data_5CJV # _model_server_result.job_id TmzaaW_ThNPckFDEWB4wcQ _model_server_result.datetime_utc '2024-11-24 12:09:18' _model_server_result.server_version 0.9.12 _model_server_result.query_name ligand _model_server_result.source_id pdb-bcif _model_server_result.entry_id 5cjv # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"E","auth_seq_id":1103}' # _entry.id 5CJV # _exptl.entry_id 5CJV _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 851.651 _entity.id 4 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description 'Isovaleryl-coenzyme A' _entity.pdbx_number_of_molecules 2 _entity.pdbx_parent_entity_id . _entity.pdbx_mutation ? _entity.pdbx_fragment ? _entity.pdbx_ec ? # _cell.angle_alpha 90 _cell.angle_beta 90 _cell.angle_gamma 120 _cell.entry_id 5CJV _cell.length_a 317.56 _cell.length_b 317.56 _cell.length_c 343.52 _cell.Z_PDB 36 _cell.pdbx_unique_axis ? # _symmetry.entry_id 5CJV _symmetry.cell_setting ? _symmetry.Int_Tables_number 155 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'H 3 2' # _pdbx_struct_assembly.method_details PISA _pdbx_struct_assembly.oligomeric_details dimeric _pdbx_struct_assembly.oligomeric_count 2 _pdbx_struct_assembly.details author_and_software_defined_assembly _pdbx_struct_assembly.id 1 # _pdbx_struct_assembly_gen.asym_id_list A,B,C,D,E,F,G,H,I,J,K,L,M _pdbx_struct_assembly_gen.assembly_id 1 _pdbx_struct_assembly_gen.oper_expression 1 # _pdbx_struct_oper_list.id 1 _pdbx_struct_oper_list.type 'identity operation' _pdbx_struct_oper_list.name 1_555 _pdbx_struct_oper_list.symmetry_operation x,y,z _pdbx_struct_oper_list.matrix[1][1] 1 _pdbx_struct_oper_list.matrix[1][2] 0 _pdbx_struct_oper_list.matrix[1][3] 0 _pdbx_struct_oper_list.matrix[2][1] 0 _pdbx_struct_oper_list.matrix[2][2] 1 _pdbx_struct_oper_list.matrix[2][3] 0 _pdbx_struct_oper_list.matrix[3][1] 0 _pdbx_struct_oper_list.matrix[3][2] 0 _pdbx_struct_oper_list.matrix[3][3] 1 _pdbx_struct_oper_list.vector[1] 0 _pdbx_struct_oper_list.vector[2] 0 _pdbx_struct_oper_list.vector[3] 0 # loop_ _struct_asym.details _struct_asym.entity_id _struct_asym.id _struct_asym.pdbx_modified _struct_asym.pdbx_blank_PDB_chainid_flag ? 4 E N N ? 4 J N N # loop_ _struct_conn.conn_type_id _struct_conn.details _struct_conn.id _struct_conn.ptnr1_label_asym_id _struct_conn.ptnr1_label_atom_id _struct_conn.ptnr1_label_comp_id _struct_conn.ptnr1_label_seq_id _struct_conn.ptnr1_auth_asym_id _struct_conn.ptnr1_auth_comp_id _struct_conn.ptnr1_auth_seq_id _struct_conn.ptnr1_symmetry _struct_conn.ptnr2_label_asym_id _struct_conn.ptnr2_label_atom_id _struct_conn.ptnr2_label_comp_id _struct_conn.ptnr2_label_seq_id _struct_conn.ptnr2_auth_asym_id _struct_conn.ptnr2_auth_comp_id _struct_conn.ptnr2_auth_seq_id _struct_conn.ptnr2_symmetry _struct_conn.pdbx_ptnr1_PDB_ins_code _struct_conn.pdbx_ptnr1_label_alt_id _struct_conn.pdbx_ptnr1_standard_comp_id _struct_conn.pdbx_ptnr2_PDB_ins_code _struct_conn.pdbx_ptnr2_label_alt_id _struct_conn.pdbx_ptnr3_PDB_ins_code _struct_conn.pdbx_ptnr3_label_alt_id _struct_conn.pdbx_ptnr3_label_asym_id _struct_conn.pdbx_ptnr3_label_atom_id _struct_conn.pdbx_ptnr3_label_comp_id _struct_conn.pdbx_ptnr3_label_seq_id _struct_conn.pdbx_PDB_id _struct_conn.pdbx_dist_value _struct_conn.pdbx_value_order metalc ? metalc1 A NE2 HIS 59 A HIS 39 1_555 C CO B12 . A B12 1101 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.423 ? metalc ? metalc2 A OG SER 243 A SER 223 1_555 G MG MG . A MG 1105 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.043 ? metalc ? metalc3 A OD1 ASP 269 A ASP 249 1_555 H MG MG . A MG 1106 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.708 ? metalc ? metalc4 A OD1 ASP 282 A ASP 262 1_555 G MG MG . A MG 1105 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.145 ? metalc ? metalc5 A OD1 ASP 282 A ASP 262 1_555 H MG MG . A MG 1106 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.843 ? metalc ? metalc6 A OE2 GLU 330 A GLU 310 1_555 G MG MG . A MG 1105 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.684 ? metalc ? metalc7 A OE2 GLU 330 A GLU 310 1_555 H MG MG . A MG 1106 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.629 ? metalc ? metalc8 A O THR 331 A THR 311 1_555 H MG MG . A MG 1106 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.957 ? metalc ? metalc9 C CO B12 . A B12 1101 1_555 D C5' 5AD . A 5AD 1102 1_555 ? ? ? ? B ? ? ? ? ? ? ? 2.181 ? metalc ? metalc10 F O2B GDP . A GDP 1104 1_555 G MG MG . A MG 1105 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.615 ? metalc ? metalc11 F O3B GDP . A GDP 1104 1_555 G MG MG . A MG 1105 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.349 ? metalc ? metalc12 B NE2 HIS 59 B HIS 39 1_555 I CO B12 . B B12 1101 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.455 ? metalc ? metalc13 B OG SER 243 B SER 223 1_555 L MG MG . B MG 1104 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.04 ? metalc ? metalc14 B O ILE 268 B ILE 248 1_555 M MG MG . B MG 1105 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.95 ? metalc ? metalc15 B OD1 ASP 269 B ASP 249 1_555 M MG MG . B MG 1105 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.795 ? metalc ? metalc16 B OD1 ASP 282 B ASP 262 1_555 L MG MG . B MG 1104 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.149 ? metalc ? metalc17 B OD1 ASP 282 B ASP 262 1_555 M MG MG . B MG 1105 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.793 ? metalc ? metalc18 B OD2 ASP 282 B ASP 262 1_555 M MG MG . B MG 1105 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.789 ? metalc ? metalc19 B OE2 GLU 330 B GLU 310 1_555 L MG MG . B MG 1104 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.689 ? metalc ? metalc20 B OE2 GLU 330 B GLU 310 1_555 M MG MG . B MG 1105 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.548 ? metalc ? metalc21 B O THR 331 B THR 311 1_555 M MG MG . B MG 1105 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.814 ? metalc ? metalc22 K O2B GDP . B GDP 1103 1_555 L MG MG . B MG 1104 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.627 ? metalc ? metalc23 K O3B GDP . B GDP 1103 1_555 L MG MG . B MG 1104 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.353 ? # _chem_comp.formula 'C26 H44 N7 O17 P3 S' _chem_comp.formula_weight 851.651 _chem_comp.id IVC _chem_comp.mon_nstd_flag . _chem_comp.name 'Isovaleryl-coenzyme A' _chem_comp.type non-polymer _chem_comp.pdbx_synonyms 'S-[2-[3-[[(2R)-4-[[[(2R,3S,4R,5R)-5-(6-aminopurin-9-yl)-4-oxidanyl-3-phosphonooxy-oxolan-2-yl]methoxy-oxidanyl-phosphoryl]oxy-oxidanyl-phosphoryl]oxy-3,3-dimethyl-2-oxidanyl-butanoyl]amino]propanoylamino]ethyl] 3-methylbutanethioate' # loop_ _chem_comp_bond.atom_id_1 _chem_comp_bond.atom_id_2 _chem_comp_bond.comp_id _chem_comp_bond.value_order _chem_comp_bond.pdbx_ordinal _chem_comp_bond.pdbx_stereo_config _chem_comp_bond.pdbx_aromatic_flag C15 N4 IVC doub 439 n y C15 N3 IVC sing 440 n y N4 C12 IVC sing 441 n y N3 C6 IVC doub 442 n y O3 C2 IVC sing 443 n n O5 P1 IVC doub 444 n n C6 C8 IVC sing 445 n y C6 N1 IVC sing 446 n y C12 N5 IVC sing 447 n n C12 C8 IVC doub 448 n y C2 C4 IVC sing 449 n n C2 C1 IVC sing 450 n n C4 N1 IVC sing 451 n n C4 O1 IVC sing 452 n n C8 N2 IVC sing 453 n y O9 P1 IVC sing 454 n n N1 C7 IVC sing 455 n y P1 O2 IVC sing 456 n n P1 O6 IVC sing 457 n n O2 C1 IVC sing 458 n n C1 C3 IVC sing 459 n n O1 C3 IVC sing 460 n n N2 C7 IVC doub 461 n y C3 C5 IVC sing 462 n n C5 O4 IVC sing 463 n n O4 P2 IVC sing 464 n n O10 P2 IVC doub 465 n n P2 O7 IVC sing 466 n n P2 O12 IVC sing 467 n n O7 P3 IVC sing 468 n n P3 O13 IVC doub 469 n n P3 O14 IVC sing 470 n n P3 O8 IVC sing 471 n n O8 C11 IVC sing 472 n n C13 C9 IVC sing 473 n n C11 C9 IVC sing 474 n n C9 C14 IVC sing 475 n n C9 C10 IVC sing 476 n n C10 O11 IVC sing 477 n n C10 C16 IVC sing 478 n n C16 O15 IVC doub 479 n n C16 N6 IVC sing 480 n n N6 C17 IVC sing 481 n n C17 C18 IVC sing 482 n n C18 C19 IVC sing 483 n n O16 C19 IVC doub 484 n n C19 N7 IVC sing 485 n n N7 C20 IVC sing 486 n n C20 C21 IVC sing 487 n n C21 S1 IVC sing 488 n n S1 C22 IVC sing 489 n n O17 C22 IVC doub 490 n n C22 C23 IVC sing 491 n n C23 C24 IVC sing 492 n n C24 C25 IVC sing 493 n n C24 C26 IVC sing 494 n n O9 H1 IVC sing 495 n n O6 H2 IVC sing 496 n n C1 H3 IVC sing 497 n n C2 H4 IVC sing 498 n n O3 H5 IVC sing 499 n n C4 H6 IVC sing 500 n n C7 H7 IVC sing 501 n n C15 H8 IVC sing 502 n n N5 H9 IVC sing 503 n n N5 H10 IVC sing 504 n n C3 H11 IVC sing 505 n n C5 H12 IVC sing 506 n n C5 H13 IVC sing 507 n n O12 H14 IVC sing 508 n n O14 H15 IVC sing 509 n n C11 H16 IVC sing 510 n n C11 H17 IVC sing 511 n n C13 H18 IVC sing 512 n n C13 H19 IVC sing 513 n n C13 H20 IVC sing 514 n n C14 H21 IVC sing 515 n n C14 H22 IVC sing 516 n n C14 H23 IVC sing 517 n n C10 H24 IVC sing 518 n n O11 H25 IVC sing 519 n n N6 H26 IVC sing 520 n n C17 H27 IVC sing 521 n n C17 H28 IVC sing 522 n n C18 H29 IVC sing 523 n n C18 H30 IVC sing 524 n n N7 H31 IVC sing 525 n n C20 H32 IVC sing 526 n n C20 H33 IVC sing 527 n n C21 H34 IVC sing 528 n n C21 H35 IVC sing 529 n n C23 H36 IVC sing 530 n n C23 H37 IVC sing 531 n n C24 H38 IVC sing 532 n n C25 H39 IVC sing 533 n n C25 H40 IVC sing 534 n n C25 H41 IVC sing 535 n n C26 H42 IVC sing 536 n n C26 H43 IVC sing 537 n n C26 H44 IVC sing 538 n n # _atom_sites.entry_id 5CJV _atom_sites.fract_transf_matrix[1][1] 0.003149 _atom_sites.fract_transf_matrix[1][2] 0.001818 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.003636 _atom_sites.fract_transf_matrix[2][3] 0 _atom_sites.fract_transf_matrix[3][1] 0 _atom_sites.fract_transf_matrix[3][2] 0 _atom_sites.fract_transf_matrix[3][3] 0.002911 _atom_sites.fract_transf_vector[1] 0 _atom_sites.fract_transf_vector[2] 0 _atom_sites.fract_transf_vector[3] 0 # loop_ _pdbx_nonpoly_scheme.asym_id _pdbx_nonpoly_scheme.entity_id _pdbx_nonpoly_scheme.mon_id _pdbx_nonpoly_scheme.pdb_strand_id _pdbx_nonpoly_scheme.ndb_seq_num _pdbx_nonpoly_scheme.pdb_seq_num _pdbx_nonpoly_scheme.auth_seq_num _pdbx_nonpoly_scheme.pdb_mon_id _pdbx_nonpoly_scheme.auth_mon_id _pdbx_nonpoly_scheme.pdb_ins_code C 2 B12 A 1 1101 1198 B12 B12 . D 3 5AD A 1 1102 1199 5AD 5AD . E 4 IVC A 1 1103 1211 IVC IVC . F 5 GDP A 1 1104 1200 GDP GDP . G 6 MG A 1 1105 1 MG MG . H 6 MG A 1 1106 3 MG MG . I 2 B12 B 1 1101 1198 B12 B12 . J 4 IVC B 1 1102 1211 IVC IVC . K 5 GDP B 1 1103 1201 GDP GDP . L 6 MG B 1 1104 2 MG MG . M 6 MG B 1 1105 4 MG MG . # loop_ _atom_site.group_PDB _atom_site.id _atom_site.type_symbol _atom_site.label_atom_id _atom_site.label_comp_id _atom_site.label_seq_id _atom_site.label_alt_id _atom_site.pdbx_PDB_ins_code _atom_site.label_asym_id _atom_site.label_entity_id _atom_site.Cartn_x _atom_site.Cartn_y _atom_site.Cartn_z _atom_site.occupancy _atom_site.B_iso_or_equiv _atom_site.pdbx_formal_charge _atom_site.auth_atom_id _atom_site.auth_comp_id _atom_site.auth_seq_id _atom_site.auth_asym_id _atom_site.pdbx_PDB_model_num HETATM 1 O O9 IVC . . . E 4 -206.289 -101.747 -35.376 1 162.82 ? O9 IVC 1103 A 1 HETATM 2 P P1 IVC . . . E 4 -205.638 -103.094 -35.363 1 163.29 ? P1 IVC 1103 A 1 HETATM 3 O O5 IVC . . . E 4 -205.352 -103.636 -36.766 1 164.6 ? O5 IVC 1103 A 1 HETATM 4 O O6 IVC . . . E 4 -204.333 -103.113 -34.559 1 161.68 ? O6 IVC 1103 A 1 HETATM 5 O O2 IVC . . . E 4 -206.602 -104.178 -34.668 1 126.28 ? O2 IVC 1103 A 1 HETATM 6 C C1 IVC . . . E 4 -208.043 -104.145 -34.582 1 124.96 ? C1 IVC 1103 A 1 HETATM 7 C C2 IVC . . . E 4 -208.671 -104.286 -35.967 1 124.48 ? C2 IVC 1103 A 1 HETATM 8 O O3 IVC . . . E 4 -207.835 -105.066 -36.814 1 125.37 ? O3 IVC 1103 A 1 HETATM 9 C C4 IVC . . . E 4 -209.958 -105.044 -35.627 1 123.53 ? C4 IVC 1103 A 1 HETATM 10 N N1 IVC . . . E 4 -211.117 -104.196 -35.364 1 119.51 ? N1 IVC 1103 A 1 HETATM 11 C C7 IVC . . . E 4 -211.668 -103.917 -34.141 1 119.06 ? C7 IVC 1103 A 1 HETATM 12 N N2 IVC . . . E 4 -212.732 -103.153 -34.194 1 117.67 ? N2 IVC 1103 A 1 HETATM 13 C C8 IVC . . . E 4 -212.893 -102.909 -35.55 1 114.95 ? C8 IVC 1103 A 1 HETATM 14 C C6 IVC . . . E 4 -211.902 -103.542 -36.283 1 115.97 ? C6 IVC 1103 A 1 HETATM 15 N N3 IVC . . . E 4 -211.754 -103.521 -37.612 1 114.7 ? N3 IVC 1103 A 1 HETATM 16 C C15 IVC . . . E 4 -212.711 -102.788 -38.189 1 112.41 ? C15 IVC 1103 A 1 HETATM 17 N N4 IVC . . . E 4 -213.722 -102.128 -37.617 1 110.35 ? N4 IVC 1103 A 1 HETATM 18 C C12 IVC . . . E 4 -213.846 -102.168 -36.272 1 112.35 ? C12 IVC 1103 A 1 HETATM 19 N N5 IVC . . . E 4 -214.861 -101.509 -35.705 1 112.74 ? N5 IVC 1103 A 1 HETATM 20 O O1 IVC . . . E 4 -209.7 -105.817 -34.468 1 124.63 ? O1 IVC 1103 A 1 HETATM 21 C C3 IVC . . . E 4 -208.426 -105.45 -33.894 1 125.66 ? C3 IVC 1103 A 1 HETATM 22 C C5 IVC . . . E 4 -208.551 -105.368 -32.393 1 125.78 ? C5 IVC 1103 A 1 HETATM 23 O O4 IVC . . . E 4 -209.468 -104.308 -32.049 1 124.82 ? O4 IVC 1103 A 1 HETATM 24 P P2 IVC . . . E 4 -209.268 -103.417 -30.737 1 117.41 ? P2 IVC 1103 A 1 HETATM 25 O O12 IVC . . . E 4 -208.199 -103.909 -29.836 1 119.36 ? O12 IVC 1103 A 1 HETATM 26 O O10 IVC . . . E 4 -208.954 -101.988 -31.178 1 115.42 ? O10 IVC 1103 A 1 HETATM 27 O O7 IVC . . . E 4 -210.656 -103.39 -29.954 1 117.1 ? O7 IVC 1103 A 1 HETATM 28 P P3 IVC . . . E 4 -211.025 -103.649 -28.425 1 117.49 ? P3 IVC 1103 A 1 HETATM 29 O O14 IVC . . . E 4 -210.197 -104.753 -27.884 1 116.42 ? O14 IVC 1103 A 1 HETATM 30 O O13 IVC . . . E 4 -212.499 -104.02 -28.355 1 119.63 ? O13 IVC 1103 A 1 HETATM 31 O O8 IVC . . . E 4 -210.835 -102.277 -27.637 1 100.6 ? O8 IVC 1103 A 1 HETATM 32 C C11 IVC . . . E 4 -209.865 -102.218 -26.582 1 99.98 ? C11 IVC 1103 A 1 HETATM 33 C C9 IVC . . . E 4 -209.5 -100.766 -26.28 1 97.97 ? C9 IVC 1103 A 1 HETATM 34 C C13 IVC . . . E 4 -208.685 -100.214 -27.455 1 92.91 ? C13 IVC 1103 A 1 HETATM 35 C C14 IVC . . . E 4 -210.795 -99.958 -26.142 1 97.38 ? C14 IVC 1103 A 1 HETATM 36 C C10 IVC . . . E 4 -208.672 -100.652 -24.975 1 103.48 ? C10 IVC 1103 A 1 HETATM 37 O O11 IVC . . . E 4 -208.4 -99.285 -24.725 1 109.03 ? O11 IVC 1103 A 1 HETATM 38 C C16 IVC . . . E 4 -209.39 -101.261 -23.782 1 101.4 ? C16 IVC 1103 A 1 HETATM 39 O O15 IVC . . . E 4 -209.356 -102.473 -23.588 1 97.5 ? O15 IVC 1103 A 1 HETATM 40 N N6 IVC . . . E 4 -210.026 -100.414 -22.976 1 103.22 ? N6 IVC 1103 A 1 HETATM 41 C C17 IVC . . . E 4 -210.703 -100.844 -21.764 1 104.61 ? C17 IVC 1103 A 1 HETATM 42 C C18 IVC . . . E 4 -210.209 -100.088 -20.552 1 105.56 ? C18 IVC 1103 A 1 HETATM 43 C C19 IVC . . . E 4 -211.093 -100.308 -19.354 1 107.34 ? C19 IVC 1103 A 1 HETATM 44 O O16 IVC . . . E 4 -212.193 -100.844 -19.46 1 108.96 ? O16 IVC 1103 A 1 HETATM 45 N N7 IVC . . . E 4 -210.612 -99.89 -18.188 1 108.22 ? N7 IVC 1103 A 1 HETATM 46 C C20 IVC . . . E 4 -211.361 -100.023 -16.949 1 109.46 ? C20 IVC 1103 A 1 HETATM 47 C C21 IVC . . . E 4 -211.07 -98.9 -15.976 1 108.82 ? C21 IVC 1103 A 1 HETATM 48 S S1 IVC . . . E 4 -212.35 -98.866 -14.693 1 76.41 ? S1 IVC 1103 A 1 HETATM 49 C C22 IVC . . . E 4 -211.746 -97.611 -13.618 1 110.94 ? C22 IVC 1103 A 1 HETATM 50 O O17 IVC . . . E 4 -210.722 -97.016 -13.813 1 107.72 ? O17 IVC 1103 A 1 HETATM 51 C C23 IVC . . . E 4 -212.645 -97.358 -12.437 1 113.05 ? C23 IVC 1103 A 1 HETATM 52 C C24 IVC . . . E 4 -211.899 -97.269 -11.11 1 115.45 ? C24 IVC 1103 A 1 HETATM 53 C C25 IVC . . . E 4 -210.805 -98.311 -10.986 1 117.06 ? C25 IVC 1103 A 1 HETATM 54 C C26 IVC . . . E 4 -211.284 -95.895 -10.976 1 116.45 ? C26 IVC 1103 A 1 # _model_server_stats.io_time_ms 36 _model_server_stats.parse_time_ms 16 _model_server_stats.create_model_time_ms 19 _model_server_stats.query_time_ms 287 _model_server_stats.encode_time_ms 12 _model_server_stats.element_count 54 #