data_5N28 # _model_server_result.job_id YaDbrIyBsFZaV1X5TRbUjw _model_server_result.datetime_utc '2024-11-04 23:08:44' _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 5n28 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"I","auth_seq_id":603}' # _entry.id 5N28 # _exptl.entry_id 5N28 _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 343.334 _entity.id 5 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description 'Coenzyme B' _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 107.8 _cell.angle_gamma 90 _cell.entry_id 5N28 _cell.length_a 103.68 _cell.length_b 81.16 _cell.length_c 154.95 _cell.Z_PDB 4 _cell.pdbx_unique_axis ? # _symmetry.entry_id 5N28 _symmetry.cell_setting ? _symmetry.Int_Tables_number 4 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 1 21 1' # _pdbx_struct_assembly.method_details PISA _pdbx_struct_assembly.oligomeric_details hexameric _pdbx_struct_assembly.oligomeric_count 6 _pdbx_struct_assembly.details 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,N,O,P,Q,R _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 ? 5 H N N ? 5 I 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 covale ? covale1 A C LYS 259 A LYS 259 1_555 A N MHS 260 A MHS 260 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.353 ? covale ? covale2 A C MHS 260 A MHS 260 1_555 A N ALA 261 A ALA 261 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.349 ? covale ? covale3 A C ARG 273 A ARG 273 1_555 A N AGM 274 A AGM 274 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.335 ? covale ? covale4 A C AGM 274 A AGM 274 1_555 A N ALA 275 A ALA 275 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.347 ? covale ? covale5 A C SER 401 A SER 401 1_555 A N MGN 402 A MGN 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.366 ? covale ? covale6 A C MGN 402 A MGN 402 1_555 A N ARG 403 A ARG 403 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.353 ? covale ? covale7 A C GLY 428 A GLY 428 1_555 A N TRX 429 A TRX 429 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.342 ? covale ? covale8 A C TRX 429 A TRX 429 1_555 A N TYR 430 A TYR 430 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.348 ? covale ? covale9 A C TYR 446 A TYR 446 1_555 A N GL3 447 A GL3 447 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.342 ? covale ? covale10 A C GL3 447 A GL3 447 1_555 A N TYR 448 A TYR 448 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.336 ? covale ? covale11 D C LYS 259 D LYS 259 1_555 D N MHS 260 D MHS 260 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.349 ? covale ? covale12 D C MHS 260 D MHS 260 1_555 D N ALA 261 D ALA 261 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.344 ? covale ? covale13 D C ARG 273 D ARG 273 1_555 D N AGM 274 D AGM 274 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.331 ? covale ? covale14 D C AGM 274 D AGM 274 1_555 D N ALA 275 D ALA 275 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.349 ? covale ? covale15 D C SER 401 D SER 401 1_555 D N MGN 402 D MGN 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.353 ? covale ? covale16 D C MGN 402 D MGN 402 1_555 D N ARG 403 D ARG 403 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.355 ? covale ? covale17 D C GLY 428 D GLY 428 1_555 D N TRX 429 D TRX 429 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.349 ? covale ? covale18 D C TRX 429 D TRX 429 1_555 D N TYR 430 D TYR 430 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.35 ? covale ? covale19 D C TYR 446 D TYR 446 1_555 D N GL3 447 D GL3 447 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.341 ? covale ? covale20 D C GL3 447 D GL3 447 1_555 D N TYR 448 D TYR 448 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.336 ? metalc ? metalc1 A OE1 GLN 150 A GLN 150 1_555 J NI F43 . A F43 604 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.08 ? metalc ? metalc2 A O GLY 218 A GLY 218 1_555 K K K . A K 605 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.702 ? metalc ? metalc3 A O ARG 219 A ARG 219 1_555 K K K . A K 605 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.897 ? metalc ? metalc4 A O CYS 221 A CYS 221 1_555 K K K . A K 605 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.433 ? metalc ? metalc5 K K K . A K 605 1_555 D O GLY 218 D GLY 218 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.992 ? metalc ? metalc6 K K K . A K 605 1_555 D O ARG 219 D ARG 219 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.972 ? metalc ? metalc7 K K K . A K 605 1_555 D O CYS 221 D CYS 221 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.716 ? metalc ? metalc8 D OE1 GLN 150 D GLN 150 1_555 L NI F43 . D F43 601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.127 ? # _chem_comp.formula 'C11 H22 N O7 P S' _chem_comp.formula_weight 343.334 _chem_comp.id TP7 _chem_comp.mon_nstd_flag . _chem_comp.name 'Coenzyme B' _chem_comp.type non-polymer _chem_comp.pdbx_synonyms 7-MERCAPTOHEPTANOYLTHREONINEPHOSPHATE # 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 N CA TP7 sing 523 n n N C1 TP7 sing 524 n n P O1P TP7 doub 525 n n P O2P TP7 sing 526 n n P O3P TP7 sing 527 n n P O4P TP7 sing 528 n n O4P CB TP7 sing 529 n n CB CA TP7 sing 530 n n CB CG TP7 sing 531 n n C O TP7 sing 532 n n C OXT TP7 doub 533 n n C CA TP7 sing 534 n n O1 C1 TP7 doub 535 n n C1 C2 TP7 sing 536 n n C2 C3 TP7 sing 537 n n C3 C4 TP7 sing 538 n n C4 C5 TP7 sing 539 n n C5 C6 TP7 sing 540 n n C6 C7 TP7 sing 541 n n C7 S7 TP7 sing 542 n n N H TP7 sing 543 n n CA HA TP7 sing 544 n n O2P H2P TP7 sing 545 n n O3P H3P TP7 sing 546 n n CB HB TP7 sing 547 n n CG HG1C TP7 sing 548 n n CG HG2C TP7 sing 549 n n CG HG3C TP7 sing 550 n n O HC TP7 sing 551 n n C2 H21C TP7 sing 552 n n C2 H22C TP7 sing 553 n n C3 H31C TP7 sing 554 n n C3 H32C TP7 sing 555 n n C4 H41C TP7 sing 556 n n C4 H42C TP7 sing 557 n n C5 H51C TP7 sing 558 n n C5 H52C TP7 sing 559 n n C6 H61C TP7 sing 560 n n C6 H62C TP7 sing 561 n n C7 H71C TP7 sing 562 n n C7 H72C TP7 sing 563 n n S7 H7 TP7 sing 564 n n # _atom_sites.entry_id 5N28 _atom_sites.fract_transf_matrix[1][1] 0.009645 _atom_sites.fract_transf_matrix[1][2] 0 _atom_sites.fract_transf_matrix[1][3] 0.003097 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.012321 _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] 0.006778 _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 G 4 COM A 1 601 553 COM COM . H 5 TP7 A 1 602 554 TP7 TP7 . I 5 TP7 A 1 603 554 TP7 TP7 . J 6 F43 A 1 604 555 F43 F43 . K 7 K A 1 605 1 K K . L 6 F43 D 1 601 555 F43 F43 . M 4 COM D 1 602 553 COM COM . N 8 HOH A 1 701 46 HOH HOH . N 8 HOH A 2 702 52 HOH HOH . N 8 HOH A 3 703 15 HOH HOH . N 8 HOH A 4 704 12 HOH HOH . N 8 HOH A 5 705 42 HOH HOH . N 8 HOH A 6 706 31 HOH HOH . N 8 HOH A 7 707 3 HOH HOH . N 8 HOH A 8 708 51 HOH HOH . N 8 HOH A 9 709 30 HOH HOH . O 8 HOH B 1 501 53 HOH HOH . O 8 HOH B 2 502 19 HOH HOH . O 8 HOH B 3 503 40 HOH HOH . O 8 HOH B 4 504 28 HOH HOH . O 8 HOH B 5 505 5 HOH HOH . O 8 HOH B 6 506 48 HOH HOH . O 8 HOH B 7 507 29 HOH HOH . O 8 HOH B 8 508 6 HOH HOH . O 8 HOH B 9 509 54 HOH HOH . P 8 HOH C 1 301 27 HOH HOH . P 8 HOH C 2 302 13 HOH HOH . P 8 HOH C 3 303 55 HOH HOH . Q 8 HOH D 1 701 32 HOH HOH . Q 8 HOH D 2 702 23 HOH HOH . Q 8 HOH D 3 703 21 HOH HOH . Q 8 HOH D 4 704 20 HOH HOH . Q 8 HOH D 5 705 4 HOH HOH . R 8 HOH E 1 501 38 HOH HOH . R 8 HOH E 2 502 35 HOH HOH . # 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 N N TP7 . . . I 5 -0.736 4.882 43.312 1 71.69 ? N TP7 603 A 1 HETATM 2 P P TP7 . . . I 5 -4.194 7.338 44.96 1 75.57 ? P TP7 603 A 1 HETATM 3 O O1P TP7 . . . I 5 -4.274 8.616 44.148 1 76.58 ? O1P TP7 603 A 1 HETATM 4 O O2P TP7 . . . I 5 -4.081 7.629 46.433 1 74.29 ? O2P TP7 603 A 1 HETATM 5 O O3P TP7 . . . I 5 -5.391 6.433 44.721 1 76.32 ? O3P TP7 603 A 1 HETATM 6 O O4P TP7 . . . I 5 -2.861 6.601 44.457 1 75.91 ? O4P TP7 603 A 1 HETATM 7 C CB TP7 . . . I 5 -2.666 5.216 44.722 1 76.06 ? CB TP7 603 A 1 HETATM 8 C C TP7 . . . I 5 -2.936 4.733 42.235 1 76.69 ? C TP7 603 A 1 HETATM 9 O O TP7 . . . I 5 -4.061 4.193 42.117 1 77.78 ? O TP7 603 A 1 HETATM 10 O OXT TP7 . . . I 5 -2.494 5.491 41.337 1 77.26 ? OXT TP7 603 A 1 HETATM 11 C CA TP7 . . . I 5 -2.116 4.484 43.486 1 74.71 ? CA TP7 603 A 1 HETATM 12 C CG TP7 . . . I 5 -1.769 5.118 45.952 1 76.3 ? CG TP7 603 A 1 HETATM 13 O O1 TP7 . . . I 5 0.341 2.938 43.747 1 69.37 ? O1 TP7 603 A 1 HETATM 14 C C1 TP7 . . . I 5 0.286 4.043 43.194 1 69.54 ? C1 TP7 603 A 1 HETATM 15 C C2 TP7 . . . I 5 1.396 4.614 42.358 1 67.94 ? C2 TP7 603 A 1 HETATM 16 C C3 TP7 . . . I 5 2.462 3.603 41.969 1 66.35 ? C3 TP7 603 A 1 HETATM 17 C C4 TP7 . . . I 5 3.558 4.23 41.106 1 65.74 ? C4 TP7 603 A 1 HETATM 18 C C5 TP7 . . . I 5 4.34 5.386 41.747 1 64.7 ? C5 TP7 603 A 1 HETATM 19 C C6 TP7 . . . I 5 5.069 5.063 43.05 1 64.33 ? C6 TP7 603 A 1 HETATM 20 C C7 TP7 . . . I 5 6.303 4.206 42.816 1 65.11 ? C7 TP7 603 A 1 HETATM 21 S S7 TP7 . . . I 5 7.065 3.843 44.41 1 65.5 ? S7 TP7 603 A 1 # _model_server_stats.io_time_ms 36 _model_server_stats.parse_time_ms 11 _model_server_stats.create_model_time_ms 18 _model_server_stats.query_time_ms 261 _model_server_stats.encode_time_ms 17 _model_server_stats.element_count 21 #