data_6B8B # _model_server_result.job_id WXERnra8xURUIt6CE2LG0g _model_server_result.datetime_utc '2025-01-11 12:02:21' _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 6b8b # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"D","auth_seq_id":303}' # _entry.id 6B8B # _exptl.entry_id 6B8B _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 427.201 _entity.id 4 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description "ADENOSINE-5'-DIPHOSPHATE" _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 101.38 _cell.angle_gamma 90 _cell.entry_id 6B8B _cell.length_a 104.03 _cell.length_b 34.78 _cell.length_c 62.71 _cell.Z_PDB 4 _cell.pdbx_unique_axis ? # _symmetry.entry_id 6B8B _symmetry.cell_setting ? _symmetry.Int_Tables_number 5 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'C 1 2 1' # _pdbx_struct_assembly.method_details PISA _pdbx_struct_assembly.oligomeric_details monomeric _pdbx_struct_assembly.oligomeric_count 1 _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 _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 # _struct_asym.details ? _struct_asym.entity_id 4 _struct_asym.id D _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 metalc ? metalc1 A OG1 THR 42 A THR 43 1_555 B MG MG . A MG 301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.031 ? metalc ? metalc2 B MG MG . A MG 301 1_555 D O2B ADP . A ADP 303 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.074 ? metalc ? metalc3 B MG MG . A MG 301 1_555 E O HOH . A HOH 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.053 ? metalc ? metalc4 B MG MG . A MG 301 1_555 E O HOH . A HOH 418 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.046 ? metalc ? metalc5 B MG MG . A MG 301 1_555 E O HOH . A HOH 433 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.913 ? metalc ? metalc6 B MG MG . A MG 301 1_555 E O HOH . A HOH 446 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.966 ? # _chem_comp.formula 'C10 H15 N5 O10 P2' _chem_comp.formula_weight 427.201 _chem_comp.id ADP _chem_comp.mon_nstd_flag n _chem_comp.name "ADENOSINE-5'-DIPHOSPHATE" _chem_comp.type non-polymer _chem_comp.pdbx_synonyms ? # 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 PB O1B ADP doub 1 n n PB O2B ADP sing 2 n n PB O3B ADP sing 3 n n PB O3A ADP sing 4 n n O2B HOB2 ADP sing 5 n n O3B HOB3 ADP sing 6 n n PA O1A ADP doub 7 n n PA O2A ADP sing 8 n n PA O3A ADP sing 9 n n PA O5' ADP sing 10 n n O2A HOA2 ADP sing 11 n n O5' C5' ADP sing 12 n n C5' C4' ADP sing 13 n n C5' "H5'1" ADP sing 14 n n C5' "H5'2" ADP sing 15 n n C4' O4' ADP sing 16 n n C4' C3' ADP sing 17 n n C4' H4' ADP sing 18 n n O4' C1' ADP sing 19 n n C3' O3' ADP sing 20 n n C3' C2' ADP sing 21 n n C3' H3' ADP sing 22 n n O3' HO3' ADP sing 23 n n C2' O2' ADP sing 24 n n C2' C1' ADP sing 25 n n C2' H2' ADP sing 26 n n O2' HO2' ADP sing 27 n n C1' N9 ADP sing 28 n n C1' H1' ADP sing 29 n n N9 C8 ADP sing 30 n y N9 C4 ADP sing 31 n y C8 N7 ADP doub 32 n y C8 H8 ADP sing 33 n n N7 C5 ADP sing 34 n y C5 C6 ADP sing 35 n y C5 C4 ADP doub 36 n y C6 N6 ADP sing 37 n n C6 N1 ADP doub 38 n y N6 HN61 ADP sing 39 n n N6 HN62 ADP sing 40 n n N1 C2 ADP sing 41 n y C2 N3 ADP doub 42 n y C2 H2 ADP sing 43 n n N3 C4 ADP sing 44 n y # _atom_sites.entry_id 6B8B _atom_sites.fract_transf_matrix[1][1] 0.009613 _atom_sites.fract_transf_matrix[1][2] 0 _atom_sites.fract_transf_matrix[1][3] 0.001935 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.028752 _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] 0.016266 _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 B 2 MG A 1 301 402 MG MG . C 3 CZJ A 1 302 1 CZJ LIG . D 4 ADP A 1 303 1 ADP ADP . E 5 HOH A 1 401 21 HOH HOH . E 5 HOH A 2 402 94 HOH HOH . E 5 HOH A 3 403 45 HOH HOH . E 5 HOH A 4 404 74 HOH HOH . E 5 HOH A 5 405 25 HOH HOH . E 5 HOH A 6 406 100 HOH HOH . E 5 HOH A 7 407 26 HOH HOH . E 5 HOH A 8 408 20 HOH HOH . E 5 HOH A 9 409 101 HOH HOH . E 5 HOH A 10 410 87 HOH HOH . E 5 HOH A 11 411 10 HOH HOH . E 5 HOH A 12 412 84 HOH HOH . E 5 HOH A 13 413 6 HOH HOH . E 5 HOH A 14 414 23 HOH HOH . E 5 HOH A 15 415 58 HOH HOH . E 5 HOH A 16 416 82 HOH HOH . E 5 HOH A 17 417 54 HOH HOH . E 5 HOH A 18 418 22 HOH HOH . E 5 HOH A 19 419 9 HOH HOH . E 5 HOH A 20 420 68 HOH HOH . E 5 HOH A 21 421 43 HOH HOH . E 5 HOH A 22 422 93 HOH HOH . E 5 HOH A 23 423 7 HOH HOH . E 5 HOH A 24 424 12 HOH HOH . E 5 HOH A 25 425 53 HOH HOH . E 5 HOH A 26 426 79 HOH HOH . E 5 HOH A 27 427 8 HOH HOH . E 5 HOH A 28 428 42 HOH HOH . E 5 HOH A 29 429 2 HOH HOH . E 5 HOH A 30 430 30 HOH HOH . E 5 HOH A 31 431 31 HOH HOH . E 5 HOH A 32 432 1 HOH HOH . E 5 HOH A 33 433 4 HOH HOH . E 5 HOH A 34 434 36 HOH HOH . E 5 HOH A 35 435 34 HOH HOH . E 5 HOH A 36 436 38 HOH HOH . E 5 HOH A 37 437 104 HOH HOH . E 5 HOH A 38 438 47 HOH HOH . E 5 HOH A 39 439 57 HOH HOH . E 5 HOH A 40 440 99 HOH HOH . E 5 HOH A 41 441 44 HOH HOH . E 5 HOH A 42 442 98 HOH HOH . E 5 HOH A 43 443 85 HOH HOH . E 5 HOH A 44 444 14 HOH HOH . E 5 HOH A 45 445 28 HOH HOH . E 5 HOH A 46 446 5 HOH HOH . E 5 HOH A 47 447 41 HOH HOH . E 5 HOH A 48 448 13 HOH HOH . E 5 HOH A 49 449 60 HOH HOH . E 5 HOH A 50 450 52 HOH HOH . E 5 HOH A 51 451 65 HOH HOH . E 5 HOH A 52 452 81 HOH HOH . E 5 HOH A 53 453 11 HOH HOH . E 5 HOH A 54 454 50 HOH HOH . E 5 HOH A 55 455 66 HOH HOH . E 5 HOH A 56 456 67 HOH HOH . E 5 HOH A 57 457 27 HOH HOH . E 5 HOH A 58 458 61 HOH HOH . E 5 HOH A 59 459 35 HOH HOH . E 5 HOH A 60 460 95 HOH HOH . E 5 HOH A 61 461 15 HOH HOH . E 5 HOH A 62 462 56 HOH HOH . E 5 HOH A 63 463 88 HOH HOH . E 5 HOH A 64 464 59 HOH HOH . E 5 HOH A 65 465 69 HOH HOH . E 5 HOH A 66 466 63 HOH HOH . E 5 HOH A 67 467 78 HOH HOH . E 5 HOH A 68 468 18 HOH HOH . E 5 HOH A 69 469 24 HOH HOH . E 5 HOH A 70 470 29 HOH HOH . E 5 HOH A 71 471 39 HOH HOH . E 5 HOH A 72 472 37 HOH HOH . E 5 HOH A 73 473 71 HOH HOH . E 5 HOH A 74 474 64 HOH HOH . E 5 HOH A 75 475 3 HOH HOH . E 5 HOH A 76 476 83 HOH HOH . E 5 HOH A 77 477 49 HOH HOH . E 5 HOH A 78 478 72 HOH HOH . E 5 HOH A 79 479 73 HOH HOH . E 5 HOH A 80 480 102 HOH HOH . E 5 HOH A 81 481 105 HOH HOH . E 5 HOH A 82 482 40 HOH HOH . E 5 HOH A 83 483 51 HOH HOH . E 5 HOH A 84 484 97 HOH HOH . E 5 HOH A 85 485 80 HOH HOH . E 5 HOH A 86 486 91 HOH HOH . E 5 HOH A 87 487 19 HOH HOH . E 5 HOH A 88 488 86 HOH HOH . E 5 HOH A 89 489 33 HOH HOH . E 5 HOH A 90 490 32 HOH HOH . E 5 HOH A 91 491 103 HOH HOH . E 5 HOH A 92 492 17 HOH HOH . E 5 HOH A 93 493 46 HOH HOH . E 5 HOH A 94 494 75 HOH HOH . E 5 HOH A 95 495 92 HOH HOH . E 5 HOH A 96 496 96 HOH HOH . E 5 HOH A 97 497 16 HOH HOH . E 5 HOH A 98 498 55 HOH HOH . E 5 HOH A 99 499 90 HOH HOH . E 5 HOH A 100 500 76 HOH HOH . E 5 HOH A 101 501 70 HOH HOH . E 5 HOH A 102 502 89 HOH HOH . E 5 HOH A 103 503 77 HOH HOH . E 5 HOH A 104 504 48 HOH HOH . E 5 HOH A 105 505 62 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 P PB ADP . . . D 4 -16.724 13.894 13.942 1 17.08 ? PB ADP 303 A 1 HETATM 2 O O1B ADP . . . D 4 -17.089 13.564 12.518 1 16.86 ? O1B ADP 303 A 1 HETATM 3 O O2B ADP . . . D 4 -15.958 12.802 14.634 1 15.29 ? O2B ADP 303 A 1 HETATM 4 O O3B ADP . . . D 4 -16.106 15.255 14.12 1 15.82 ? O3B ADP 303 A 1 HETATM 5 P PA ADP . . . D 4 -18.654 13.372 16.036 1 19.69 ? PA ADP 303 A 1 HETATM 6 O O1A ADP . . . D 4 -19.174 11.967 15.8 1 20.11 ? O1A ADP 303 A 1 HETATM 7 O O2A ADP . . . D 4 -17.658 13.602 17.129 1 18.6 ? O2A ADP 303 A 1 HETATM 8 O O3A ADP . . . D 4 -18.182 14.017 14.635 1 15.85 ? O3A ADP 303 A 1 HETATM 9 O O5' ADP . . . D 4 -19.917 14.315 16.378 1 18.38 ? O5' ADP 303 A 1 HETATM 10 C C5' ADP . . . D 4 -21.083 14.377 15.565 1 25.84 ? C5' ADP 303 A 1 HETATM 11 C C4' ADP . . . D 4 -22.084 15.338 16.202 1 27.74 ? C4' ADP 303 A 1 HETATM 12 O O4' ADP . . . D 4 -22.604 14.738 17.387 1 27.48 ? O4' ADP 303 A 1 HETATM 13 C C3' ADP . . . D 4 -21.46 16.656 16.628 1 31.8 ? C3' ADP 303 A 1 HETATM 14 O O3' ADP . . . D 4 -22.369 17.726 16.356 1 27.24 ? O3' ADP 303 A 1 HETATM 15 C C2' ADP . . . D 4 -21.277 16.544 18.122 1 33.77 ? C2' ADP 303 A 1 HETATM 16 O O2' ADP . . . D 4 -21.376 17.813 18.776 1 38.96 ? O2' ADP 303 A 1 HETATM 17 C C1' ADP . . . D 4 -22.416 15.617 18.5 1 28.54 ? C1' ADP 303 A 1 HETATM 18 N N9 ADP . . . D 4 -22.127 14.817 19.702 1 30.39 ? N9 ADP 303 A 1 HETATM 19 C C8 ADP . . . D 4 -21.092 13.971 19.861 1 35.8 ? C8 ADP 303 A 1 HETATM 20 N N7 ADP . . . D 4 -21.145 13.387 21.085 1 31.91 ? N7 ADP 303 A 1 HETATM 21 C C5 ADP . . . D 4 -22.228 13.862 21.72 1 35.15 ? C5 ADP 303 A 1 HETATM 22 C C6 ADP . . . D 4 -22.867 13.66 23.038 1 31.88 ? C6 ADP 303 A 1 HETATM 23 N N6 ADP . . . D 4 -22.33 12.811 23.942 1 44.72 ? N6 ADP 303 A 1 HETATM 24 N N1 ADP . . . D 4 -23.995 14.353 23.297 1 27.82 ? N1 ADP 303 A 1 HETATM 25 C C2 ADP . . . D 4 -24.538 15.205 22.407 1 30.86 ? C2 ADP 303 A 1 HETATM 26 N N3 ADP . . . D 4 -24.01 15.433 21.192 1 34.05 ? N3 ADP 303 A 1 HETATM 27 C C4 ADP . . . D 4 -22.876 14.804 20.802 1 36.53 ? C4 ADP 303 A 1 HETATM 28 H "H5'1" ADP . . . D 4 -21.527 13.384 15.476 1 30.98 ? "H5'1" ADP 303 A 1 HETATM 29 H "H5'2" ADP . . . D 4 -20.82 14.725 14.564 1 30.98 ? "H5'2" ADP 303 A 1 HETATM 30 H H4' ADP . . . D 4 -22.896 15.538 15.489 1 33.26 ? H4' ADP 303 A 1 HETATM 31 H H3' ADP . . . D 4 -20.492 16.805 16.13 1 38.13 ? H3' ADP 303 A 1 HETATM 32 H HO3' ADP . . . D 4 -21.971 18.565 16.628 1 32.66 ? HO3' ADP 303 A 1 HETATM 33 H H2' ADP . . . D 4 -20.316 16.06 18.343 1 40.49 ? H2' ADP 303 A 1 HETATM 34 H HO2' ADP . . . D 4 -20.678 18.398 18.451 1 46.73 ? HO2' ADP 303 A 1 HETATM 35 H H1' ADP . . . D 4 -23.323 16.218 18.659 1 34.22 ? H1' ADP 303 A 1 HETATM 36 H H8 ADP . . . D 4 -20.326 13.784 19.119 1 42.93 ? H8 ADP 303 A 1 HETATM 37 H HN61 ADP . . . D 4 -22.774 12.682 24.84 1 53.63 ? HN61 ADP 303 A 1 HETATM 38 H HN62 ADP . . . D 4 -21.484 12.305 23.719 1 53.63 ? HN62 ADP 303 A 1 HETATM 39 H H2 ADP . . . D 4 -25.445 15.729 22.681 1 37 ? H2 ADP 303 A 1 # _model_server_stats.io_time_ms 12 _model_server_stats.parse_time_ms 13 _model_server_stats.create_model_time_ms 4 _model_server_stats.query_time_ms 317 _model_server_stats.encode_time_ms 13 _model_server_stats.element_count 39 #