data_2G5I # _model_server_result.job_id UuwdkG0_20u6g0bQ_mvYpQ _model_server_result.datetime_utc '2024-11-28 05:39:55' _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 2g5i # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"E","auth_seq_id":601}' # _entry.id 2G5I # _exptl.entry_id 2G5I _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 90 _cell.entry_id 2G5I _cell.length_a 76.86 _cell.length_b 85.279 _cell.length_c 183.625 _cell.Z_PDB 4 _cell.pdbx_unique_axis ? # _symmetry.entry_id 2G5I _symmetry.cell_setting ? _symmetry.Int_Tables_number 19 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 21 21 21' # _pdbx_struct_assembly.method_details PISA _pdbx_struct_assembly.oligomeric_details trimeric _pdbx_struct_assembly.oligomeric_count 3 _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 # _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 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 metalc ? metalc1 B NE2 HIS 12 B HIS 12 1_555 D MG MG . B MG 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.427 ? metalc ? metalc2 B OE2 GLU 124 B GLU 124 1_555 D MG MG . B MG 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.795 ? metalc ? metalc3 B OE1 GLU 124 B GLU 124 1_555 D MG MG . B MG 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.719 ? metalc ? metalc4 B OE2 GLU 150 B GLU 150 1_555 D MG MG . B MG 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.727 ? metalc ? metalc5 D MG MG . B MG 501 1_555 G O HOH . B HOH 603 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.565 ? # _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 2G5I _atom_sites.fract_transf_matrix[1][1] 0.013011 _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] 0.011726 _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] 0.005446 _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 MG B 1 501 501 MG MG . E 5 ADP B 1 601 601 ADP ADP . F 6 HOH A 1 486 4 HOH HOH . F 6 HOH A 2 487 9 HOH HOH . F 6 HOH A 3 488 10 HOH HOH . F 6 HOH A 4 489 11 HOH HOH . F 6 HOH A 5 490 13 HOH HOH . F 6 HOH A 6 491 19 HOH HOH . F 6 HOH A 7 492 25 HOH HOH . F 6 HOH A 8 493 26 HOH HOH . F 6 HOH A 9 494 28 HOH HOH . F 6 HOH A 10 495 31 HOH HOH . F 6 HOH A 11 496 35 HOH HOH . F 6 HOH A 12 497 37 HOH HOH . F 6 HOH A 13 498 39 HOH HOH . F 6 HOH A 14 499 41 HOH HOH . F 6 HOH A 15 500 45 HOH HOH . F 6 HOH A 16 501 46 HOH HOH . F 6 HOH A 17 502 48 HOH HOH . F 6 HOH A 18 503 49 HOH HOH . F 6 HOH A 19 504 52 HOH HOH . F 6 HOH A 20 505 53 HOH HOH . F 6 HOH A 21 506 54 HOH HOH . F 6 HOH A 22 507 56 HOH HOH . F 6 HOH A 23 508 62 HOH HOH . F 6 HOH A 24 509 63 HOH HOH . F 6 HOH A 25 510 65 HOH HOH . F 6 HOH A 26 511 67 HOH HOH . F 6 HOH A 27 512 69 HOH HOH . F 6 HOH A 28 513 74 HOH HOH . F 6 HOH A 29 514 75 HOH HOH . F 6 HOH A 30 515 76 HOH HOH . F 6 HOH A 31 516 77 HOH HOH . F 6 HOH A 32 517 78 HOH HOH . F 6 HOH A 33 518 81 HOH HOH . F 6 HOH A 34 519 82 HOH HOH . F 6 HOH A 35 520 83 HOH HOH . F 6 HOH A 36 521 84 HOH HOH . F 6 HOH A 37 522 85 HOH HOH . F 6 HOH A 38 523 86 HOH HOH . F 6 HOH A 39 524 87 HOH HOH . F 6 HOH A 40 525 88 HOH HOH . F 6 HOH A 41 526 89 HOH HOH . F 6 HOH A 42 527 90 HOH HOH . G 6 HOH B 1 602 1 HOH HOH . G 6 HOH B 2 603 2 HOH HOH . G 6 HOH B 3 604 3 HOH HOH . G 6 HOH B 4 605 5 HOH HOH . G 6 HOH B 5 606 8 HOH HOH . G 6 HOH B 6 607 12 HOH HOH . G 6 HOH B 7 608 15 HOH HOH . G 6 HOH B 8 609 16 HOH HOH . G 6 HOH B 9 610 17 HOH HOH . G 6 HOH B 10 611 18 HOH HOH . G 6 HOH B 11 612 21 HOH HOH . G 6 HOH B 12 613 22 HOH HOH . G 6 HOH B 13 614 24 HOH HOH . G 6 HOH B 14 615 27 HOH HOH . G 6 HOH B 15 616 29 HOH HOH . G 6 HOH B 16 617 30 HOH HOH . G 6 HOH B 17 618 33 HOH HOH . G 6 HOH B 18 619 34 HOH HOH . G 6 HOH B 19 620 36 HOH HOH . G 6 HOH B 20 621 38 HOH HOH . G 6 HOH B 21 622 40 HOH HOH . G 6 HOH B 22 623 42 HOH HOH . G 6 HOH B 23 624 43 HOH HOH . G 6 HOH B 24 625 44 HOH HOH . G 6 HOH B 25 626 47 HOH HOH . G 6 HOH B 26 627 55 HOH HOH . G 6 HOH B 27 628 57 HOH HOH . G 6 HOH B 28 629 58 HOH HOH . G 6 HOH B 29 630 59 HOH HOH . G 6 HOH B 30 631 60 HOH HOH . G 6 HOH B 31 632 64 HOH HOH . G 6 HOH B 32 633 66 HOH HOH . G 6 HOH B 33 634 68 HOH HOH . G 6 HOH B 34 635 70 HOH HOH . G 6 HOH B 35 636 71 HOH HOH . G 6 HOH B 36 637 72 HOH HOH . G 6 HOH B 37 638 73 HOH HOH . G 6 HOH B 38 639 79 HOH HOH . G 6 HOH B 39 640 80 HOH HOH . H 6 HOH C 1 101 6 HOH HOH . H 6 HOH C 2 102 7 HOH HOH . H 6 HOH C 3 103 14 HOH HOH . H 6 HOH C 4 104 20 HOH HOH . H 6 HOH C 5 105 23 HOH HOH . H 6 HOH C 6 106 32 HOH HOH . H 6 HOH C 7 107 50 HOH HOH . H 6 HOH C 8 108 51 HOH HOH . H 6 HOH C 9 109 61 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 . . . E 5 6.781 2.589 -19.531 0.7 43.17 ? PB ADP 601 B 1 HETATM 2 O O1B ADP . . . E 5 7.403 2.354 -20.846 0.7 42.57 ? O1B ADP 601 B 1 HETATM 3 O O2B ADP . . . E 5 5.476 1.668 -19.408 0.7 42.79 ? O2B ADP 601 B 1 HETATM 4 O O3B ADP . . . E 5 7.823 2.189 -18.375 0.7 42.33 ? O3B ADP 601 B 1 HETATM 5 P PA ADP . . . E 5 5.273 4.808 -20.354 0.7 41.62 ? PA ADP 601 B 1 HETATM 6 O O1A ADP . . . E 5 4.108 3.942 -20.611 0.7 38.53 ? O1A ADP 601 B 1 HETATM 7 O O2A ADP . . . E 5 4.798 6.156 -19.609 0.7 39.69 ? O2A ADP 601 B 1 HETATM 8 O O3A ADP . . . E 5 6.374 4.16 -19.314 0.7 43.04 ? O3A ADP 601 B 1 HETATM 9 O O5' ADP . . . E 5 5.957 5.283 -21.75 0.7 37.27 ? O5' ADP 601 B 1 HETATM 10 C C5' ADP . . . E 5 6.316 4.143 -22.545 0.7 34.48 ? C5' ADP 601 B 1 HETATM 11 C C4' ADP . . . E 5 7.02 4.545 -23.857 0.7 33.01 ? C4' ADP 601 B 1 HETATM 12 O O4' ADP . . . E 5 6.115 4.368 -24.994 0.7 31.88 ? O4' ADP 601 B 1 HETATM 13 C C3' ADP . . . E 5 7.456 6.024 -23.878 0.7 32.11 ? C3' ADP 601 B 1 HETATM 14 O O3' ADP . . . E 5 8.725 6.147 -24.531 0.7 28.6 ? O3' ADP 601 B 1 HETATM 15 C C2' ADP . . . E 5 6.34 6.753 -24.616 0.7 32.01 ? C2' ADP 601 B 1 HETATM 16 O O2' ADP . . . E 5 6.862 7.877 -25.33 0.7 32.1 ? O2' ADP 601 B 1 HETATM 17 C C1' ADP . . . E 5 5.814 5.674 -25.58 0.7 31.53 ? C1' ADP 601 B 1 HETATM 18 N N9 ADP . . . E 5 4.361 5.807 -25.802 0.7 32.54 ? N9 ADP 601 B 1 HETATM 19 C C8 ADP . . . E 5 3.378 6.102 -24.882 0.7 33.17 ? C8 ADP 601 B 1 HETATM 20 N N7 ADP . . . E 5 2.205 6.127 -25.464 0.7 33.49 ? N7 ADP 601 B 1 HETATM 21 C C5 ADP . . . E 5 2.364 5.84 -26.783 0.7 33.39 ? C5 ADP 601 B 1 HETATM 22 C C6 ADP . . . E 5 1.496 5.725 -27.913 0.7 33 ? C6 ADP 601 B 1 HETATM 23 N N6 ADP . . . E 5 0.129 5.906 -27.781 0.7 34.01 ? N6 ADP 601 B 1 HETATM 24 N N1 ADP . . . E 5 2.036 5.411 -29.116 0.7 32.86 ? N1 ADP 601 B 1 HETATM 25 C C2 ADP . . . E 5 3.354 5.231 -29.269 0.7 33.48 ? C2 ADP 601 B 1 HETATM 26 N N3 ADP . . . E 5 4.195 5.335 -28.247 0.7 33.1 ? N3 ADP 601 B 1 HETATM 27 C C4 ADP . . . E 5 3.751 5.636 -27.007 0.7 33.08 ? C4 ADP 601 B 1 # _model_server_stats.io_time_ms 25 _model_server_stats.parse_time_ms 94 _model_server_stats.create_model_time_ms 11 _model_server_stats.query_time_ms 342 _model_server_stats.encode_time_ms 12 _model_server_stats.element_count 27 #