HEADER APOPTOSIS 17-JUN-15 5C3F TITLE CRYSTAL STRUCTURE OF MCL-1 BOUND TO BID-MM COMPND MOL_ID: 1; COMPND 2 MOLECULE: INDUCED MYELOID LEUKEMIA CELL DIFFERENTIATION PROTEIN MCL- COMPND 3 1; COMPND 4 CHAIN: A; COMPND 5 SYNONYM: BCL-2-LIKE PROTEIN 3,BCL2-L-3,BCL-2-RELATED PROTEIN COMPND 6 EAT/MCL1,MCL1/EAT; COMPND 7 ENGINEERED: YES; COMPND 8 MOL_ID: 2; COMPND 9 MOLECULE: BID-MM; 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: MCL1, BCL2L3; 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 COMPLEX, BCL-2 FAMILY, BH3, STAPLED PEPTIDE, APOPTOSIS EXPDTA X-RAY DIFFRACTION AUTHOR J.A.MILES,D.J.YEO,P.ROWELL,S.RODRIGUEZ-MARIN,C.M.PASK,S.L.WARRINER, AUTHOR 2 T.A.EDWARDS,A.J.WILSON REVDAT 3 10-JAN-24 5C3F 1 REMARK REVDAT 2 18-OCT-17 5C3F 1 JRNL REVDAT 1 20-APR-16 5C3F 0 JRNL AUTH J.A.MILES,D.J.YEO,P.ROWELL,S.RODRIGUEZ-MARIN,C.M.PASK, JRNL AUTH 2 S.L.WARRINER,T.A.EDWARDS,A.J.WILSON JRNL TITL HYDROCARBON CONSTRAINED PEPTIDES - UNDERSTANDING JRNL TITL 2 PREORGANISATION AND BINDING AFFINITY. JRNL REF CHEM SCI V. 7 3694 2016 JRNL REFN ISSN 2041-6520 JRNL PMID 28970875 JRNL DOI 10.1039/C5SC04048E REMARK 2 REMARK 2 RESOLUTION. 1.43 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.9_1692 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) : 1.43 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 46.54 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.340 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.0 REMARK 3 NUMBER OF REFLECTIONS : 32015 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.163 REMARK 3 R VALUE (WORKING SET) : 0.162 REMARK 3 FREE R VALUE : 0.177 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.770 REMARK 3 FREE R VALUE TEST SET COUNT : 1528 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 46.5634 - 3.1801 0.98 2939 138 0.1592 0.1635 REMARK 3 2 3.1801 - 2.5242 0.99 2825 139 0.1462 0.1563 REMARK 3 3 2.5242 - 2.2051 0.99 2788 153 0.1375 0.1594 REMARK 3 4 2.2051 - 2.0035 1.00 2791 148 0.1421 0.1496 REMARK 3 5 2.0035 - 1.8599 0.99 2762 129 0.1496 0.1718 REMARK 3 6 1.8599 - 1.7502 1.00 2753 157 0.1711 0.2141 REMARK 3 7 1.7502 - 1.6626 1.00 2739 150 0.1796 0.2080 REMARK 3 8 1.6626 - 1.5902 0.99 2741 133 0.2113 0.2196 REMARK 3 9 1.5902 - 1.5290 0.99 2720 138 0.2291 0.2985 REMARK 3 10 1.5290 - 1.4762 0.99 2729 133 0.2429 0.2848 REMARK 3 11 1.4762 - 1.4301 0.98 2700 110 0.2668 0.2644 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) : 0.150 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 18.560 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) : 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 : 0.004 1445 REMARK 3 ANGLE : 0.680 1941 REMARK 3 CHIRALITY : 0.051 217 REMARK 3 PLANARITY : 0.003 247 REMARK 3 DIHEDRAL : 15.249 556 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 5C3F COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 17-JUN-15. REMARK 100 THE DEPOSITION ID IS D_1000210959. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 08-MAY-14 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 8.0 REMARK 200 NUMBER OF CRYSTALS USED : NULL REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : DIAMOND REMARK 200 BEAMLINE : I03 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9763 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : PSI PILATUS 6M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : XDS, XIA2 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 32047 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.430 REMARK 200 RESOLUTION RANGE LOW (A) : 46.540 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.0 REMARK 200 DATA REDUNDANCY : 4.200 REMARK 200 R MERGE (I) : 0.06200 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 13.5000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.43 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.47 REMARK 200 COMPLETENESS FOR SHELL (%) : 97.8 REMARK 200 DATA REDUNDANCY IN SHELL : 3.50 REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 2.200 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: REFMAC REMARK 200 STARTING MODEL: 2NL9 REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 40.83 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.08 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 18% PEG 20000, 0.1 M TRIS PH 8.0, REMARK 280 VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 277K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 21 21 2 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,-Y,Z REMARK 290 3555 -X+1/2,Y+1/2,-Z 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 0.00000 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 40.41500 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 18.51000 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 40.41500 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 18.51000 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: 2130 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 8940 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -16.0 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 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 ASP A 323 REMARK 465 LEU A 324 REMARK 465 GLU A 325 REMARK 465 GLY A 326 REMARK 465 GLY A 327 REMARK 465 TRP B 102 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 O HOH A 566 O HOH A 590 1.91 REMARK 500 O HOH A 503 O HOH A 573 1.91 REMARK 500 O HOH A 525 O HOH A 633 2.02 REMARK 500 O HOH A 649 O HOH A 672 2.18 REMARK 500 REMARK 500 REMARK: NULL REMARK 525 REMARK 525 SOLVENT REMARK 525 REMARK 525 THE SOLVENT MOLECULES HAVE CHAIN IDENTIFIERS THAT REMARK 525 INDICATE THE POLYMER CHAIN WITH WHICH THEY ARE MOST REMARK 525 CLOSELY ASSOCIATED. THE REMARK LISTS ALL THE SOLVENT REMARK 525 MOLECULES WHICH ARE MORE THAN 5A AWAY FROM THE REMARK 525 NEAREST POLYMER CHAIN (M = MODEL NUMBER; REMARK 525 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE REMARK 525 NUMBER; I=INSERTION CODE): REMARK 525 REMARK 525 M RES CSSEQI REMARK 525 HOH A 677 DISTANCE = 5.94 ANGSTROMS REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue GOL A 401 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residues NLE B 92 and NLE B 96 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residues NLE B 96 and NLE B 97 DBREF 5C3F A 173 327 UNP Q07820 MCL1_HUMAN 173 327 DBREF 5C3F B 79 102 PDB 5C3F 5C3F 79 102 SEQADV 5C3F SER A 172 UNP Q07820 EXPRESSION TAG SEQRES 1 A 156 SER GLU LEU TYR ARG GLN SER LEU GLU ILE ILE SER ARG SEQRES 2 A 156 TYR LEU ARG GLU GLN ALA THR GLY ALA LYS ASP THR LYS SEQRES 3 A 156 PRO MET GLY ARG SER GLY ALA THR SER ARG LYS ALA LEU SEQRES 4 A 156 GLU THR LEU ARG ARG VAL GLY ASP GLY VAL GLN ARG ASN SEQRES 5 A 156 HIS GLU THR ALA PHE GLN GLY MET LEU ARG LYS LEU ASP SEQRES 6 A 156 ILE LYS ASN GLU ASP ASP VAL LYS SER LEU SER ARG VAL SEQRES 7 A 156 MET ILE HIS VAL PHE SER ASP GLY VAL THR ASN TRP GLY SEQRES 8 A 156 ARG ILE VAL THR LEU ILE SER PHE GLY ALA PHE VAL ALA SEQRES 9 A 156 LYS HIS LEU LYS THR ILE ASN GLN GLU SER CYS ILE GLU SEQRES 10 A 156 PRO LEU ALA GLU SER ILE THR ASP VAL LEU VAL ARG THR SEQRES 11 A 156 LYS ARG ASP TRP LEU VAL LYS GLN ARG GLY TRP ASP GLY SEQRES 12 A 156 PHE VAL GLU PHE PHE HIS VAL GLU ASP LEU GLU GLY GLY SEQRES 1 B 24 ACE GLU ASP ILE ILE ARG ASN ILE ALA ARG HIS LEU ALA SEQRES 2 B 24 NLE VAL GLY ASP NLE NLE ASP ARG SER ILE TRP HET ACE B 79 3 HET NLE B 92 16 HET NLE B 96 16 HET NLE B 97 18 HET GOL A 401 14 HETNAM ACE ACETYL GROUP HETNAM NLE NORLEUCINE HETNAM GOL GLYCEROL HETSYN GOL GLYCERIN; PROPANE-1,2,3-TRIOL FORMUL 2 ACE C2 H4 O FORMUL 2 NLE 3(C6 H13 N O2) FORMUL 3 GOL C3 H8 O3 FORMUL 4 HOH *190(H2 O) HELIX 1 AA1 SER A 172 GLY A 192 1 21 HELIX 2 AA2 SER A 202 HIS A 224 1 23 HELIX 3 AA3 HIS A 224 ASP A 236 1 13 HELIX 4 AA4 ASN A 239 ASP A 242 5 4 HELIX 5 AA5 VAL A 243 PHE A 254 1 12 HELIX 6 AA6 SER A 255 GLY A 257 5 3 HELIX 7 AA7 ASN A 260 ILE A 281 1 22 HELIX 8 AA8 GLN A 283 SER A 285 5 3 HELIX 9 AA9 CYS A 286 GLN A 309 1 24 HELIX 10 AB1 ARG A 310 HIS A 320 1 11 HELIX 11 AB2 GLU B 80 ILE B 101 1 22 LINK C ACE B 79 N GLU B 80 1555 1555 1.35 LINK C ALA B 91 N NLE B 92 1555 1555 1.33 LINK C NLE B 92 N VAL B 93 1555 1555 1.35 LINK CE NLE B 92 CE NLE B 96 1555 1555 1.49 LINK C ASP B 95 N NLE B 96 1555 1555 1.29 LINK C NLE B 96 N NLE B 97 1555 1555 1.28 LINK C NLE B 97 N ASP B 98 1555 1555 1.32 SITE 1 AC1 6 ARG A 176 ARG A 187 HOH A 523 HOH A 525 SITE 2 AC1 6 HOH A 539 HOH A 544 SITE 1 AC2 12 ASP A 256 ARG B 88 HIS B 89 LEU B 90 SITE 2 AC2 12 ALA B 91 VAL B 93 GLY B 94 ASP B 95 SITE 3 AC2 12 NLE B 97 ASP B 98 ARG B 99 SER B 100 SITE 1 AC3 12 VAL A 216 ASP A 256 VAL A 265 PHE A 319 SITE 2 AC3 12 NLE B 92 VAL B 93 GLY B 94 ASP B 95 SITE 3 AC3 12 ASP B 98 ARG B 99 SER B 100 ILE B 101 CRYST1 80.830 37.020 56.920 90.00 90.00 90.00 P 21 21 2 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 0.012372 0.000000 0.000000 0.00000 SCALE2 0.000000 0.027012 0.000000 0.00000 SCALE3 0.000000 0.000000 0.017569 0.00000