data_6KVQ # _model_server_result.job_id YaJA-uGIGw6WMom1ivPtTg _model_server_result.datetime_utc '2025-04-21 13:36:38' _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 6kvq # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"B","auth_seq_id":401}' # _entry.id 6KVQ # _exptl.entry_id 6KVQ _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 111.24 _cell.angle_gamma 90 _cell.entry_id 6KVQ _cell.length_a 72.268 _cell.length_b 49.686 _cell.length_c 88.592 _cell.Z_PDB 4 _cell.pdbx_unique_axis ? # _symmetry.entry_id 6KVQ _symmetry.cell_setting ? _symmetry.Int_Tables_number 5 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'C 1 2 1' # _pdbx_struct_assembly.method_details PISA _pdbx_struct_assembly.oligomeric_details monomeric _pdbx_struct_assembly.oligomeric_count 1 _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 # _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 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 O LEU 192 A LEU 200 1_555 C CA CA . A CA 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.334 ? metalc ? metalc2 A O VAL 195 A VAL 203 1_555 C CA CA . A CA 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.284 ? metalc ? metalc3 A OD1 ASN 200 A ASN 208 1_555 C CA CA . A CA 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.415 ? metalc ? metalc4 A O LEU 201 A LEU 209 1_555 C CA CA . A CA 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.28 ? metalc ? metalc5 C CA CA . A CA 402 1_555 D O30 DVX . A DVX 403 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.337 ? metalc ? metalc6 C CA CA . A CA 402 1_555 E O HOH . A HOH 630 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.352 ? # _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 151 n n PB O2B GDP sing 152 n n PB O3B GDP sing 153 n n PB O3A GDP sing 154 n n O2B HOB2 GDP sing 155 n n O3B HOB3 GDP sing 156 n n O3A PA GDP sing 157 n n PA O1A GDP doub 158 n n PA O2A GDP sing 159 n n PA O5' GDP sing 160 n n O2A HOA2 GDP sing 161 n n O5' C5' GDP sing 162 n n C5' C4' GDP sing 163 n n C5' H5' GDP sing 164 n n C5' "H5''" GDP sing 165 n n C4' O4' GDP sing 166 n n C4' C3' GDP sing 167 n n C4' H4' GDP sing 168 n n O4' C1' GDP sing 169 n n C3' O3' GDP sing 170 n n C3' C2' GDP sing 171 n n C3' H3' GDP sing 172 n n O3' HO3' GDP sing 173 n n C2' O2' GDP sing 174 n n C2' C1' GDP sing 175 n n C2' H2' GDP sing 176 n n O2' HO2' GDP sing 177 n n C1' N9 GDP sing 178 n n C1' H1' GDP sing 179 n n N9 C8 GDP sing 180 n y N9 C4 GDP sing 181 n y C8 N7 GDP doub 182 n y C8 H8 GDP sing 183 n n N7 C5 GDP sing 184 n y C5 C6 GDP sing 185 n n C5 C4 GDP doub 186 n y C6 O6 GDP doub 187 n n C6 N1 GDP sing 188 n n N1 C2 GDP sing 189 n n N1 HN1 GDP sing 190 n n C2 N2 GDP sing 191 n n C2 N3 GDP doub 192 n n N2 HN21 GDP sing 193 n n N2 HN22 GDP sing 194 n n N3 C4 GDP sing 195 n n # _atom_sites.entry_id 6KVQ _atom_sites.fract_transf_matrix[1][1] 0.013837 _atom_sites.fract_transf_matrix[1][2] 0 _atom_sites.fract_transf_matrix[1][3] 0.005378 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.020126 _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] 0.01211 _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 1 GDP GDP . C 3 CA A 1 402 1 CA CA . D 4 DVX A 1 403 1 DVX YZZ . E 5 HOH A 1 501 154 HOH HOH . E 5 HOH A 2 502 150 HOH HOH . E 5 HOH A 3 503 199 HOH HOH . E 5 HOH A 4 504 85 HOH HOH . E 5 HOH A 5 505 65 HOH HOH . E 5 HOH A 6 506 86 HOH HOH . E 5 HOH A 7 507 33 HOH HOH . E 5 HOH A 8 508 43 HOH HOH . E 5 HOH A 9 509 87 HOH HOH . E 5 HOH A 10 510 125 HOH HOH . E 5 HOH A 11 511 145 HOH HOH . E 5 HOH A 12 512 149 HOH HOH . E 5 HOH A 13 513 121 HOH HOH . E 5 HOH A 14 514 133 HOH HOH . E 5 HOH A 15 515 89 HOH HOH . E 5 HOH A 16 516 114 HOH HOH . E 5 HOH A 17 517 165 HOH HOH . E 5 HOH A 18 518 5 HOH HOH . E 5 HOH A 19 519 191 HOH HOH . E 5 HOH A 20 520 59 HOH HOH . E 5 HOH A 21 521 79 HOH HOH . E 5 HOH A 22 522 42 HOH HOH . E 5 HOH A 23 523 62 HOH HOH . E 5 HOH A 24 524 167 HOH HOH . E 5 HOH A 25 525 19 HOH HOH . E 5 HOH A 26 526 169 HOH HOH . E 5 HOH A 27 527 131 HOH HOH . E 5 HOH A 28 528 162 HOH HOH . E 5 HOH A 29 529 160 HOH HOH . E 5 HOH A 30 530 177 HOH HOH . E 5 HOH A 31 531 46 HOH HOH . E 5 HOH A 32 532 152 HOH HOH . E 5 HOH A 33 533 128 HOH HOH . E 5 HOH A 34 534 39 HOH HOH . E 5 HOH A 35 535 6 HOH HOH . E 5 HOH A 36 536 37 HOH HOH . E 5 HOH A 37 537 29 HOH HOH . E 5 HOH A 38 538 98 HOH HOH . E 5 HOH A 39 539 24 HOH HOH . E 5 HOH A 40 540 14 HOH HOH . E 5 HOH A 41 541 22 HOH HOH . E 5 HOH A 42 542 92 HOH HOH . E 5 HOH A 43 543 193 HOH HOH . E 5 HOH A 44 544 106 HOH HOH . E 5 HOH A 45 545 83 HOH HOH . E 5 HOH A 46 546 97 HOH HOH . E 5 HOH A 47 547 55 HOH HOH . E 5 HOH A 48 548 155 HOH HOH . E 5 HOH A 49 549 178 HOH HOH . E 5 HOH A 50 550 31 HOH HOH . E 5 HOH A 51 551 21 HOH HOH . E 5 HOH A 52 552 99 HOH HOH . E 5 HOH A 53 553 75 HOH HOH . E 5 HOH A 54 554 81 HOH HOH . E 5 HOH A 55 555 36 HOH HOH . E 5 HOH A 56 556 63 HOH HOH . E 5 HOH A 57 557 129 HOH HOH . E 5 HOH A 58 558 44 HOH HOH . E 5 HOH A 59 559 141 HOH HOH . E 5 HOH A 60 560 127 HOH HOH . E 5 HOH A 61 561 53 HOH HOH . E 5 HOH A 62 562 54 HOH HOH . E 5 HOH A 63 563 8 HOH HOH . E 5 HOH A 64 564 11 HOH HOH . E 5 HOH A 65 565 47 HOH HOH . E 5 HOH A 66 566 51 HOH HOH . E 5 HOH A 67 567 148 HOH HOH . E 5 HOH A 68 568 157 HOH HOH . E 5 HOH A 69 569 164 HOH HOH . E 5 HOH A 70 570 17 HOH HOH . E 5 HOH A 71 571 52 HOH HOH . E 5 HOH A 72 572 182 HOH HOH . E 5 HOH A 73 573 35 HOH HOH . E 5 HOH A 74 574 115 HOH HOH . E 5 HOH A 75 575 100 HOH HOH . E 5 HOH A 76 576 72 HOH HOH . E 5 HOH A 77 577 30 HOH HOH . E 5 HOH A 78 578 134 HOH HOH . E 5 HOH A 79 579 38 HOH HOH . E 5 HOH A 80 580 69 HOH HOH . E 5 HOH A 81 581 66 HOH HOH . E 5 HOH A 82 582 109 HOH HOH . E 5 HOH A 83 583 187 HOH HOH . E 5 HOH A 84 584 56 HOH HOH . E 5 HOH A 85 585 15 HOH HOH . E 5 HOH A 86 586 68 HOH HOH . E 5 HOH A 87 587 82 HOH HOH . E 5 HOH A 88 588 32 HOH HOH . E 5 HOH A 89 589 122 HOH HOH . E 5 HOH A 90 590 26 HOH HOH . E 5 HOH A 91 591 20 HOH HOH . E 5 HOH A 92 592 76 HOH HOH . E 5 HOH A 93 593 103 HOH HOH . E 5 HOH A 94 594 119 HOH HOH . E 5 HOH A 95 595 18 HOH HOH . E 5 HOH A 96 596 78 HOH HOH . E 5 HOH A 97 597 190 HOH HOH . E 5 HOH A 98 598 95 HOH HOH . E 5 HOH A 99 599 195 HOH HOH . E 5 HOH A 100 600 48 HOH HOH . E 5 HOH A 101 601 4 HOH HOH . E 5 HOH A 102 602 110 HOH HOH . E 5 HOH A 103 603 171 HOH HOH . E 5 HOH A 104 604 185 HOH HOH . E 5 HOH A 105 605 130 HOH HOH . E 5 HOH A 106 606 40 HOH HOH . E 5 HOH A 107 607 12 HOH HOH . E 5 HOH A 108 608 77 HOH HOH . E 5 HOH A 109 609 41 HOH HOH . E 5 HOH A 110 610 91 HOH HOH . E 5 HOH A 111 611 84 HOH HOH . E 5 HOH A 112 612 96 HOH HOH . E 5 HOH A 113 613 27 HOH HOH . E 5 HOH A 114 614 153 HOH HOH . E 5 HOH A 115 615 64 HOH HOH . E 5 HOH A 116 616 58 HOH HOH . E 5 HOH A 117 617 23 HOH HOH . E 5 HOH A 118 618 88 HOH HOH . E 5 HOH A 119 619 111 HOH HOH . E 5 HOH A 120 620 50 HOH HOH . E 5 HOH A 121 621 142 HOH HOH . E 5 HOH A 122 622 57 HOH HOH . E 5 HOH A 123 623 166 HOH HOH . E 5 HOH A 124 624 105 HOH HOH . E 5 HOH A 125 625 28 HOH HOH . E 5 HOH A 126 626 45 HOH HOH . E 5 HOH A 127 627 94 HOH HOH . E 5 HOH A 128 628 93 HOH HOH . E 5 HOH A 129 629 180 HOH HOH . E 5 HOH A 130 630 7 HOH HOH . E 5 HOH A 131 631 158 HOH HOH . E 5 HOH A 132 632 102 HOH HOH . E 5 HOH A 133 633 140 HOH HOH . E 5 HOH A 134 634 123 HOH HOH . E 5 HOH A 135 635 60 HOH HOH . E 5 HOH A 136 636 70 HOH HOH . E 5 HOH A 137 637 135 HOH HOH . E 5 HOH A 138 638 108 HOH HOH . E 5 HOH A 139 639 192 HOH HOH . E 5 HOH A 140 640 161 HOH HOH . E 5 HOH A 141 641 143 HOH HOH . E 5 HOH A 142 642 120 HOH HOH . E 5 HOH A 143 643 147 HOH HOH . E 5 HOH A 144 644 184 HOH HOH . E 5 HOH A 145 645 173 HOH HOH . E 5 HOH A 146 646 107 HOH HOH . E 5 HOH A 147 647 124 HOH HOH . E 5 HOH A 148 648 139 HOH HOH . E 5 HOH A 149 649 126 HOH HOH . E 5 HOH A 150 650 174 HOH HOH . E 5 HOH A 151 651 49 HOH HOH . E 5 HOH A 152 652 117 HOH HOH . E 5 HOH A 153 653 113 HOH HOH . E 5 HOH A 154 654 116 HOH HOH . E 5 HOH A 155 655 146 HOH HOH . E 5 HOH A 156 656 118 HOH HOH . E 5 HOH A 157 657 186 HOH HOH . E 5 HOH A 158 658 163 HOH HOH . E 5 HOH A 159 659 132 HOH HOH . E 5 HOH A 160 660 198 HOH HOH . E 5 HOH A 161 661 156 HOH HOH . E 5 HOH A 162 662 159 HOH HOH . E 5 HOH A 163 663 194 HOH HOH . E 5 HOH A 164 664 172 HOH HOH . E 5 HOH A 165 665 144 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 -21.338 -10.422 14.391 1 19.1 ? PB GDP 401 A 1 HETATM 2 O O1B GDP . . . B 2 -21.831 -11.661 13.719 1 23.78 ? O1B GDP 401 A 1 HETATM 3 O O2B GDP . . . B 2 -19.907 -10.065 14.012 1 24.23 ? O2B GDP 401 A 1 HETATM 4 O O3B GDP . . . B 2 -22.242 -9.247 14.156 1 18.59 ? O3B GDP 401 A 1 HETATM 5 O O3A GDP . . . B 2 -21.362 -10.796 15.969 1 17.37 ? O3A GDP 401 A 1 HETATM 6 P PA GDP . . . B 2 -21.333 -9.754 17.201 1 21.2 ? PA GDP 401 A 1 HETATM 7 O O1A GDP . . . B 2 -20.315 -8.663 16.956 1 21.44 ? O1A GDP 401 A 1 HETATM 8 O O2A GDP . . . B 2 -22.74 -9.275 17.52 1 21.22 ? O2A GDP 401 A 1 HETATM 9 O O5' GDP . . . B 2 -20.862 -10.736 18.37 1 21.43 ? O5' GDP 401 A 1 HETATM 10 C C5' GDP . . . B 2 -19.598 -11.388 18.299 1 19.86 ? C5' GDP 401 A 1 HETATM 11 C C4' GDP . . . B 2 -18.954 -11.442 19.679 1 21.5 ? C4' GDP 401 A 1 HETATM 12 O O4' GDP . . . B 2 -18.595 -10.124 20.073 1 19.52 ? O4' GDP 401 A 1 HETATM 13 C C3' GDP . . . B 2 -19.915 -11.932 20.731 1 25.15 ? C3' GDP 401 A 1 HETATM 14 O O3' GDP . . . B 2 -19.813 -13.357 20.776 1 30.28 ? O3' GDP 401 A 1 HETATM 15 C C2' GDP . . . B 2 -19.405 -11.265 21.985 1 21.1 ? C2' GDP 401 A 1 HETATM 16 O O2' GDP . . . B 2 -18.305 -11.998 22.53 1 21.88 ? O2' GDP 401 A 1 HETATM 17 C C1' GDP . . . B 2 -18.762 -10.001 21.505 1 18.58 ? C1' GDP 401 A 1 HETATM 18 N N9 GDP . . . B 2 -19.523 -8.748 21.615 1 20.98 ? N9 GDP 401 A 1 HETATM 19 C C8 GDP . . . B 2 -20.614 -8.404 20.899 1 20.81 ? C8 GDP 401 A 1 HETATM 20 N N7 GDP . . . B 2 -20.984 -7.137 21.182 1 20.02 ? N7 GDP 401 A 1 HETATM 21 C C5 GDP . . . B 2 -20.08 -6.654 22.072 1 22.76 ? C5 GDP 401 A 1 HETATM 22 C C6 GDP . . . B 2 -19.85 -5.389 22.795 1 24.04 ? C6 GDP 401 A 1 HETATM 23 O O6 GDP . . . B 2 -20.613 -4.417 22.611 1 22.6 ? O6 GDP 401 A 1 HETATM 24 N N1 GDP . . . B 2 -18.797 -5.305 23.624 1 22.28 ? N1 GDP 401 A 1 HETATM 25 C C2 GDP . . . B 2 -17.94 -6.334 23.834 1 23.39 ? C2 GDP 401 A 1 HETATM 26 N N2 GDP . . . B 2 -16.907 -6.178 24.699 1 23.47 ? N2 GDP 401 A 1 HETATM 27 N N3 GDP . . . B 2 -18.078 -7.524 23.211 1 21.7 ? N3 GDP 401 A 1 HETATM 28 C C4 GDP . . . B 2 -19.108 -7.719 22.345 1 23.28 ? C4 GDP 401 A 1 # _model_server_stats.io_time_ms 13 _model_server_stats.parse_time_ms 11 _model_server_stats.create_model_time_ms 4 _model_server_stats.query_time_ms 314 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 28 #