data_4NM0 # _model_server_result.job_id -JBxddMitzr0aFU0tRr-VQ _model_server_result.datetime_utc '2024-11-07 03:37:30' _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 4nm0 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"J","auth_seq_id":408}' # _entry.id 4NM0 # _exptl.entry_id 4NM0 _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 427.201 _entity.id 5 _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 90 _cell.angle_gamma 120 _cell.entry_id 4NM0 _cell.length_a 81.303 _cell.length_b 81.303 _cell.length_c 280.829 _cell.Z_PDB 12 _cell.pdbx_unique_axis ? # _symmetry.entry_id 4NM0 _symmetry.cell_setting ? _symmetry.Int_Tables_number 178 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 61 2 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,N _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 5 _struct_asym.id J _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 OD1 ASN 186 A ASN 186 1_555 I MG MG . A MG 407 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.44 ? metalc ? metalc2 A OD2 ASP 200 A ASP 200 1_555 I MG MG . A MG 407 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.678 ? metalc ? metalc3 H MG MG . A MG 406 1_555 J O1B ADP . A ADP 408 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.048 ? metalc ? metalc4 I MG MG . A MG 407 1_555 J O3B ADP . A ADP 408 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.072 ? metalc ? metalc5 I MG MG . A MG 407 1_555 J O1A ADP . A ADP 408 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.8 ? # _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 4NM0 _atom_sites.fract_transf_matrix[1][1] 0.0123 _atom_sites.fract_transf_matrix[1][2] 0.007101 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.014202 _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] 0.003561 _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 3 GOL A 1 401 1 GOL GOL . D 3 GOL A 1 402 2 GOL GOL . E 3 GOL A 1 403 3 GOL GOL . F 3 GOL A 1 404 5 GOL GOL . G 3 GOL A 1 405 9 GOL GOL . H 4 MG A 1 406 1 MG MG . I 4 MG A 1 407 2 MG MG . J 5 ADP A 1 408 1 ADP ADP . K 6 DTT A 1 409 1 DTT DTT . L 7 CL A 1 410 1 CL CL . M 8 HOH A 1 501 1 HOH HOH . M 8 HOH A 2 502 2 HOH HOH . M 8 HOH A 3 503 3 HOH HOH . M 8 HOH A 4 504 5 HOH HOH . M 8 HOH A 5 505 6 HOH HOH . M 8 HOH A 6 506 7 HOH HOH . M 8 HOH A 7 507 8 HOH HOH . M 8 HOH A 8 508 9 HOH HOH . M 8 HOH A 9 509 10 HOH HOH . M 8 HOH A 10 510 11 HOH HOH . M 8 HOH A 11 511 12 HOH HOH . M 8 HOH A 12 512 13 HOH HOH . M 8 HOH A 13 513 14 HOH HOH . M 8 HOH A 14 514 15 HOH HOH . M 8 HOH A 15 515 16 HOH HOH . M 8 HOH A 16 516 17 HOH HOH . M 8 HOH A 17 517 18 HOH HOH . M 8 HOH A 18 518 19 HOH HOH . M 8 HOH A 19 519 20 HOH HOH . M 8 HOH A 20 520 22 HOH HOH . M 8 HOH A 21 521 23 HOH HOH . M 8 HOH A 22 522 24 HOH HOH . M 8 HOH A 23 523 25 HOH HOH . M 8 HOH A 24 524 26 HOH HOH . M 8 HOH A 25 525 27 HOH HOH . M 8 HOH A 26 526 28 HOH HOH . M 8 HOH A 27 527 29 HOH HOH . M 8 HOH A 28 528 30 HOH HOH . M 8 HOH A 29 529 31 HOH HOH . M 8 HOH A 30 530 33 HOH HOH . M 8 HOH A 31 531 34 HOH HOH . M 8 HOH A 32 532 35 HOH HOH . M 8 HOH A 33 533 36 HOH HOH . M 8 HOH A 34 534 37 HOH HOH . M 8 HOH A 35 535 38 HOH HOH . M 8 HOH A 36 536 39 HOH HOH . M 8 HOH A 37 537 41 HOH HOH . M 8 HOH A 38 538 42 HOH HOH . M 8 HOH A 39 539 43 HOH HOH . M 8 HOH A 40 540 44 HOH HOH . M 8 HOH A 41 541 45 HOH HOH . M 8 HOH A 42 542 46 HOH HOH . M 8 HOH A 43 543 47 HOH HOH . M 8 HOH A 44 544 49 HOH HOH . M 8 HOH A 45 545 50 HOH HOH . M 8 HOH A 46 546 52 HOH HOH . M 8 HOH A 47 547 53 HOH HOH . M 8 HOH A 48 548 54 HOH HOH . M 8 HOH A 49 549 57 HOH HOH . M 8 HOH A 50 550 58 HOH HOH . M 8 HOH A 51 551 59 HOH HOH . M 8 HOH A 52 552 60 HOH HOH . M 8 HOH A 53 553 61 HOH HOH . M 8 HOH A 54 554 62 HOH HOH . M 8 HOH A 55 555 63 HOH HOH . M 8 HOH A 56 556 64 HOH HOH . M 8 HOH A 57 557 65 HOH HOH . M 8 HOH A 58 558 67 HOH HOH . M 8 HOH A 59 559 68 HOH HOH . M 8 HOH A 60 560 69 HOH HOH . M 8 HOH A 61 561 70 HOH HOH . M 8 HOH A 62 562 71 HOH HOH . M 8 HOH A 63 563 72 HOH HOH . M 8 HOH A 64 564 73 HOH HOH . M 8 HOH A 65 565 75 HOH HOH . M 8 HOH A 66 566 76 HOH HOH . M 8 HOH A 67 567 78 HOH HOH . M 8 HOH A 68 568 79 HOH HOH . M 8 HOH A 69 569 80 HOH HOH . M 8 HOH A 70 570 81 HOH HOH . M 8 HOH A 71 571 84 HOH HOH . M 8 HOH A 72 572 86 HOH HOH . M 8 HOH A 73 573 87 HOH HOH . M 8 HOH A 74 574 89 HOH HOH . M 8 HOH A 75 575 91 HOH HOH . M 8 HOH A 76 576 92 HOH HOH . M 8 HOH A 77 577 93 HOH HOH . M 8 HOH A 78 578 94 HOH HOH . M 8 HOH A 79 579 95 HOH HOH . M 8 HOH A 80 580 96 HOH HOH . M 8 HOH A 81 581 97 HOH HOH . M 8 HOH A 82 582 98 HOH HOH . M 8 HOH A 83 583 99 HOH HOH . M 8 HOH A 84 584 101 HOH HOH . M 8 HOH A 85 585 102 HOH HOH . M 8 HOH A 86 586 103 HOH HOH . M 8 HOH A 87 587 108 HOH HOH . M 8 HOH A 88 588 109 HOH HOH . M 8 HOH A 89 589 110 HOH HOH . M 8 HOH A 90 590 114 HOH HOH . M 8 HOH A 91 591 115 HOH HOH . M 8 HOH A 92 592 116 HOH HOH . M 8 HOH A 93 593 118 HOH HOH . M 8 HOH A 94 594 119 HOH HOH . M 8 HOH A 95 595 120 HOH HOH . M 8 HOH A 96 596 121 HOH HOH . M 8 HOH A 97 597 123 HOH HOH . M 8 HOH A 98 598 125 HOH HOH . M 8 HOH A 99 599 126 HOH HOH . M 8 HOH A 100 600 127 HOH HOH . M 8 HOH A 101 601 128 HOH HOH . M 8 HOH A 102 602 129 HOH HOH . M 8 HOH A 103 603 131 HOH HOH . M 8 HOH A 104 604 133 HOH HOH . M 8 HOH A 105 605 135 HOH HOH . M 8 HOH A 106 606 137 HOH HOH . M 8 HOH A 107 607 138 HOH HOH . M 8 HOH A 108 608 139 HOH HOH . M 8 HOH A 109 609 140 HOH HOH . M 8 HOH A 110 610 141 HOH HOH . M 8 HOH A 111 611 142 HOH HOH . M 8 HOH A 112 612 144 HOH HOH . M 8 HOH A 113 613 145 HOH HOH . M 8 HOH A 114 614 146 HOH HOH . M 8 HOH A 115 615 148 HOH HOH . M 8 HOH A 116 616 149 HOH HOH . M 8 HOH A 117 617 152 HOH HOH . M 8 HOH A 118 618 153 HOH HOH . M 8 HOH A 119 619 154 HOH HOH . M 8 HOH A 120 620 156 HOH HOH . M 8 HOH A 121 621 157 HOH HOH . M 8 HOH A 122 622 158 HOH HOH . M 8 HOH A 123 623 159 HOH HOH . M 8 HOH A 124 624 160 HOH HOH . M 8 HOH A 125 625 161 HOH HOH . M 8 HOH A 126 626 162 HOH HOH . M 8 HOH A 127 627 163 HOH HOH . M 8 HOH A 128 628 164 HOH HOH . M 8 HOH A 129 629 165 HOH HOH . M 8 HOH A 130 630 166 HOH HOH . M 8 HOH A 131 631 167 HOH HOH . M 8 HOH A 132 632 168 HOH HOH . M 8 HOH A 133 633 171 HOH HOH . M 8 HOH A 134 634 172 HOH HOH . M 8 HOH A 135 635 173 HOH HOH . M 8 HOH A 136 636 174 HOH HOH . M 8 HOH A 137 637 175 HOH HOH . M 8 HOH A 138 638 176 HOH HOH . M 8 HOH A 139 639 177 HOH HOH . M 8 HOH A 140 640 178 HOH HOH . M 8 HOH A 141 641 180 HOH HOH . M 8 HOH A 142 642 183 HOH HOH . M 8 HOH A 143 643 184 HOH HOH . M 8 HOH A 144 644 186 HOH HOH . M 8 HOH A 145 645 189 HOH HOH . M 8 HOH A 146 646 192 HOH HOH . M 8 HOH A 147 647 193 HOH HOH . M 8 HOH A 148 648 194 HOH HOH . M 8 HOH A 149 649 195 HOH HOH . M 8 HOH A 150 650 196 HOH HOH . M 8 HOH A 151 651 197 HOH HOH . M 8 HOH A 152 652 198 HOH HOH . M 8 HOH A 153 653 199 HOH HOH . N 8 HOH B 1 501 4 HOH HOH . N 8 HOH B 2 502 21 HOH HOH . N 8 HOH B 3 503 32 HOH HOH . N 8 HOH B 4 504 48 HOH HOH . N 8 HOH B 5 505 90 HOH HOH . N 8 HOH B 6 506 106 HOH HOH . N 8 HOH B 7 507 111 HOH HOH . N 8 HOH B 8 508 122 HOH HOH . N 8 HOH B 9 509 130 HOH HOH . N 8 HOH B 10 510 181 HOH HOH . N 8 HOH B 11 511 191 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 . . . J 5 -11.335 44.73 -12.222 0.71 92.85 ? PB ADP 408 A 1 HETATM 2 O O1B ADP . . . J 5 -12.591 44.651 -13.055 0.71 91.7 ? O1B ADP 408 A 1 HETATM 3 O O2B ADP . . . J 5 -11.039 46.177 -11.908 0.71 92.59 ? O2B ADP 408 A 1 HETATM 4 O O3B ADP . . . J 5 -10.18 44.143 -12.999 0.71 92.77 ? O3B ADP 408 A 1 HETATM 5 P PA ADP . . . J 5 -10.434 43.154 -10.074 0.71 69.52 ? PA ADP 408 A 1 HETATM 6 O O1A ADP . . . J 5 -9.525 42.415 -11.029 0.71 72.17 ? O1A ADP 408 A 1 HETATM 7 O O2A ADP . . . J 5 -11.109 42.166 -9.153 0.71 68.95 ? O2A ADP 408 A 1 HETATM 8 O O3A ADP . . . J 5 -11.545 43.968 -10.855 0.71 208.21 ? O3A ADP 408 A 1 HETATM 9 O O5' ADP . . . J 5 -9.554 44.159 -9.231 0.71 67.92 ? O5' ADP 408 A 1 HETATM 10 C C5' ADP . . . J 5 -8.518 44.847 -9.893 0.71 67.06 ? C5' ADP 408 A 1 HETATM 11 C C4' ADP . . . J 5 -7.255 44.673 -9.149 0.71 67.1 ? C4' ADP 408 A 1 HETATM 12 O O4' ADP . . . J 5 -7.537 44.722 -7.671 0.71 68.19 ? O4' ADP 408 A 1 HETATM 13 C C3' ADP . . . J 5 -6.643 43.37 -9.462 0.71 65.42 ? C3' ADP 408 A 1 HETATM 14 O O3' ADP . . . J 5 -5.502 43.539 -10.36 0.71 62.53 ? O3' ADP 408 A 1 HETATM 15 C C2' ADP . . . J 5 -6.192 42.788 -8.213 0.71 68.12 ? C2' ADP 408 A 1 HETATM 16 O O2' ADP . . . J 5 -4.737 42.88 -8.112 0.71 71.21 ? O2' ADP 408 A 1 HETATM 17 C C1' ADP . . . J 5 -6.824 43.526 -7.105 0.71 65.84 ? C1' ADP 408 A 1 HETATM 18 N N9 ADP . . . J 5 -7.701 42.669 -6.466 0.71 59.62 ? N9 ADP 408 A 1 HETATM 19 C C8 ADP . . . J 5 -8.945 42.345 -6.832 0.71 56.58 ? C8 ADP 408 A 1 HETATM 20 N N7 ADP . . . J 5 -9.447 41.486 -5.971 0.71 53.34 ? N7 ADP 408 A 1 HETATM 21 C C5 ADP . . . J 5 -8.547 41.224 -5.033 0.71 52.58 ? C5 ADP 408 A 1 HETATM 22 C C6 ADP . . . J 5 -8.52 40.423 -3.916 0.71 49.89 ? C6 ADP 408 A 1 HETATM 23 N N6 ADP . . . J 5 -9.646 39.646 -3.573 0.71 50.13 ? N6 ADP 408 A 1 HETATM 24 N N1 ADP . . . J 5 -7.423 40.381 -3.15 0.71 47.41 ? N1 ADP 408 A 1 HETATM 25 C C2 ADP . . . J 5 -6.338 41.112 -3.45 0.71 45.53 ? C2 ADP 408 A 1 HETATM 26 N N3 ADP . . . J 5 -6.333 41.904 -4.536 0.71 47.82 ? N3 ADP 408 A 1 HETATM 27 C C4 ADP . . . J 5 -7.405 41.979 -5.334 0.71 53.98 ? C4 ADP 408 A 1 # _model_server_stats.io_time_ms 13 _model_server_stats.parse_time_ms 9 _model_server_stats.create_model_time_ms 4 _model_server_stats.query_time_ms 321 _model_server_stats.encode_time_ms 16 _model_server_stats.element_count 27 #