 0 3 HET 2JN B 3 9 HET UZA B 10 12 HET NH2 B 14 1 HET ZN A1101 1 HET CL A1102 1 HETNAM ACE ACETYL GROUP HETNAM 2JN 2-METHYL-D-NORLEUCINE HETNAM UZA (2S,6E)-2-AMINO-2-METHYLNON-6-ENOIC ACID HETNAM NH2 AMINO GROUP HETNAM ZN ZINC ION HETNAM CL CHLORIDE ION FORMUL 2 ACE C2 H4 O FORMUL 2 2JN C7 H15 N O2 FORMUL 2 UZA C10 H19 N O2 FORMUL 2 NH2 H2 N FORMUL 3 ZN ZN 2+ FORMUL 4 CL CL 1- FORMUL 5 HOH *92(H2 O) HELIX 1 AA1 ASP A 922 ILE A 942 1 21 HELIX 2 AA2 PRO A 946 GLU A 949 5 4 HELIX 3 AA3 TYR A 950 ILE A 972 1 23 HELIX 4 AA4 PRO A 973 LEU A 975 5 3 HELIX 5 AA5 PRO A 976 SER A 978 5 3 HELIX 6 AA6 THR A 979 TYR A 1007 1 29 HELIX 7 AA7 LEU A 1012 GLY A 1047 1 36 HELIX 8 AA8 ASN B 1 LEU B 2 5 2 HELIX 9 AA9 GLU B 4 GLU B 4 5 1 HELIX 10 AB1 LEU B 5 GLU B 11 1 7 LINK C ACE B 0 N ASN B 1 1555 1555 1.33 LINK C LEU B 2 N 2JN B 3 1555 1555 1.33 LINK C 2JN B 3 N GLU B 4 1555 1555 1.33 LINK CAI 2JN B 3 C05 UZA B 10 1555 1555 1.49 LINK C LEU B 9 N UZA B 10 1555 1555 1.33 LINK C UZA B 10 N GLU B 11 1555 1555 1.34 LINK C ASN B 13 N NH2 B 14 1555 1555 1.33 LINK OE1 GLU A 937 ZN ZN A1101 1555 1555 1.98 LINK OE2 GLU A 956 ZN ZN A1101 1555 1555 1.91 LINK ND1 HIS A 980 ZN ZN A1101 1555 2454 2.11 LINK ZN ZN A1101 O HOH A1216 1555 1555 1.88 SITE 1 AC1 4 GLU A 937 GLU A 956 HIS A 980 HOH A1216 SITE 1 AC2 4 HIS A1025 ASP A1039 HOH A1254 HOH A1256 CRYST1 47.489 53.094 53.419 90.00 90.00 90.00 P 21 21 21 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 0.021058 0.000000 0.000000 0.00000 SCALE2 0.000000 0.018835 0.000000 0.00000 SCALE3 0.000000 0.000000 0.018720 0.00000