data_3RRE # _model_server_result.job_id vkrSafaD1iZlGmqbg3aN0Q _model_server_result.datetime_utc '2024-11-22 10:24:34' _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 3rre # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"G","auth_seq_id":495}' # _entry.id 3RRE # _exptl.entry_id 3RRE _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 3 _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 90 _cell.entry_id 3RRE _cell.length_a 122.309 _cell.length_b 122.309 _cell.length_c 155.312 _cell.Z_PDB 16 _cell.pdbx_unique_axis ? # _symmetry.entry_id 3RRE _symmetry.cell_setting ? _symmetry.Int_Tables_number 97 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'I 4 2 2' # _pdbx_struct_assembly.method_details PISA _pdbx_struct_assembly.oligomeric_details hexadecameric _pdbx_struct_assembly.oligomeric_count 16 _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 _pdbx_struct_assembly_gen.assembly_id 1 _pdbx_struct_assembly_gen.oper_expression 1,2,3,4,5,6,7,8 # 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' 2_555 -x,-y,z -1 0 0 0 -1 0 0 0 1 0 0 0 3 'crystal symmetry operation' 3_555 -y,x,z 0 -1 0 1 0 0 0 0 1 0 0 0 4 'crystal symmetry operation' 4_555 y,-x,z 0 1 0 -1 0 0 0 0 1 0 0 0 5 'crystal symmetry operation' 5_555 -x,y,-z -1 0 0 0 1 0 0 0 -1 0 0 0 6 'crystal symmetry operation' 6_555 x,-y,-z 1 0 0 0 -1 0 0 0 -1 0 0 0 7 'crystal symmetry operation' 7_555 y,x,-z 0 1 0 1 0 0 0 0 -1 0 0 0 8 'crystal symmetry operation' 8_555 -y,-x,-z 0 -1 0 -1 0 0 0 0 -1 0 0 0 # loop_ _struct_asym.details _struct_asym.entity_id _struct_asym.id _struct_asym.pdbx_modified _struct_asym.pdbx_blank_PDB_chainid_flag ? 5 E N N ? 5 F N N ? 5 G 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 OD1 ASN 64 A ASN 52 1_555 C K K . A K 491 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.796 ? metalc ? metalc2 A O ASP 126 A ASP 114 1_555 C K K . A K 491 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.974 ? metalc ? metalc3 A OD2 ASP 126 A ASP 114 1_555 C K K . A K 491 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 3.363 ? metalc ? metalc4 A O PHE 129 A PHE 117 1_555 C K K . A K 491 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.748 ? metalc ? metalc5 A O VAL 158 A VAL 146 1_555 C K K . A K 491 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.982 ? metalc ? metalc6 A O VAL 160 A VAL 148 1_555 C K K . A K 491 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.747 ? metalc ? metalc7 A OG SER 162 A SER 150 1_555 C K K . A K 491 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 3 ? metalc ? metalc8 D MG MG . A MG 492 1_555 E O1B ADP . A ADP 493 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.034 ? metalc ? metalc9 D MG MG . A MG 492 1_555 E O1A ADP . A ADP 493 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.106 ? metalc ? metalc10 D MG MG . A MG 492 1_555 I O HOH . A HOH 530 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.182 ? metalc ? metalc11 D MG MG . A MG 492 1_555 I O HOH . A HOH 542 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.227 ? metalc ? metalc12 D MG MG . A MG 492 1_555 I O HOH . A HOH 612 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.063 ? # _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 3RRE _atom_sites.fract_transf_matrix[1][1] 0.008176 _atom_sites.fract_transf_matrix[1][2] 0 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.008176 _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] 0.006439 _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 K A 1 491 1 K K . D 4 MG A 1 492 2 MG MG . E 5 ADP A 1 493 3 ADP ADP . F 5 ADP A 1 494 4 ADP ADP . G 5 ADP A 1 495 5 ADP ADP . H 6 GOL A 1 496 6 GOL GOL . I 7 HOH A 1 497 1 HOH HOH . I 7 HOH A 2 498 2 HOH HOH . I 7 HOH A 3 499 3 HOH HOH . I 7 HOH A 4 500 4 HOH HOH . I 7 HOH A 5 501 5 HOH HOH . I 7 HOH A 6 502 6 HOH HOH . I 7 HOH A 7 503 8 HOH HOH . I 7 HOH A 8 504 9 HOH HOH . I 7 HOH A 9 505 10 HOH HOH . I 7 HOH A 10 506 11 HOH HOH . I 7 HOH A 11 507 12 HOH HOH . I 7 HOH A 12 508 13 HOH HOH . I 7 HOH A 13 509 14 HOH HOH . I 7 HOH A 14 510 15 HOH HOH . I 7 HOH A 15 511 16 HOH HOH . I 7 HOH A 16 512 17 HOH HOH . I 7 HOH A 17 513 18 HOH HOH . I 7 HOH A 18 514 19 HOH HOH . I 7 HOH A 19 515 20 HOH HOH . I 7 HOH A 20 516 21 HOH HOH . I 7 HOH A 21 517 22 HOH HOH . I 7 HOH A 22 518 23 HOH HOH . I 7 HOH A 23 519 24 HOH HOH . I 7 HOH A 24 520 25 HOH HOH . I 7 HOH A 25 521 26 HOH HOH . I 7 HOH A 26 522 27 HOH HOH . I 7 HOH A 27 523 28 HOH HOH . I 7 HOH A 28 524 29 HOH HOH . I 7 HOH A 29 525 30 HOH HOH . I 7 HOH A 30 526 31 HOH HOH . I 7 HOH A 31 527 32 HOH HOH . I 7 HOH A 32 528 33 HOH HOH . I 7 HOH A 33 529 34 HOH HOH . I 7 HOH A 34 530 35 HOH HOH . I 7 HOH A 35 531 36 HOH HOH . I 7 HOH A 36 532 37 HOH HOH . I 7 HOH A 37 533 38 HOH HOH . I 7 HOH A 38 534 39 HOH HOH . I 7 HOH A 39 535 40 HOH HOH . I 7 HOH A 40 536 41 HOH HOH . I 7 HOH A 41 537 42 HOH HOH . I 7 HOH A 42 538 43 HOH HOH . I 7 HOH A 43 539 44 HOH HOH . I 7 HOH A 44 540 45 HOH HOH . I 7 HOH A 45 541 46 HOH HOH . I 7 HOH A 46 542 47 HOH HOH . I 7 HOH A 47 543 48 HOH HOH . I 7 HOH A 48 544 49 HOH HOH . I 7 HOH A 49 545 50 HOH HOH . I 7 HOH A 50 546 51 HOH HOH . I 7 HOH A 51 547 52 HOH HOH . I 7 HOH A 52 548 53 HOH HOH . I 7 HOH A 53 549 54 HOH HOH . I 7 HOH A 54 550 55 HOH HOH . I 7 HOH A 55 551 56 HOH HOH . I 7 HOH A 56 552 57 HOH HOH . I 7 HOH A 57 553 58 HOH HOH . I 7 HOH A 58 554 59 HOH HOH . I 7 HOH A 59 555 60 HOH HOH . I 7 HOH A 60 556 61 HOH HOH . I 7 HOH A 61 557 62 HOH HOH . I 7 HOH A 62 558 63 HOH HOH . I 7 HOH A 63 559 64 HOH HOH . I 7 HOH A 64 560 65 HOH HOH . I 7 HOH A 65 561 66 HOH HOH . I 7 HOH A 66 562 67 HOH HOH . I 7 HOH A 67 563 68 HOH HOH . I 7 HOH A 68 564 69 HOH HOH . I 7 HOH A 69 565 70 HOH HOH . I 7 HOH A 70 566 71 HOH HOH . I 7 HOH A 71 567 72 HOH HOH . I 7 HOH A 72 568 73 HOH HOH . I 7 HOH A 73 569 74 HOH HOH . I 7 HOH A 74 570 75 HOH HOH . I 7 HOH A 75 571 76 HOH HOH . I 7 HOH A 76 572 77 HOH HOH . I 7 HOH A 77 573 78 HOH HOH . I 7 HOH A 78 574 79 HOH HOH . I 7 HOH A 79 575 80 HOH HOH . I 7 HOH A 80 576 81 HOH HOH . I 7 HOH A 81 577 82 HOH HOH . I 7 HOH A 82 578 83 HOH HOH . I 7 HOH A 83 579 84 HOH HOH . I 7 HOH A 84 580 85 HOH HOH . I 7 HOH A 85 581 86 HOH HOH . I 7 HOH A 86 582 87 HOH HOH . I 7 HOH A 87 583 88 HOH HOH . I 7 HOH A 88 584 89 HOH HOH . I 7 HOH A 89 585 90 HOH HOH . I 7 HOH A 90 586 91 HOH HOH . I 7 HOH A 91 587 92 HOH HOH . I 7 HOH A 92 588 93 HOH HOH . I 7 HOH A 93 589 94 HOH HOH . I 7 HOH A 94 590 95 HOH HOH . I 7 HOH A 95 591 96 HOH HOH . I 7 HOH A 96 592 97 HOH HOH . I 7 HOH A 97 593 98 HOH HOH . I 7 HOH A 98 594 99 HOH HOH . I 7 HOH A 99 595 100 HOH HOH . I 7 HOH A 100 596 101 HOH HOH . I 7 HOH A 101 597 102 HOH HOH . I 7 HOH A 102 598 103 HOH HOH . I 7 HOH A 103 599 105 HOH HOH . I 7 HOH A 104 600 106 HOH HOH . I 7 HOH A 105 601 107 HOH HOH . I 7 HOH A 106 602 108 HOH HOH . I 7 HOH A 107 603 109 HOH HOH . I 7 HOH A 108 604 110 HOH HOH . I 7 HOH A 109 605 111 HOH HOH . I 7 HOH A 110 606 112 HOH HOH . I 7 HOH A 111 607 113 HOH HOH . I 7 HOH A 112 608 114 HOH HOH . I 7 HOH A 113 609 115 HOH HOH . I 7 HOH A 114 610 116 HOH HOH . I 7 HOH A 115 611 117 HOH HOH . I 7 HOH A 116 612 118 HOH HOH . I 7 HOH A 117 613 119 HOH HOH . I 7 HOH A 118 614 120 HOH HOH . I 7 HOH A 119 615 121 HOH HOH . I 7 HOH A 120 616 122 HOH HOH . I 7 HOH A 121 617 123 HOH HOH . I 7 HOH A 122 618 124 HOH HOH . I 7 HOH A 123 619 125 HOH HOH . I 7 HOH A 124 620 126 HOH HOH . I 7 HOH A 125 621 127 HOH HOH . I 7 HOH A 126 622 128 HOH HOH . I 7 HOH A 127 623 129 HOH HOH . I 7 HOH A 128 624 130 HOH HOH . I 7 HOH A 129 625 131 HOH HOH . I 7 HOH A 130 626 132 HOH HOH . I 7 HOH A 131 627 133 HOH HOH . I 7 HOH A 132 628 134 HOH HOH . I 7 HOH A 133 629 135 HOH HOH . I 7 HOH A 134 630 136 HOH HOH . I 7 HOH A 135 631 137 HOH HOH . I 7 HOH A 136 632 138 HOH HOH . I 7 HOH A 137 633 139 HOH HOH . I 7 HOH A 138 634 140 HOH HOH . J 7 HOH B 1 8 7 HOH HOH . J 7 HOH B 2 104 104 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 . . . G 5 -8.821 -23.959 -45.71 1 83.05 ? PB ADP 495 A 1 HETATM 2 O O1B ADP . . . G 5 -10.177 -23.952 -45.019 1 84.43 ? O1B ADP 495 A 1 HETATM 3 O O2B ADP . . . G 5 -8.769 -23.019 -46.9 1 84.13 ? O2B ADP 495 A 1 HETATM 4 O O3B ADP . . . G 5 -7.612 -23.903 -44.791 1 80.52 ? O3B ADP 495 A 1 HETATM 5 P PA ADP . . . G 5 -10.192 -26.199 -46.646 1 81.26 ? PA ADP 495 A 1 HETATM 6 O O1A ADP . . . G 5 -9.781 -27.409 -47.457 1 80.47 ? O1A ADP 495 A 1 HETATM 7 O O2A ADP . . . G 5 -11.294 -25.214 -47.046 1 80.67 ? O2A ADP 495 A 1 HETATM 8 O O3A ADP . . . G 5 -8.798 -25.409 -46.415 1 81.74 ? O3A ADP 495 A 1 HETATM 9 O O5' ADP . . . G 5 -10.566 -26.763 -45.176 1 76.87 ? O5' ADP 495 A 1 HETATM 10 C C5' ADP . . . G 5 -11.791 -26.601 -44.48 1 72.53 ? C5' ADP 495 A 1 HETATM 11 C C4' ADP . . . G 5 -12.319 -28.012 -44.223 1 70.82 ? C4' ADP 495 A 1 HETATM 12 O O4' ADP . . . G 5 -11.378 -28.882 -43.557 1 66.9 ? O4' ADP 495 A 1 HETATM 13 C C3' ADP . . . G 5 -13.587 -27.94 -43.38 1 68.91 ? C3' ADP 495 A 1 HETATM 14 O O3' ADP . . . G 5 -14.653 -28.469 -44.166 1 70.29 ? O3' ADP 495 A 1 HETATM 15 C C2' ADP . . . G 5 -13.328 -28.788 -42.158 1 67.01 ? C2' ADP 495 A 1 HETATM 16 O O2' ADP . . . G 5 -14.215 -29.895 -42.043 1 69.91 ? O2' ADP 495 A 1 HETATM 17 C C1' ADP . . . G 5 -11.933 -29.343 -42.316 1 63.71 ? C1' ADP 495 A 1 HETATM 18 N N9 ADP . . . G 5 -11.139 -28.936 -41.138 1 56.57 ? N9 ADP 495 A 1 HETATM 19 C C8 ADP . . . G 5 -10.201 -27.984 -41.033 1 53.4 ? C8 ADP 495 A 1 HETATM 20 N N7 ADP . . . G 5 -9.716 -27.934 -39.758 1 50.62 ? N7 ADP 495 A 1 HETATM 21 C C5 ADP . . . G 5 -10.342 -28.873 -39.044 1 50.77 ? C5 ADP 495 A 1 HETATM 22 C C6 ADP . . . G 5 -10.324 -29.383 -37.649 1 51.13 ? C6 ADP 495 A 1 HETATM 23 N N6 ADP . . . G 5 -9.497 -28.873 -36.699 1 47.96 ? N6 ADP 495 A 1 HETATM 24 N N1 ADP . . . G 5 -11.207 -30.37 -37.344 1 51.46 ? N1 ADP 495 A 1 HETATM 25 C C2 ADP . . . G 5 -12.058 -30.9 -38.247 1 51.17 ? C2 ADP 495 A 1 HETATM 26 N N3 ADP . . . G 5 -12.108 -30.481 -39.512 1 51.15 ? N3 ADP 495 A 1 HETATM 27 C C4 ADP . . . G 5 -11.294 -29.506 -39.957 1 52.59 ? C4 ADP 495 A 1 # _model_server_stats.io_time_ms 12 _model_server_stats.parse_time_ms 8 _model_server_stats.create_model_time_ms 4 _model_server_stats.query_time_ms 253 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 27 #