data_3RT7 # _model_server_result.job_id AgP8CbADmpTesJGHMk0Wlw _model_server_result.datetime_utc '2024-11-22 08:52:41' _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 3rt7 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"F","auth_seq_id":494}' # _entry.id 3RT7 # _exptl.entry_id 3RT7 _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 589.342 _entity.id 5 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description "ADENOSINE-5'-DIPHOSPHATE-GLUCOSE" _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 3RT7 _cell.length_a 122.138 _cell.length_b 122.138 _cell.length_c 155.337 _cell.Z_PDB 16 _cell.pdbx_unique_axis ? # _symmetry.entry_id 3RT7 _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 _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_554 -x,y,-z-1 -1 0 0 0 1 0 0 0 -1 0 0 -155.337 6 'crystal symmetry operation' 6_554 x,-y,-z-1 1 0 0 0 -1 0 0 0 -1 0 0 -155.337 7 'crystal symmetry operation' 7_554 y,x,-z-1 0 1 0 1 0 0 0 0 -1 0 0 -155.337 8 'crystal symmetry operation' 8_554 -y,-x,-z-1 0 -1 0 -1 0 0 0 0 -1 0 0 -155.337 # 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 ? ? ? ? ? ? ? ? ? ? ? ? 2.849 ? metalc ? metalc2 A O ASP 126 A ASP 114 1_555 C K K . A K 491 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.994 ? metalc ? metalc3 A OD2 ASP 126 A ASP 114 1_555 C K K . A K 491 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 3.364 ? metalc ? metalc4 A O PHE 129 A PHE 117 1_555 C K K . A K 491 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.745 ? metalc ? metalc5 A O VAL 158 A VAL 146 1_555 C K K . A K 491 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.888 ? metalc ? metalc6 A O VAL 160 A VAL 148 1_555 C K K . A K 491 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.788 ? metalc ? metalc7 A OG SER 162 A SER 150 1_555 C K K . A K 491 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.934 ? metalc ? metalc8 D MG MG . A MG 492 1_555 F O1A ADQ . A ADQ 494 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.064 ? metalc ? metalc9 D MG MG . A MG 492 1_555 F O3B ADQ . A ADQ 494 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.274 ? metalc ? metalc10 D MG MG . A MG 492 1_555 I O HOH . A HOH 535 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.3 ? metalc ? metalc11 D MG MG . A MG 492 1_555 I O HOH . A HOH 552 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.298 ? metalc ? metalc12 D MG MG . A MG 492 1_555 I O HOH . A HOH 553 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.381 ? # _chem_comp.formula 'C16 H25 N5 O15 P2' _chem_comp.formula_weight 589.342 _chem_comp.id ADQ _chem_comp.mon_nstd_flag . _chem_comp.name "ADENOSINE-5'-DIPHOSPHATE-GLUCOSE" _chem_comp.type non-polymer _chem_comp.pdbx_synonyms "ADENOSINE-5'-MONOPHOSPHATE GLUCOPYRANOSYL-MONOPHOSPHATE ESTER" # 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 ADQ doub 1 n n PB O2B ADQ sing 2 n n PB O3B ADQ sing 3 n n PB O3A ADQ sing 4 n n O2B HOB2 ADQ sing 5 n n O3B C1' ADQ sing 6 n n PA O1A ADQ doub 7 n n PA O2A ADQ sing 8 n n PA O3A ADQ sing 9 n n PA O5D ADQ sing 10 n n O2A HOA2 ADQ sing 11 n n O5D C5D ADQ sing 12 n n C5D C4D ADQ sing 13 n n C5D "H5'1" ADQ sing 14 n n C5D "H5'2" ADQ sing 15 n n C4D O4D ADQ sing 16 n n C4D C3D ADQ sing 17 n n C4D H4D ADQ sing 18 n n O4D C1D ADQ sing 19 n n C3D O3D ADQ sing 20 n n C3D C2D ADQ sing 21 n n C3D H3D ADQ sing 22 n n O3D HO3' ADQ sing 23 n n C2D O2D ADQ sing 24 n n C2D C1D ADQ sing 25 n n C2D H2D ADQ sing 26 n n O2D HO2' ADQ sing 27 n n C1D N9 ADQ sing 28 n n C1D H1D ADQ sing 29 n n N9 C8 ADQ sing 30 n y N9 C4 ADQ sing 31 n y C8 N7 ADQ doub 32 n y C8 H8 ADQ sing 33 n n N7 C5 ADQ sing 34 n y C5 C6 ADQ sing 35 n y C5 C4 ADQ doub 36 n y C6 N6 ADQ sing 37 n n C6 N1 ADQ doub 38 n y N6 HN61 ADQ sing 39 n n N6 HN62 ADQ sing 40 n n N1 C2 ADQ sing 41 n y C2 N3 ADQ doub 42 n y C2 H2 ADQ sing 43 n n N3 C4 ADQ sing 44 n y C1' C2' ADQ sing 45 n n C1' O5' ADQ sing 46 n n C1' H1' ADQ sing 47 n n C2' C3' ADQ sing 48 n n C2' O2' ADQ sing 49 n n C2' H2' ADQ sing 50 n n C3' C4' ADQ sing 51 n n C3' O3' ADQ sing 52 n n C3' H3' ADQ sing 53 n n C4' C5' ADQ sing 54 n n C4' O4' ADQ sing 55 n n C4' H4' ADQ sing 56 n n C5' C6' ADQ sing 57 n n C5' O5' ADQ sing 58 n n C5' H5' ADQ sing 59 n n C6' O6' ADQ sing 60 n n C6' "H6'1" ADQ sing 61 n n C6' "H6'2" ADQ sing 62 n n O2' HO2A ADQ sing 63 n n O3' HO3A ADQ sing 64 n n O4' HO4' ADQ sing 65 n n O6' HO6' ADQ sing 66 n n # _atom_sites.entry_id 3RT7 _atom_sites.fract_transf_matrix[1][1] 0.008187 _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] 0.008187 _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] 0.006438 _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 ADQ A 1 493 3 ADQ ADQ . F 5 ADQ A 1 494 4 ADQ ADQ . G 5 ADQ A 1 495 5 ADQ ADQ . 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 7 HOH HOH . I 7 HOH A 8 504 8 HOH HOH . I 7 HOH A 9 505 9 HOH HOH . I 7 HOH A 10 506 10 HOH HOH . I 7 HOH A 11 507 11 HOH HOH . I 7 HOH A 12 508 12 HOH HOH . I 7 HOH A 13 509 13 HOH HOH . I 7 HOH A 14 510 14 HOH HOH . I 7 HOH A 15 511 15 HOH HOH . I 7 HOH A 16 512 16 HOH HOH . I 7 HOH A 17 513 17 HOH HOH . I 7 HOH A 18 514 18 HOH HOH . I 7 HOH A 19 515 19 HOH HOH . I 7 HOH A 20 516 20 HOH HOH . I 7 HOH A 21 517 21 HOH HOH . I 7 HOH A 22 518 22 HOH HOH . I 7 HOH A 23 519 23 HOH HOH . I 7 HOH A 24 520 24 HOH HOH . I 7 HOH A 25 521 25 HOH HOH . I 7 HOH A 26 522 26 HOH HOH . I 7 HOH A 27 523 27 HOH HOH . I 7 HOH A 28 524 28 HOH HOH . I 7 HOH A 29 525 29 HOH HOH . I 7 HOH A 30 526 30 HOH HOH . I 7 HOH A 31 527 31 HOH HOH . I 7 HOH A 32 528 32 HOH HOH . I 7 HOH A 33 529 33 HOH HOH . I 7 HOH A 34 530 34 HOH HOH . I 7 HOH A 35 531 35 HOH HOH . I 7 HOH A 36 532 36 HOH HOH . I 7 HOH A 37 533 37 HOH HOH . I 7 HOH A 38 534 38 HOH HOH . I 7 HOH A 39 535 39 HOH HOH . I 7 HOH A 40 536 40 HOH HOH . I 7 HOH A 41 537 41 HOH HOH . I 7 HOH A 42 538 42 HOH HOH . I 7 HOH A 43 539 43 HOH HOH . I 7 HOH A 44 540 44 HOH HOH . I 7 HOH A 45 541 45 HOH HOH . I 7 HOH A 46 542 46 HOH HOH . I 7 HOH A 47 543 47 HOH HOH . I 7 HOH A 48 544 48 HOH HOH . I 7 HOH A 49 545 49 HOH HOH . I 7 HOH A 50 546 50 HOH HOH . I 7 HOH A 51 547 51 HOH HOH . I 7 HOH A 52 548 52 HOH HOH . I 7 HOH A 53 549 53 HOH HOH . I 7 HOH A 54 550 54 HOH HOH . I 7 HOH A 55 551 55 HOH HOH . I 7 HOH A 56 552 56 HOH HOH . I 7 HOH A 57 553 57 HOH HOH . I 7 HOH A 58 554 58 HOH HOH . I 7 HOH A 59 555 59 HOH HOH . I 7 HOH A 60 556 60 HOH HOH . I 7 HOH A 61 557 61 HOH HOH . I 7 HOH A 62 558 62 HOH HOH . I 7 HOH A 63 559 63 HOH HOH . I 7 HOH A 64 560 64 HOH HOH . I 7 HOH A 65 561 65 HOH HOH . I 7 HOH A 66 562 66 HOH HOH . I 7 HOH A 67 563 67 HOH HOH . I 7 HOH A 68 564 68 HOH HOH . I 7 HOH A 69 565 69 HOH HOH . I 7 HOH A 70 566 70 HOH HOH . I 7 HOH A 71 567 71 HOH HOH . I 7 HOH A 72 568 72 HOH HOH . I 7 HOH A 73 569 73 HOH HOH . I 7 HOH A 74 570 74 HOH HOH . I 7 HOH A 75 571 75 HOH HOH . I 7 HOH A 76 572 76 HOH HOH . I 7 HOH A 77 573 77 HOH HOH . I 7 HOH A 78 574 78 HOH HOH . I 7 HOH A 79 575 79 HOH HOH . I 7 HOH A 80 576 80 HOH HOH . I 7 HOH A 81 577 81 HOH HOH . I 7 HOH A 82 578 82 HOH HOH . I 7 HOH A 83 579 83 HOH HOH . I 7 HOH A 84 580 84 HOH HOH . I 7 HOH A 85 581 85 HOH HOH . I 7 HOH A 86 582 86 HOH HOH . I 7 HOH A 87 583 87 HOH HOH . I 7 HOH A 88 584 88 HOH HOH . I 7 HOH A 89 585 89 HOH HOH . I 7 HOH A 90 586 90 HOH HOH . I 7 HOH A 91 587 91 HOH HOH . I 7 HOH A 92 588 92 HOH HOH . I 7 HOH A 93 589 93 HOH HOH . I 7 HOH A 94 590 94 HOH HOH . I 7 HOH A 95 591 95 HOH HOH . I 7 HOH A 96 592 96 HOH HOH . I 7 HOH A 97 593 97 HOH HOH . I 7 HOH A 98 594 98 HOH HOH . I 7 HOH A 99 595 99 HOH HOH . I 7 HOH A 100 596 100 HOH HOH . I 7 HOH A 101 597 101 HOH HOH . I 7 HOH A 102 598 102 HOH HOH . I 7 HOH A 103 599 103 HOH HOH . I 7 HOH A 104 600 104 HOH HOH . I 7 HOH A 105 601 105 HOH HOH . I 7 HOH A 106 602 106 HOH HOH . I 7 HOH A 107 603 107 HOH HOH . I 7 HOH A 108 604 108 HOH HOH . I 7 HOH A 109 605 109 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 ADQ . . . F 5 -21.387 -5.785 -36.528 1 61.53 ? PB ADQ 494 A 1 HETATM 2 O O1B ADQ . . . F 5 -20.519 -5.01 -37.469 1 59.49 ? O1B ADQ 494 A 1 HETATM 3 O O2B ADQ . . . F 5 -20.913 -7.101 -36.012 1 62.41 ? O2B ADQ 494 A 1 HETATM 4 O O3B ADQ . . . F 5 -21.69 -4.901 -35.203 1 61.63 ? O3B ADQ 494 A 1 HETATM 5 P PA ADQ . . . F 5 -23.928 -4.928 -37.5 1 54.86 ? PA ADQ 494 A 1 HETATM 6 O O1A ADQ . . . F 5 -24.04 -3.875 -36.451 1 56.83 ? O1A ADQ 494 A 1 HETATM 7 O O2A ADQ . . . F 5 -25.065 -5.78 -38.049 1 64.47 ? O2A ADQ 494 A 1 HETATM 8 O O3A ADQ . . . F 5 -22.865 -6.104 -37.148 1 59.61 ? O3A ADQ 494 A 1 HETATM 9 O O5D ADQ . . . F 5 -23.452 -4.13 -38.824 1 52.71 ? O5D ADQ 494 A 1 HETATM 10 C C5D ADQ . . . F 5 -23.219 -4.815 -40.07 1 49.66 ? C5D ADQ 494 A 1 HETATM 11 C C4D ADQ . . . F 5 -23.195 -3.766 -41.209 1 49.01 ? C4D ADQ 494 A 1 HETATM 12 O O4D ADQ . . . F 5 -22.816 -4.431 -42.41 1 52 ? O4D ADQ 494 A 1 HETATM 13 C C3D ADQ . . . F 5 -24.583 -3.227 -41.538 1 50.01 ? C3D ADQ 494 A 1 HETATM 14 O O3D ADQ . . . F 5 -24.582 -1.973 -42.215 1 47.21 ? O3D ADQ 494 A 1 HETATM 15 C C2D ADQ . . . F 5 -25.168 -4.196 -42.529 1 51.58 ? C2D ADQ 494 A 1 HETATM 16 O O2D ADQ . . . F 5 -26.17 -3.587 -43.313 1 49.4 ? O2D ADQ 494 A 1 HETATM 17 C C1D ADQ . . . F 5 -23.94 -4.58 -43.331 1 53.25 ? C1D ADQ 494 A 1 HETATM 18 N N9 ADQ . . . F 5 -24.035 -5.966 -43.892 1 54.27 ? N9 ADQ 494 A 1 HETATM 19 C C8 ADQ . . . F 5 -23.844 -7.127 -43.208 1 55.11 ? C8 ADQ 494 A 1 HETATM 20 N N7 ADQ . . . F 5 -23.989 -8.209 -44.02 1 52.2 ? N7 ADQ 494 A 1 HETATM 21 C C5 ADQ . . . F 5 -24.247 -7.729 -45.252 1 52.84 ? C5 ADQ 494 A 1 HETATM 22 C C6 ADQ . . . F 5 -24.498 -8.318 -46.565 1 51.09 ? C6 ADQ 494 A 1 HETATM 23 N N6 ADQ . . . F 5 -24.493 -9.663 -46.705 1 52.67 ? N6 ADQ 494 A 1 HETATM 24 N N1 ADQ . . . F 5 -24.73 -7.482 -47.597 1 52.97 ? N1 ADQ 494 A 1 HETATM 25 C C2 ADQ . . . F 5 -24.76 -6.137 -47.484 1 51.82 ? C2 ADQ 494 A 1 HETATM 26 N N3 ADQ . . . F 5 -24.558 -5.526 -46.297 1 54.43 ? N3 ADQ 494 A 1 HETATM 27 C C4 ADQ . . . F 5 -24.288 -6.255 -45.174 1 54.04 ? C4 ADQ 494 A 1 # _model_server_stats.io_time_ms 13 _model_server_stats.parse_time_ms 10 _model_server_stats.create_model_time_ms 4 _model_server_stats.query_time_ms 280 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 27 #