HEADER DE NOVO PROTEIN 18-MAR-20 6W70 TITLE CRYSTAL STRUCTURE OF APIXABAN-BOUND ABLE COMPND MOL_ID: 1; COMPND 2 MOLECULE: DE NOVO DESIGNED ABLE; COMPND 3 CHAIN: A, C; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: SYNTHETIC CONSTRUCT; SOURCE 3 ORGANISM_TAXID: 32630; SOURCE 4 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 5 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 6 EXPRESSION_SYSTEM_STRAIN: BL21(DE3); SOURCE 7 EXPRESSION_SYSTEM_VECTOR_TYPE: BL21(DE3); SOURCE 8 EXPRESSION_SYSTEM_PLASMID: PET11 KEYWDS 4-HELIX BUNDLE, DE NOVO, LIGAND-BINDING, DE NOVO PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR N.F.POLIZZI REVDAT 4 03-APR-24 6W70 1 REMARK REVDAT 3 06-MAR-24 6W70 1 REMARK REVDAT 2 23-SEP-20 6W70 1 JRNL REVDAT 1 26-AUG-20 6W70 0 JRNL AUTH N.F.POLIZZI,W.F.DEGRADO JRNL TITL A DEFINED STRUCTURAL UNIT ENABLES DE NOVO DESIGN OF JRNL TITL 2 SMALL-MOLECULE-BINDING PROTEINS. JRNL REF SCIENCE V. 369 1227 2020 JRNL REFN ESSN 1095-9203 JRNL PMID 32883865 JRNL DOI 10.1126/SCIENCE.ABB8330 REMARK 2 REMARK 2 RESOLUTION. 1.30 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.16_3549 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) : 1.30 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 41.26 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.360 REMARK 3 COMPLETENESS FOR RANGE (%) : 98.8 REMARK 3 NUMBER OF REFLECTIONS : 54876 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.162 REMARK 3 R VALUE (WORKING SET) : 0.161 REMARK 3 FREE R VALUE : 0.183 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.920 REMARK 3 FREE R VALUE TEST SET COUNT : 2702 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 41.2590 - 3.4563 1.00 2850 136 0.1619 0.1627 REMARK 3 2 3.4563 - 2.7435 1.00 2808 139 0.1587 0.1610 REMARK 3 3 2.7435 - 2.3968 1.00 2788 137 0.1463 0.1478 REMARK 3 4 2.3968 - 2.1777 1.00 2780 146 0.1358 0.1756 REMARK 3 5 2.1777 - 2.0216 1.00 2801 152 0.1464 0.1610 REMARK 3 6 2.0216 - 1.9024 1.00 2759 150 0.1477 0.1752 REMARK 3 7 1.9024 - 1.8071 1.00 2781 142 0.1519 0.1981 REMARK 3 8 1.8071 - 1.7284 1.00 2774 142 0.1477 0.1965 REMARK 3 9 1.7284 - 1.6619 1.00 2756 139 0.1483 0.1894 REMARK 3 10 1.6619 - 1.6046 1.00 2789 136 0.1447 0.2059 REMARK 3 11 1.6046 - 1.5544 1.00 2807 145 0.1516 0.1882 REMARK 3 12 1.5544 - 1.5100 1.00 2735 164 0.1546 0.1953 REMARK 3 13 1.5100 - 1.4702 1.00 2764 126 0.1561 0.2064 REMARK 3 14 1.4702 - 1.4343 1.00 2793 137 0.1611 0.1870 REMARK 3 15 1.4343 - 1.4017 1.00 2759 147 0.1702 0.2325 REMARK 3 16 1.4017 - 1.3719 1.00 2797 141 0.1852 0.2653 REMARK 3 17 1.3719 - 1.3444 1.00 2701 143 0.2681 0.3107 REMARK 3 18 1.3444 - 1.3191 0.97 2700 157 0.3805 0.3686 REMARK 3 19 1.3191 - 1.2960 0.80 2232 123 0.5274 0.5236 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) : 0.180 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 19.330 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 20.10 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 : NULL NULL REMARK 3 ANGLE : NULL NULL REMARK 3 CHIRALITY : NULL NULL REMARK 3 PLANARITY : NULL NULL REMARK 3 DIHEDRAL : NULL NULL 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 6W70 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 19-MAR-20. REMARK 100 THE DEPOSITION ID IS D_1000247724. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 24-JUL-19 REMARK 200 TEMPERATURE (KELVIN) : 100 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 : 24-ID-E REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.97918 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS EIGER X 16M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : SCALA 3.3.22 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 54993 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.292 REMARK 200 RESOLUTION RANGE LOW (A) : 41.259 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 97.5 REMARK 200 DATA REDUNDANCY : 10.70 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : 0.11100 REMARK 200 FOR THE DATA SET : 27.9000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.29 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.35 REMARK 200 COMPLETENESS FOR SHELL (%) : 82.6 REMARK 200 DATA REDUNDANCY IN SHELL : 4.00 REMARK 200 R MERGE FOR SHELL (I) : 0.59500 REMARK 200 R SYM FOR SHELL (I) : 0.59500 REMARK 200 FOR SHELL : 1.100 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: DESIGNED MODEL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 40.32 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.06 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 2.6 M AMSO4, 0.1 M NA ACETATE, VAPOR REMARK 280 DIFFUSION, HANGING DROP, TEMPERATURE 298K 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 39.22250 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: MONOMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 APPLY THE FOLLOWING TO CHAINS: A 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: MONOMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 APPLY THE FOLLOWING TO CHAINS: 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 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 GLU A 51 CD OE1 OE2 REMARK 470 GLU A 102 CD OE1 OE2 REMARK 470 GLN A 106 CD OE1 NE2 REMARK 470 LYS A 124 CE NZ REMARK 470 VAL C 2 CG1 CG2 REMARK 470 LYS C 3 CG CD CE NZ REMARK 470 GLU C 5 CD OE1 OE2 REMARK 470 GLU C 58 CD OE1 OE2 REMARK 470 LYS C 59 CG CD CE NZ REMARK 470 ARG C 62 CZ NH1 NH2 REMARK 470 GLU C 63 CG CD OE1 OE2 REMARK 470 GLN C 106 CD OE1 NE2 REMARK 470 LYS C 110 CD CE NZ REMARK 470 LYS C 124 CE NZ 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 560 DISTANCE = 5.96 ANGSTROMS REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue SO4 A 301 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue ACT A 302 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue GG2 A 303 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue ACT A 304 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue GG2 C 201 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 6W6X RELATED DB: PDB REMARK 900 APO-STRUCTURE OF ABLE DBREF 6W70 A 1 126 PDB 6W70 6W70 1 126 DBREF 6W70 C 1 126 PDB 6W70 6W70 1 126 SEQRES 1 A 126 SER VAL LYS SER GLU TYR ALA GLU ALA ALA ALA VAL GLY SEQRES 2 A 126 GLN GLU ALA VAL ALA VAL PHE ASN THR MET LYS ALA ALA SEQRES 3 A 126 PHE GLN ASN GLY ASP LYS GLU ALA VAL ALA GLN TYR LEU SEQRES 4 A 126 ALA ARG LEU ALA SER LEU TYR THR ARG HIS GLU GLU LEU SEQRES 5 A 126 LEU ASN ARG ILE LEU GLU LYS ALA ARG ARG GLU GLY ASN SEQRES 6 A 126 LYS GLU ALA VAL THR LEU MET ASN GLU PHE THR ALA THR SEQRES 7 A 126 PHE GLN THR GLY LYS SER ILE PHE ASN ALA MET VAL ALA SEQRES 8 A 126 ALA PHE LYS ASN GLY ASP ASP ASP SER PHE GLU SER TYR SEQRES 9 A 126 LEU GLN ALA LEU GLU LYS VAL THR ALA LYS GLY GLU THR SEQRES 10 A 126 LEU ALA ASP GLN ILE ALA LYS ALA LEU SEQRES 1 C 126 SER VAL LYS SER GLU TYR ALA GLU ALA ALA ALA VAL GLY SEQRES 2 C 126 GLN GLU ALA VAL ALA VAL PHE ASN THR MET LYS ALA ALA SEQRES 3 C 126 PHE GLN ASN GLY ASP LYS GLU ALA VAL ALA GLN TYR LEU SEQRES 4 C 126 ALA ARG LEU ALA SER LEU TYR THR ARG HIS GLU GLU LEU SEQRES 5 C 126 LEU ASN ARG ILE LEU GLU LYS ALA ARG ARG GLU GLY ASN SEQRES 6 C 126 LYS GLU ALA VAL THR LEU MET ASN GLU PHE THR ALA THR SEQRES 7 C 126 PHE GLN THR GLY LYS SER ILE PHE ASN ALA MET VAL ALA SEQRES 8 C 126 ALA PHE LYS ASN GLY ASP ASP ASP SER PHE GLU SER TYR SEQRES 9 C 126 LEU GLN ALA LEU GLU LYS VAL THR ALA LYS GLY GLU THR SEQRES 10 C 126 LEU ALA ASP GLN ILE ALA LYS ALA LEU HET SO4 A 301 5 HET ACT A 302 7 HET GG2 A 303 59 HET ACT A 304 7 HET GG2 C 201 59 HETNAM SO4 SULFATE ION HETNAM ACT ACETATE ION HETNAM GG2 1-(4-METHOXYPHENYL)-7-OXO-6-[4-(2-OXOPIPERIDIN-1-YL) HETNAM 2 GG2 PHENYL]-4,5,6,7-TETRAHYDRO-1H-PYRAZOLO[3,4-C]PYRIDINE- HETNAM 3 GG2 3-CARBOXAMIDE FORMUL 3 SO4 O4 S 2- FORMUL 4 ACT 2(C2 H3 O2 1-) FORMUL 5 GG2 2(C25 H25 N5 O4) FORMUL 8 HOH *272(H2 O) HELIX 1 AA1 SER A 1 ASN A 29 1 29 HELIX 2 AA2 ASP A 31 GLU A 63 1 33 HELIX 3 AA3 ASN A 65 GLY A 96 1 32 HELIX 4 AA4 ASP A 97 LEU A 126 1 30 HELIX 5 AA5 VAL C 2 ASN C 29 1 28 HELIX 6 AA6 ASP C 31 GLU C 63 1 33 HELIX 7 AA7 ASN C 65 ASN C 95 1 31 HELIX 8 AA8 ASP C 97 LEU C 126 1 30 SITE 1 AC1 4 THR A 70 ASN A 73 HOH A 418 HOH A 467 SITE 1 AC2 3 SER A 84 ASN A 87 HOH A 435 SITE 1 AC3 15 TYR A 6 ALA A 10 GLY A 13 GLN A 14 SITE 2 AC3 15 TYR A 46 HIS A 49 ILE A 56 PHE A 75 SITE 3 AC3 15 PHE A 79 THR A 112 GLU A 116 ALA A 119 SITE 4 AC3 15 HOH A 408 HOH A 444 HOH A 509 SITE 1 AC4 6 ALA A 91 LYS A 94 ASN A 95 HOH A 433 SITE 2 AC4 6 HOH A 490 LYS C 94 SITE 1 AC5 15 TYR C 6 ALA C 10 GLY C 13 GLN C 14 SITE 2 AC5 15 TYR C 46 HIS C 49 ILE C 56 PHE C 75 SITE 3 AC5 15 THR C 112 GLY C 115 GLU C 116 ALA C 119 SITE 4 AC5 15 HOH C 310 HOH C 339 HOH C 371 CRYST1 35.194 78.445 43.133 90.00 106.95 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 0.028414 0.000000 0.008662 0.00000 SCALE2 0.000000 0.012748 0.000000 0.00000 SCALE3 0.000000 0.000000 0.024237 0.00000