data_5N2A # _model_server_result.job_id GeIzmXNNvF8ylcSpBIuXVA _model_server_result.datetime_utc '2025-02-27 22:38:50' _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 5n2a # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"E","auth_seq_id":602}' # _entry.id 5N2A # _exptl.entry_id 5N2A _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 1 _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 5N2A _cell.length_a 127.699 _cell.length_b 127.699 _cell.length_c 160.376 _cell.Z_PDB 6 _cell.pdbx_unique_axis ? # _symmetry.entry_id 5N2A _symmetry.cell_setting ? _symmetry.Int_Tables_number 154 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 32 2 1' # _pdbx_struct_assembly.method_details PISA _pdbx_struct_assembly.oligomeric_details hexameric _pdbx_struct_assembly.oligomeric_count 6 _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 _pdbx_struct_assembly_gen.assembly_id 1 _pdbx_struct_assembly_gen.oper_expression 1,2 # loop_ _pdbx_struct_oper_list.id _pdbx_struct_oper_list.type _pdbx_struct_oper_list.name _pdbx_struct_oper_list.symmetry_operation _pdbx_struct_oper_list.matrix[1][1] _pdbx_struct_oper_list.matrix[1][2] _pdbx_struct_oper_list.matrix[1][3] _pdbx_struct_oper_list.matrix[2][1] _pdbx_struct_oper_list.matrix[2][2] _pdbx_struct_oper_list.matrix[2][3] _pdbx_struct_oper_list.matrix[3][1] _pdbx_struct_oper_list.matrix[3][2] _pdbx_struct_oper_list.matrix[3][3] _pdbx_struct_oper_list.vector[1] _pdbx_struct_oper_list.vector[2] _pdbx_struct_oper_list.vector[3] 1 'identity operation' 1_555 x,y,z 1 0 0 0 1 0 0 0 1 0 0 0 2 'crystal symmetry operation' 5_555 x-y,-y,-z+1/3 1 0 0 0 -1 0 0 0 -1 0 0 53.458667 # _struct_asym.details ? _struct_asym.entity_id 5 _struct_asym.id E _struct_asym.pdbx_modified N _struct_asym.pdbx_blank_PDB_chainid_flag 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 ? ? ? ? ? ? ? ? ? ? ? ? 1.359 ? 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 ? ? ? ? ? ? ? ? ? ? ? ? 1.331 ? covale ? covale4 A C AGM 274 A AGM 274 1_555 A N ALA 275 A ALA 275 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.364 ? covale ? covale5 A C SER 401 A SER 401 1_555 A N MGN 402 A MGN 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.362 ? covale ? covale6 A C MGN 402 A MGN 402 1_555 A N ARG 403 A ARG 403 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.355 ? covale ? covale7 A C GLY 428 A GLY 428 1_555 A N TRX 429 A TRX 429 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.343 ? 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 ? ? ? ? ? ? ? ? ? ? ? ? 1.349 ? covale ? covale10 A C GL3 447 A GL3 447 1_555 A N TYR 448 A TYR 448 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.337 ? metalc ? metalc1 A OE1 GLN 150 A GLN 150 1_555 F NI F43 . A F43 603 5_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.196 ? metalc ? metalc2 A O GLY 218 A GLY 218 1_555 G K K . A K 604 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.705 ? metalc ? metalc3 A O GLY 218 A GLY 218 1_555 G K K . A K 604 5_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.732 ? metalc ? metalc4 A O ARG 219 A ARG 219 1_555 G K K . A K 604 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 3.178 ? metalc ? metalc5 A O ARG 219 A ARG 219 1_555 G K K . A K 604 5_555 ? ? ? ? ? ? ? ? ? ? ? ? 3.155 ? metalc ? metalc6 A O CYS 221 A CYS 221 1_555 G K K . A K 604 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.783 ? metalc ? metalc7 A O CYS 221 A CYS 221 1_555 G K K . A K 604 5_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.762 ? # _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 521 n n N C1 TP7 sing 522 n n P O1P TP7 doub 523 n n P O2P TP7 sing 524 n n P O3P TP7 sing 525 n n P O4P TP7 sing 526 n n O4P CB TP7 sing 527 n n CB CA TP7 sing 528 n n CB CG TP7 sing 529 n n C O TP7 sing 530 n n C OXT TP7 doub 531 n n C CA TP7 sing 532 n n O1 C1 TP7 doub 533 n n C1 C2 TP7 sing 534 n n C2 C3 TP7 sing 535 n n C3 C4 TP7 sing 536 n n C4 C5 TP7 sing 537 n n C5 C6 TP7 sing 538 n n C6 C7 TP7 sing 539 n n C7 S7 TP7 sing 540 n n N H TP7 sing 541 n n CA HA TP7 sing 542 n n O2P H2P TP7 sing 543 n n O3P H3P TP7 sing 544 n n CB HB TP7 sing 545 n n CG HG1C TP7 sing 546 n n CG HG2C TP7 sing 547 n n CG HG3C TP7 sing 548 n n O HC TP7 sing 549 n n C2 H21C TP7 sing 550 n n C2 H22C TP7 sing 551 n n C3 H31C TP7 sing 552 n n C3 H32C TP7 sing 553 n n C4 H41C TP7 sing 554 n n C4 H42C TP7 sing 555 n n C5 H51C TP7 sing 556 n n C5 H52C TP7 sing 557 n n C6 H61C TP7 sing 558 n n C6 H62C TP7 sing 559 n n C7 H71C TP7 sing 560 n n C7 H72C TP7 sing 561 n n S7 H7 TP7 sing 562 n n # _atom_sites.entry_id 5N2A _atom_sites.fract_transf_matrix[1][1] 0.007831 _atom_sites.fract_transf_matrix[1][2] 0.004521 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.009042 _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] 0.006235 _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 D 4 COM A 1 601 553 COM COM . E 5 TP7 A 1 602 554 TP7 TP7 . F 6 F43 A 1 603 555 F43 F43 . G 7 K A 1 604 1 K K . H 8 BR C 1 301 1 BR BR . # 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 . . . E 5 -36.021 3.278 12.557 1 83.73 ? N TP7 602 A 1 HETATM 2 P P TP7 . . . E 5 -38.726 -0.087 11.584 1 89.53 ? P TP7 602 A 1 HETATM 3 O O1P TP7 . . . E 5 -39.816 0.163 10.567 1 90.95 ? O1P TP7 602 A 1 HETATM 4 O O2P TP7 . . . E 5 -39.305 -0.371 12.955 1 88.54 ? O2P TP7 602 A 1 HETATM 5 O O3P TP7 . . . E 5 -37.85 -1.227 11.121 1 89.67 ? O3P TP7 602 A 1 HETATM 6 O O4P TP7 . . . E 5 -37.801 1.229 11.664 1 88.23 ? O4P TP7 602 A 1 HETATM 7 C CB TP7 . . . E 5 -38.301 2.449 12.203 1 86.14 ? CB TP7 602 A 1 HETATM 8 C C TP7 . . . E 5 -37.196 2.158 14.426 1 82.42 ? C TP7 602 A 1 HETATM 9 O O TP7 . . . E 5 -38.011 2.347 15.361 1 82.16 ? O TP7 602 A 1 HETATM 10 O OXT TP7 . . . E 5 -36.311 1.269 14.468 1 80.96 ? OXT TP7 602 A 1 HETATM 11 C CA TP7 . . . E 5 -37.304 3.038 13.203 1 84.26 ? CA TP7 602 A 1 HETATM 12 C CG TP7 . . . E 5 -38.635 3.388 11.048 1 85.74 ? CG TP7 602 A 1 HETATM 13 O O1 TP7 . . . E 5 -36.127 5.53 12.434 1 82.74 ? O1 TP7 602 A 1 HETATM 14 C C1 TP7 . . . E 5 -35.486 4.487 12.392 1 82.72 ? C1 TP7 602 A 1 HETATM 15 C C2 TP7 . . . E 5 -33.997 4.48 12.131 1 81.75 ? C2 TP7 602 A 1 HETATM 16 C C3 TP7 . . . E 5 -33.39 5.877 12.196 1 81.35 ? C3 TP7 602 A 1 HETATM 17 C C4 TP7 . . . E 5 -31.91 5.855 11.824 1 81.2 ? C4 TP7 602 A 1 HETATM 18 C C5 TP7 . . . E 5 -31.645 5.719 10.325 1 81.2 ? C5 TP7 602 A 1 HETATM 19 C C6 TP7 . . . E 5 -32.348 6.765 9.466 1 81.91 ? C6 TP7 602 A 1 HETATM 20 C C7 TP7 . . . E 5 -31.672 8.123 9.59 1 82.61 ? C7 TP7 602 A 1 HETATM 21 S S7 TP7 . . . E 5 -32.367 9.217 8.337 1 83.52 ? S7 TP7 602 A 1 # _model_server_stats.io_time_ms 0 _model_server_stats.parse_time_ms 16 _model_server_stats.create_model_time_ms 14 _model_server_stats.query_time_ms 399 _model_server_stats.encode_time_ms 3 _model_server_stats.element_count 21 #