data_5CJV
#
_model_server_result.job_id            F_hZaZH-Fb3pyJqDgfY9_A 
_model_server_result.datetime_utc      '2024-11-24 11:27:52' 
_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":"J","auth_seq_id":1102}' 
#
_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 . . . J 4 -251.551 -65.345 -28.097 1 171.6 ? O9 IVC 1102 B 1 
HETATM 2 P P1 IVC . . . J 4 -251.749 -66.781 -27.607 1 171.6 ? P1 IVC 1102 B 1 
HETATM 3 O O5 IVC . . . J 4 -251.906 -67.756 -28.73 1 170.69 ? O5 IVC 1102 B 1 
HETATM 4 O O6 IVC . . . J 4 -252.932 -66.801 -26.637 1 171.78 ? O6 IVC 1102 B 1 
HETATM 5 O O2 IVC . . . J 4 -250.442 -67.139 -26.729 1 151.55 ? O2 IVC 1102 B 1 
HETATM 6 C C1 IVC . . . J 4 -250.259 -68.309 -25.904 1 149.44 ? C1 IVC 1102 B 1 
HETATM 7 C C2 IVC . . . J 4 -249.069 -69.139 -26.381 1 147.47 ? C2 IVC 1102 B 1 
HETATM 8 O O3 IVC . . . J 4 -248.998 -69.155 -27.803 1 147.52 ? O3 IVC 1102 B 1 
HETATM 9 C C4 IVC . . . J 4 -247.91 -68.339 -25.787 1 145.99 ? C4 IVC 1102 B 1 
HETATM 10 N N1 IVC . . . J 4 -246.709 -69.128 -25.53 1 142.14 ? N1 IVC 1102 B 1 
HETATM 11 C C7 IVC . . . J 4 -246.623 -70.282 -24.795 1 140.53 ? C7 IVC 1102 B 1 
HETATM 12 N N2 IVC . . . J 4 -245.413 -70.781 -24.721 1 138.05 ? N2 IVC 1102 B 1 
HETATM 13 C C8 IVC . . . J 4 -244.646 -69.893 -25.461 1 136.25 ? C8 IVC 1102 B 1 
HETATM 14 C C6 IVC . . . J 4 -245.431 -68.87 -25.968 1 138.44 ? C6 IVC 1102 B 1 
HETATM 15 N N3 IVC . . . J 4 -245.021 -67.844 -26.722 1 136.14 ? N3 IVC 1102 B 1 
HETATM 16 C C15 IVC . . . J 4 -243.706 -67.913 -26.949 1 133.9 ? C15 IVC 1102 B 1 
HETATM 17 N N4 IVC . . . J 4 -242.828 -68.831 -26.53 1 132.07 ? N4 IVC 1102 B 1 
HETATM 18 C C12 IVC . . . J 4 -243.273 -69.856 -25.77 1 132.39 ? C12 IVC 1102 B 1 
HETATM 19 N N5 IVC . . . J 4 -242.392 -70.771 -25.358 1 130.38 ? N5 IVC 1102 B 1 
HETATM 20 O O1 IVC . . . J 4 -248.372 -67.819 -24.553 1 148.18 ? O1 IVC 1102 B 1 
HETATM 21 C C3 IVC . . . J 4 -249.818 -67.811 -24.527 1 149.16 ? C3 IVC 1102 B 1 
HETATM 22 C C5 IVC . . . J 4 -250.311 -68.616 -23.349 1 149.65 ? C5 IVC 1102 B 1 
HETATM 23 O O4 IVC . . . J 4 -249.725 -69.934 -23.381 1 150.34 ? O4 IVC 1102 B 1 
HETATM 24 P P2 IVC . . . J 4 -250.484 -71.21 -22.788 1 185.15 ? P2 IVC 1102 B 1 
HETATM 25 O O12 IVC . . . J 4 -249.776 -71.614 -21.496 1 185.07 ? O12 IVC 1102 B 1 
HETATM 26 O O10 IVC . . . J 4 -250.519 -72.37 -23.711 1 183.38 ? O10 IVC 1102 B 1 
HETATM 27 O O7 IVC . . . J 4 -251.971 -70.771 -22.417 1 183.08 ? O7 IVC 1102 B 1 
#
_model_server_stats.io_time_ms              37 
_model_server_stats.parse_time_ms           15 
_model_server_stats.create_model_time_ms    25 
_model_server_stats.query_time_ms           283 
_model_server_stats.encode_time_ms          5 
_model_server_stats.element_count           27 
#