data_6JTG # _model_server_result.job_id NXSWL_VbSFeOuBVkpHozIQ _model_server_result.datetime_utc '2024-10-18 19:23:47' _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 6jtg # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"B","auth_seq_id":401}' # _entry.id 6JTG # _exptl.entry_id 6JTG _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 443.201 _entity.id 2 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description "GUANOSINE-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 6JTG _cell.length_a 77.89 _cell.length_b 77.89 _cell.length_c 171.547 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 6JTG _symmetry.cell_setting ? _symmetry.Int_Tables_number 96 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 43 21 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 _pdbx_struct_assembly_gen.assembly_id 1 _pdbx_struct_assembly_gen.oper_expression 1,2 # 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' 8_554 -y,-x,-z-1/2 0 -1 0 -1 0 0 0 0 -1 0 0 -85.7735 # _struct_asym.details ? _struct_asym.entity_id 2 _struct_asym.id B _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 OG SER 36 A SER 36 1_555 E K K . A K 404 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.731 ? metalc ? metalc2 A OG1 THR 40 A THR 40 1_555 C MG MG . A MG 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.856 ? metalc ? metalc3 A O GLY 55 A GLY 55 1_555 E K K . A K 404 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.678 ? metalc ? metalc4 A O GLU 58 A GLU 58 1_555 E K K . A K 404 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.96 ? metalc ? metalc5 A OG1 THR 61 A THR 61 1_555 C MG MG . A MG 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.175 ? metalc ? metalc6 B O3B GDP . A GDP 401 1_555 C MG MG . A MG 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.317 ? metalc ? metalc7 B O1B GDP . A GDP 401 1_555 D BE BEF . A BEF 403 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.718 ? metalc ? metalc8 B O1B GDP . A GDP 401 1_555 E K K . A K 404 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.72 ? metalc ? metalc9 B O1A GDP . A GDP 401 1_555 E K K . A K 404 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 3.281 ? # _chem_comp.formula 'C10 H15 N5 O11 P2' _chem_comp.formula_weight 443.201 _chem_comp.id GDP _chem_comp.mon_nstd_flag n _chem_comp.name "GUANOSINE-5'-DIPHOSPHATE" _chem_comp.type 'rna linking' _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 GDP doub 86 n n PB O2B GDP sing 87 n n PB O3B GDP sing 88 n n PB O3A GDP sing 89 n n O2B HOB2 GDP sing 90 n n O3B HOB3 GDP sing 91 n n O3A PA GDP sing 92 n n PA O1A GDP doub 93 n n PA O2A GDP sing 94 n n PA O5' GDP sing 95 n n O2A HOA2 GDP sing 96 n n O5' C5' GDP sing 97 n n C5' C4' GDP sing 98 n n C5' H5' GDP sing 99 n n C5' "H5''" GDP sing 100 n n C4' O4' GDP sing 101 n n C4' C3' GDP sing 102 n n C4' H4' GDP sing 103 n n O4' C1' GDP sing 104 n n C3' O3' GDP sing 105 n n C3' C2' GDP sing 106 n n C3' H3' GDP sing 107 n n O3' HO3' GDP sing 108 n n C2' O2' GDP sing 109 n n C2' C1' GDP sing 110 n n C2' H2' GDP sing 111 n n O2' HO2' GDP sing 112 n n C1' N9 GDP sing 113 n n C1' H1' GDP sing 114 n n N9 C8 GDP sing 115 n y N9 C4 GDP sing 116 n y C8 N7 GDP doub 117 n y C8 H8 GDP sing 118 n n N7 C5 GDP sing 119 n y C5 C6 GDP sing 120 n n C5 C4 GDP doub 121 n y C6 O6 GDP doub 122 n n C6 N1 GDP sing 123 n n N1 C2 GDP sing 124 n n N1 HN1 GDP sing 125 n n C2 N2 GDP sing 126 n n C2 N3 GDP doub 127 n n N2 HN21 GDP sing 128 n n N2 HN22 GDP sing 129 n n N3 C4 GDP sing 130 n n # _atom_sites.entry_id 6JTG _atom_sites.fract_transf_matrix[1][1] 0.012839 _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] 0.012839 _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] 0.005829 _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 GDP A 1 401 1000 GDP GDP . C 3 MG A 1 402 1003 MG MG . D 4 BEF A 1 403 1001 BEF BEF . E 5 K A 1 404 1004 K K . F 6 HOH A 1 501 111 HOH HOH . F 6 HOH A 2 502 23 HOH HOH . F 6 HOH A 3 503 120 HOH HOH . F 6 HOH A 4 504 58 HOH HOH . F 6 HOH A 5 505 146 HOH HOH . F 6 HOH A 6 506 21 HOH HOH . F 6 HOH A 7 507 32 HOH HOH . F 6 HOH A 8 508 66 HOH HOH . F 6 HOH A 9 509 42 HOH HOH . F 6 HOH A 10 510 125 HOH HOH . F 6 HOH A 11 511 123 HOH HOH . F 6 HOH A 12 512 124 HOH HOH . F 6 HOH A 13 513 143 HOH HOH . F 6 HOH A 14 514 100 HOH HOH . F 6 HOH A 15 515 27 HOH HOH . F 6 HOH A 16 516 15 HOH HOH . F 6 HOH A 17 517 5 HOH HOH . F 6 HOH A 18 518 97 HOH HOH . F 6 HOH A 19 519 36 HOH HOH . F 6 HOH A 20 520 24 HOH HOH . F 6 HOH A 21 521 39 HOH HOH . F 6 HOH A 22 522 108 HOH HOH . F 6 HOH A 23 523 61 HOH HOH . F 6 HOH A 24 524 48 HOH HOH . F 6 HOH A 25 525 38 HOH HOH . F 6 HOH A 26 526 76 HOH HOH . F 6 HOH A 27 527 37 HOH HOH . F 6 HOH A 28 528 73 HOH HOH . F 6 HOH A 29 529 96 HOH HOH . F 6 HOH A 30 530 20 HOH HOH . F 6 HOH A 31 531 91 HOH HOH . F 6 HOH A 32 532 121 HOH HOH . F 6 HOH A 33 533 128 HOH HOH . F 6 HOH A 34 534 51 HOH HOH . F 6 HOH A 35 535 65 HOH HOH . F 6 HOH A 36 536 1 HOH HOH . F 6 HOH A 37 537 2 HOH HOH . F 6 HOH A 38 538 9 HOH HOH . F 6 HOH A 39 539 82 HOH HOH . F 6 HOH A 40 540 30 HOH HOH . F 6 HOH A 41 541 68 HOH HOH . F 6 HOH A 42 542 45 HOH HOH . F 6 HOH A 43 543 7 HOH HOH . F 6 HOH A 44 544 104 HOH HOH . F 6 HOH A 45 545 8 HOH HOH . F 6 HOH A 46 546 99 HOH HOH . F 6 HOH A 47 547 62 HOH HOH . F 6 HOH A 48 548 84 HOH HOH . F 6 HOH A 49 549 44 HOH HOH . F 6 HOH A 50 550 34 HOH HOH . F 6 HOH A 51 551 12 HOH HOH . F 6 HOH A 52 552 16 HOH HOH . F 6 HOH A 53 553 57 HOH HOH . F 6 HOH A 54 554 14 HOH HOH . F 6 HOH A 55 555 33 HOH HOH . F 6 HOH A 56 556 149 HOH HOH . F 6 HOH A 57 557 11 HOH HOH . F 6 HOH A 58 558 106 HOH HOH . F 6 HOH A 59 559 31 HOH HOH . F 6 HOH A 60 560 102 HOH HOH . F 6 HOH A 61 561 4 HOH HOH . F 6 HOH A 62 562 77 HOH HOH . F 6 HOH A 63 563 19 HOH HOH . F 6 HOH A 64 564 26 HOH HOH . F 6 HOH A 65 565 29 HOH HOH . F 6 HOH A 66 566 92 HOH HOH . F 6 HOH A 67 567 116 HOH HOH . F 6 HOH A 68 568 54 HOH HOH . F 6 HOH A 69 569 145 HOH HOH . F 6 HOH A 70 570 35 HOH HOH . F 6 HOH A 71 571 144 HOH HOH . F 6 HOH A 72 572 40 HOH HOH . F 6 HOH A 73 573 98 HOH HOH . F 6 HOH A 74 574 136 HOH HOH . F 6 HOH A 75 575 53 HOH HOH . F 6 HOH A 76 576 10 HOH HOH . F 6 HOH A 77 577 22 HOH HOH . F 6 HOH A 78 578 75 HOH HOH . F 6 HOH A 79 579 94 HOH HOH . F 6 HOH A 80 580 69 HOH HOH . F 6 HOH A 81 581 28 HOH HOH . F 6 HOH A 82 582 41 HOH HOH . F 6 HOH A 83 583 127 HOH HOH . F 6 HOH A 84 584 105 HOH HOH . F 6 HOH A 85 585 86 HOH HOH . F 6 HOH A 86 586 151 HOH HOH . F 6 HOH A 87 587 49 HOH HOH . F 6 HOH A 88 588 46 HOH HOH . F 6 HOH A 89 589 79 HOH HOH . F 6 HOH A 90 590 3 HOH HOH . F 6 HOH A 91 591 87 HOH HOH . F 6 HOH A 92 592 126 HOH HOH . F 6 HOH A 93 593 95 HOH HOH . F 6 HOH A 94 594 109 HOH HOH . F 6 HOH A 95 595 101 HOH HOH . F 6 HOH A 96 596 47 HOH HOH . F 6 HOH A 97 597 67 HOH HOH . F 6 HOH A 98 598 55 HOH HOH . F 6 HOH A 99 599 71 HOH HOH . F 6 HOH A 100 600 60 HOH HOH . F 6 HOH A 101 601 78 HOH HOH . F 6 HOH A 102 602 103 HOH HOH . F 6 HOH A 103 603 88 HOH HOH . F 6 HOH A 104 604 141 HOH HOH . F 6 HOH A 105 605 130 HOH HOH . F 6 HOH A 106 606 56 HOH HOH . F 6 HOH A 107 607 80 HOH HOH . F 6 HOH A 108 608 129 HOH HOH . F 6 HOH A 109 609 72 HOH HOH . F 6 HOH A 110 610 43 HOH HOH . F 6 HOH A 111 611 148 HOH HOH . F 6 HOH A 112 612 113 HOH HOH . F 6 HOH A 113 613 83 HOH HOH . F 6 HOH A 114 614 114 HOH HOH . F 6 HOH A 115 615 89 HOH HOH . F 6 HOH A 116 616 70 HOH HOH . F 6 HOH A 117 617 90 HOH HOH . F 6 HOH A 118 618 107 HOH HOH . F 6 HOH A 119 619 139 HOH HOH . F 6 HOH A 120 620 52 HOH HOH . F 6 HOH A 121 621 147 HOH HOH . F 6 HOH A 122 622 74 HOH HOH . F 6 HOH A 123 623 25 HOH HOH . F 6 HOH A 124 624 131 HOH HOH . F 6 HOH A 125 625 132 HOH HOH . F 6 HOH A 126 626 152 HOH HOH . F 6 HOH A 127 627 50 HOH HOH . F 6 HOH A 128 628 142 HOH HOH . F 6 HOH A 129 629 134 HOH HOH . F 6 HOH A 130 630 112 HOH HOH . F 6 HOH A 131 631 133 HOH HOH . F 6 HOH A 132 632 119 HOH HOH . F 6 HOH A 133 633 118 HOH HOH . F 6 HOH A 134 634 117 HOH HOH . F 6 HOH A 135 635 81 HOH HOH . F 6 HOH A 136 636 6 HOH HOH . F 6 HOH A 137 637 138 HOH HOH . F 6 HOH A 138 638 135 HOH HOH . F 6 HOH A 139 639 137 HOH HOH . F 6 HOH A 140 640 85 HOH HOH . F 6 HOH A 141 641 64 HOH HOH . F 6 HOH A 142 642 93 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 GDP . . . B 2 -10.677 0.872 -32.601 1 21.31 ? PB GDP 401 A 1 HETATM 2 O O1B GDP . . . B 2 -11.748 0.738 -33.632 1 18.64 ? O1B GDP 401 A 1 HETATM 3 O O2B GDP . . . B 2 -10.17 2.293 -32.646 1 22.81 ? O2B GDP 401 A 1 HETATM 4 O O3B GDP . . . B 2 -11.106 0.515 -31.19 1 18.4 ? O3B GDP 401 A 1 HETATM 5 O O3A GDP . . . B 2 -9.433 0.012 -33.072 1 24.55 ? O3A GDP 401 A 1 HETATM 6 P PA GDP . . . B 2 -9.112 -1.506 -32.712 1 22.27 ? PA GDP 401 A 1 HETATM 7 O O1A GDP . . . B 2 -10.313 -2.382 -33.017 1 23.42 ? O1A GDP 401 A 1 HETATM 8 O O2A GDP . . . B 2 -8.589 -1.56 -31.301 1 20.96 ? O2A GDP 401 A 1 HETATM 9 O O5' GDP . . . B 2 -7.835 -1.759 -33.629 1 21.65 ? O5' GDP 401 A 1 HETATM 10 C C5' GDP . . . B 2 -7.85 -2.023 -35.016 1 25.58 ? C5' GDP 401 A 1 HETATM 11 C C4' GDP . . . B 2 -6.544 -2.792 -35.252 1 31.42 ? C4' GDP 401 A 1 HETATM 12 O O4' GDP . . . B 2 -5.36 -1.983 -35.204 1 25.07 ? O4' GDP 401 A 1 HETATM 13 C C3' GDP . . . B 2 -6.321 -3.851 -34.179 1 31.64 ? C3' GDP 401 A 1 HETATM 14 O O3' GDP . . . B 2 -6.882 -5.079 -34.618 1 35.56 ? O3' GDP 401 A 1 HETATM 15 C C2' GDP . . . B 2 -4.827 -3.997 -34.071 1 34.15 ? C2' GDP 401 A 1 HETATM 16 O O2' GDP . . . B 2 -4.451 -5.204 -34.733 1 42.77 ? O2' GDP 401 A 1 HETATM 17 C C1' GDP . . . B 2 -4.259 -2.823 -34.856 1 29.4 ? C1' GDP 401 A 1 HETATM 18 N N9 GDP . . . B 2 -3.338 -2.04 -34.014 1 29.41 ? N9 GDP 401 A 1 HETATM 19 C C8 GDP . . . B 2 -3.674 -1.366 -32.898 1 25.93 ? C8 GDP 401 A 1 HETATM 20 N N7 GDP . . . B 2 -2.602 -0.713 -32.373 1 26.71 ? N7 GDP 401 A 1 HETATM 21 C C5 GDP . . . B 2 -1.547 -0.989 -33.166 1 27.42 ? C5 GDP 401 A 1 HETATM 22 C C6 GDP . . . B 2 -0.116 -0.636 -33.192 1 26.43 ? C6 GDP 401 A 1 HETATM 23 O O6 GDP . . . B 2 0.394 0.104 -32.321 1 26.15 ? O6 GDP 401 A 1 HETATM 24 N N1 GDP . . . B 2 0.614 -1.126 -34.195 1 30.91 ? N1 GDP 401 A 1 HETATM 25 C C2 GDP . . . B 2 0.122 -1.93 -35.149 1 28.51 ? C2 GDP 401 A 1 HETATM 26 N N2 GDP . . . B 2 0.95 -2.38 -36.119 1 28.95 ? N2 GDP 401 A 1 HETATM 27 N N3 GDP . . . B 2 -1.178 -2.286 -35.187 1 29.92 ? N3 GDP 401 A 1 HETATM 28 C C4 GDP . . . B 2 -2.04 -1.853 -34.248 1 29.14 ? C4 GDP 401 A 1 # _model_server_stats.io_time_ms 51 _model_server_stats.parse_time_ms 35 _model_server_stats.create_model_time_ms 3 _model_server_stats.query_time_ms 263 _model_server_stats.encode_time_ms 5 _model_server_stats.element_count 28 #