data_2DGN # _model_server_result.job_id Yz_Dxs5fimQJyg0zl1T-9A _model_server_result.datetime_utc '2024-11-18 12:43:26' _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 2dgn # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"D","auth_seq_id":1452}' # _entry.id 2DGN # _exptl.entry_id 2DGN _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 443.201 _entity.id 4 _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 2DGN _cell.length_a 70.112 _cell.length_b 70.112 _cell.length_c 199.033 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 2DGN _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,PQS _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 _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_775 -y+2,-x+2,-z+1/2 0 -1 0 -1 0 0 0 0 -1 140.224 140.224 99.5165 # _struct_asym.details ? _struct_asym.entity_id 4 _struct_asym.id D _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 ASP 43 A ASP 43 1_555 B MG MG . A MG 1454 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.255 ? metalc ? metalc2 A O GLY 70 A GLY 70 1_555 B MG MG . A MG 1454 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.116 ? metalc ? metalc3 E O HOH . A HOH 513 1_555 B MG MG . A MG 1454 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.234 ? metalc ? metalc4 C O16 DOI . A DOI 1451 1_555 B MG MG . A MG 1454 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.04 ? metalc ? metalc5 D O2A GDP . A GDP 1452 1_555 B MG MG . A MG 1454 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.074 ? metalc ? metalc6 D O2B GDP . A GDP 1452 1_555 B MG MG . A MG 1454 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.042 ? # _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 125 n n PB O2B GDP sing 126 n n PB O3B GDP sing 127 n n PB O3A GDP sing 128 n n O2B HOB2 GDP sing 129 n n O3B HOB3 GDP sing 130 n n O3A PA GDP sing 131 n n PA O1A GDP doub 132 n n PA O2A GDP sing 133 n n PA O5' GDP sing 134 n n O2A HOA2 GDP sing 135 n n O5' C5' GDP sing 136 n n C5' C4' GDP sing 137 n n C5' H5' GDP sing 138 n n C5' "H5''" GDP sing 139 n n C4' O4' GDP sing 140 n n C4' C3' GDP sing 141 n n C4' H4' GDP sing 142 n n O4' C1' GDP sing 143 n n C3' O3' GDP sing 144 n n C3' C2' GDP sing 145 n n C3' H3' GDP sing 146 n n O3' HO3' GDP sing 147 n n C2' O2' GDP sing 148 n n C2' C1' GDP sing 149 n n C2' H2' GDP sing 150 n n O2' HO2' GDP sing 151 n n C1' N9 GDP sing 152 n n C1' H1' GDP sing 153 n n N9 C8 GDP sing 154 n y N9 C4 GDP sing 155 n y C8 N7 GDP doub 156 n y C8 H8 GDP sing 157 n n N7 C5 GDP sing 158 n y C5 C6 GDP sing 159 n n C5 C4 GDP doub 160 n y C6 O6 GDP doub 161 n n C6 N1 GDP sing 162 n n N1 C2 GDP sing 163 n n N1 HN1 GDP sing 164 n n C2 N2 GDP sing 165 n n C2 N3 GDP doub 166 n n N2 HN21 GDP sing 167 n n N2 HN22 GDP sing 168 n n N3 C4 GDP sing 169 n n # _atom_sites.entry_id 2DGN _atom_sites.fract_transf_matrix[1][1] 0.014263 _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] 0.014263 _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] 0.005024 _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 MG A 1 1454 1454 MG MG . C 3 DOI A 1 1451 1451 DOI DOI . D 4 GDP A 1 1452 1452 GDP GDP . E 5 HOH A 1 501 501 HOH HOH . E 5 HOH A 2 502 502 HOH HOH . E 5 HOH A 3 503 503 HOH HOH . E 5 HOH A 4 504 504 HOH HOH . E 5 HOH A 5 505 505 HOH HOH . E 5 HOH A 6 506 506 HOH HOH . E 5 HOH A 7 507 507 HOH HOH . E 5 HOH A 8 508 508 HOH HOH . E 5 HOH A 9 509 509 HOH HOH . E 5 HOH A 10 510 510 HOH HOH . E 5 HOH A 11 511 511 HOH HOH . E 5 HOH A 12 512 512 HOH HOH . E 5 HOH A 13 513 513 HOH HOH . E 5 HOH A 14 514 514 HOH HOH . E 5 HOH A 15 515 515 HOH HOH . E 5 HOH A 16 516 516 HOH HOH . E 5 HOH A 17 517 517 HOH HOH . E 5 HOH A 18 518 518 HOH HOH . E 5 HOH A 19 519 519 HOH HOH . E 5 HOH A 20 520 520 HOH HOH . E 5 HOH A 21 521 521 HOH HOH . E 5 HOH A 22 522 522 HOH HOH . E 5 HOH A 23 523 523 HOH HOH . E 5 HOH A 24 524 524 HOH HOH . E 5 HOH A 25 525 525 HOH HOH . E 5 HOH A 26 526 526 HOH HOH . E 5 HOH A 27 527 527 HOH HOH . E 5 HOH A 28 528 528 HOH HOH . E 5 HOH A 29 529 529 HOH HOH . E 5 HOH A 30 530 530 HOH HOH . E 5 HOH A 31 531 531 HOH HOH . E 5 HOH A 32 532 532 HOH HOH . E 5 HOH A 33 533 533 HOH HOH . E 5 HOH A 34 534 534 HOH HOH . E 5 HOH A 35 535 535 HOH HOH . E 5 HOH A 36 536 536 HOH HOH . E 5 HOH A 37 537 537 HOH HOH . E 5 HOH A 38 538 538 HOH HOH . E 5 HOH A 39 539 539 HOH HOH . E 5 HOH A 40 540 540 HOH HOH . E 5 HOH A 41 541 541 HOH HOH . E 5 HOH A 42 542 542 HOH HOH . E 5 HOH A 43 543 543 HOH HOH . E 5 HOH A 44 544 544 HOH HOH . E 5 HOH A 45 545 545 HOH HOH . E 5 HOH A 46 546 546 HOH HOH . E 5 HOH A 47 547 547 HOH HOH . E 5 HOH A 48 548 548 HOH HOH . E 5 HOH A 49 549 549 HOH HOH . E 5 HOH A 50 550 550 HOH HOH . E 5 HOH A 51 551 551 HOH HOH . E 5 HOH A 52 552 552 HOH HOH . E 5 HOH A 53 553 553 HOH HOH . E 5 HOH A 54 554 554 HOH HOH . E 5 HOH A 55 555 555 HOH HOH . E 5 HOH A 56 556 556 HOH HOH . E 5 HOH A 57 557 557 HOH HOH . E 5 HOH A 58 558 558 HOH HOH . E 5 HOH A 59 559 559 HOH HOH . E 5 HOH A 60 560 560 HOH HOH . E 5 HOH A 61 561 561 HOH HOH . E 5 HOH A 62 562 562 HOH HOH . E 5 HOH A 63 563 563 HOH HOH . E 5 HOH A 64 564 564 HOH HOH . E 5 HOH A 65 565 565 HOH HOH . E 5 HOH A 66 566 566 HOH HOH . E 5 HOH A 67 567 567 HOH HOH . E 5 HOH A 68 568 568 HOH HOH . E 5 HOH A 69 569 569 HOH HOH . E 5 HOH A 70 570 570 HOH HOH . E 5 HOH A 71 571 571 HOH HOH . E 5 HOH A 72 572 572 HOH HOH . E 5 HOH A 73 573 573 HOH HOH . E 5 HOH A 74 574 574 HOH HOH . E 5 HOH A 75 575 575 HOH HOH . E 5 HOH A 76 576 576 HOH HOH . E 5 HOH A 77 577 577 HOH HOH . E 5 HOH A 78 578 578 HOH HOH . E 5 HOH A 79 579 579 HOH HOH . E 5 HOH A 80 580 580 HOH HOH . E 5 HOH A 81 581 581 HOH HOH . E 5 HOH A 82 582 582 HOH HOH . E 5 HOH A 83 583 583 HOH HOH . E 5 HOH A 84 584 584 HOH HOH . E 5 HOH A 85 585 585 HOH HOH . E 5 HOH A 86 586 586 HOH HOH . E 5 HOH A 87 587 587 HOH HOH . E 5 HOH A 88 588 588 HOH HOH . E 5 HOH A 89 589 589 HOH HOH . E 5 HOH A 90 590 590 HOH HOH . E 5 HOH A 91 591 591 HOH HOH . E 5 HOH A 92 592 592 HOH HOH . E 5 HOH A 93 593 593 HOH HOH . E 5 HOH A 94 594 594 HOH HOH . E 5 HOH A 95 595 595 HOH HOH . E 5 HOH A 96 597 597 HOH HOH . E 5 HOH A 97 598 598 HOH HOH . E 5 HOH A 98 599 599 HOH HOH . E 5 HOH A 99 600 600 HOH HOH . E 5 HOH A 100 601 601 HOH HOH . E 5 HOH A 101 602 602 HOH HOH . E 5 HOH A 102 603 603 HOH HOH . E 5 HOH A 103 604 604 HOH HOH . E 5 HOH A 104 605 605 HOH HOH . E 5 HOH A 105 606 606 HOH HOH . E 5 HOH A 106 607 607 HOH HOH . E 5 HOH A 107 608 608 HOH HOH . E 5 HOH A 108 609 609 HOH HOH . E 5 HOH A 109 610 610 HOH HOH . E 5 HOH A 110 611 611 HOH HOH . E 5 HOH A 111 612 612 HOH HOH . E 5 HOH A 112 613 613 HOH HOH . E 5 HOH A 113 614 614 HOH HOH . E 5 HOH A 114 615 615 HOH HOH . E 5 HOH A 115 616 616 HOH HOH . E 5 HOH A 116 617 617 HOH HOH . E 5 HOH A 117 618 618 HOH HOH . E 5 HOH A 118 619 619 HOH HOH . E 5 HOH A 119 620 620 HOH HOH . E 5 HOH A 120 621 621 HOH HOH . E 5 HOH A 121 622 622 HOH HOH . E 5 HOH A 122 623 623 HOH HOH . E 5 HOH A 123 624 624 HOH HOH . E 5 HOH A 124 625 625 HOH HOH . E 5 HOH A 125 626 626 HOH HOH . E 5 HOH A 126 627 627 HOH HOH . E 5 HOH A 127 628 628 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 . . . D 4 63.934 53.045 36.519 1 19.6 ? PB GDP 1452 A 1 HETATM 2 O O1B GDP . . . D 4 63.688 51.979 37.569 1 10.61 ? O1B GDP 1452 A 1 HETATM 3 O O2B GDP . . . D 4 63.251 54.367 36.813 1 18.69 ? O2B GDP 1452 A 1 HETATM 4 O O3B GDP . . . D 4 65.417 53.226 36.212 1 23.94 ? O3B GDP 1452 A 1 HETATM 5 O O3A GDP . . . D 4 63.247 52.461 35.166 1 20.73 ? O3A GDP 1452 A 1 HETATM 6 P PA GDP . . . D 4 61.649 52.476 34.852 1 24.46 ? PA GDP 1452 A 1 HETATM 7 O O1A GDP . . . D 4 61.108 51.261 35.497 1 29.38 ? O1A GDP 1452 A 1 HETATM 8 O O2A GDP . . . D 4 61.117 53.802 35.256 1 28.17 ? O2A GDP 1452 A 1 HETATM 9 O O5' GDP . . . D 4 61.447 52.356 33.277 1 24.89 ? O5' GDP 1452 A 1 HETATM 10 C C5' GDP . . . D 4 62.266 51.506 32.483 1 23.45 ? C5' GDP 1452 A 1 HETATM 11 C C4' GDP . . . D 4 61.408 50.506 31.738 1 27.42 ? C4' GDP 1452 A 1 HETATM 12 O O4' GDP . . . D 4 62.214 49.667 30.872 1 28.56 ? O4' GDP 1452 A 1 HETATM 13 C C3' GDP . . . D 4 60.595 49.569 32.623 1 27.73 ? C3' GDP 1452 A 1 HETATM 14 O O3' GDP . . . D 4 59.238 49.53 32.203 1 33.06 ? O3' GDP 1452 A 1 HETATM 15 C C2' GDP . . . D 4 61.297 48.227 32.474 1 26.88 ? C2' GDP 1452 A 1 HETATM 16 O O2' GDP . . . D 4 60.407 47.145 32.645 1 25.87 ? O2' GDP 1452 A 1 HETATM 17 C C1' GDP . . . D 4 61.842 48.317 31.048 1 26.14 ? C1' GDP 1452 A 1 HETATM 18 N N9 GDP . . . D 4 63.04 47.509 30.861 1 28.84 ? N9 GDP 1452 A 1 HETATM 19 C C8 GDP . . . D 4 64.162 47.529 31.652 1 27.51 ? C8 GDP 1452 A 1 HETATM 20 N N7 GDP . . . D 4 65.17 46.886 31.13 1 31.68 ? N7 GDP 1452 A 1 HETATM 21 C C5 GDP . . . D 4 64.684 46.411 29.919 1 32.51 ? C5 GDP 1452 A 1 HETATM 22 C C6 GDP . . . D 4 65.317 45.63 28.915 1 30.43 ? C6 GDP 1452 A 1 HETATM 23 O O6 GDP . . . D 4 66.468 45.187 28.894 1 27.63 ? O6 GDP 1452 A 1 HETATM 24 N N1 GDP . . . D 4 64.457 45.37 27.855 1 31.88 ? N1 GDP 1452 A 1 HETATM 25 C C2 GDP . . . D 4 63.157 45.798 27.767 1 28.42 ? C2 GDP 1452 A 1 HETATM 26 N N2 GDP . . . D 4 62.491 45.436 26.662 1 24.19 ? N2 GDP 1452 A 1 HETATM 27 N N3 GDP . . . D 4 62.555 46.524 28.694 1 30.36 ? N3 GDP 1452 A 1 HETATM 28 C C4 GDP . . . D 4 63.371 46.79 29.736 1 30.55 ? C4 GDP 1452 A 1 # _model_server_stats.io_time_ms 7 _model_server_stats.parse_time_ms 6 _model_server_stats.create_model_time_ms 3 _model_server_stats.query_time_ms 243 _model_server_stats.encode_time_ms 3 _model_server_stats.element_count 28 #