data_7OHL # _model_server_result.job_id lHRQPbxKO8nWzcnKF3Dolg _model_server_result.datetime_utc '2025-07-13 14:28:20' _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 7ohl # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"B","auth_seq_id":401}' # _entry.id 7OHL # _exptl.entry_id 7OHL _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 110.819 _cell.angle_gamma 90 _cell.entry_id 7OHL _cell.length_a 72.02 _cell.length_b 51.49 _cell.length_c 88.02 _cell.Z_PDB 4 _cell.pdbx_unique_axis ? # _symmetry.entry_id 7OHL _symmetry.cell_setting ? _symmetry.Int_Tables_number 5 _symmetry.space_group_name_Hall 'C 2y' _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,F _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 OE1 GLN 58 A GLN 48 1_555 E K K . A K 404 3_545 ? ? ? ? ? ? ? ? ? ? ? ? 2.878 ? metalc ? metalc2 A O LEU 210 A LEU 200 1_555 E K K . A K 404 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.522 ? metalc ? metalc3 A O VAL 213 A VAL 203 1_555 E K K . A K 404 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.548 ? metalc ? metalc4 A OD1 ASN 218 A ASN 208 1_555 E K K . A K 404 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.74 ? metalc ? metalc5 A O LEU 219 A LEU 209 1_555 E K K . A K 404 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.576 ? metalc ? metalc6 B O3B GDP . A GDP 401 1_555 C BE BEF . A BEF 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.433 ? metalc ? metalc7 B O1B GDP . A GDP 401 1_555 D MN MN . A MN 403 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.222 ? metalc ? metalc8 C F3 BEF . A BEF 402 1_555 D MN MN . A MN 403 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.182 ? metalc ? metalc9 D MN MN . A MN 403 1_555 F O HOH . A HOH 521 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.262 ? metalc ? metalc10 D MN MN . A MN 403 1_555 F O HOH . A HOH 538 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.205 ? metalc ? metalc11 D MN MN . A MN 403 1_555 F O HOH . A HOH 568 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.174 ? metalc ? metalc12 D MN MN . A MN 403 1_555 F O HOH . A HOH 573 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.189 ? metalc ? metalc13 E K K . A K 404 1_555 F O HOH . A HOH 508 3_455 ? ? ? ? ? ? ? ? ? ? ? ? 2.964 ? metalc ? metalc14 E K K . A K 404 1_555 F O HOH . A HOH 585 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.614 ? # _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 73 n n PB O2B GDP sing 74 n n PB O3B GDP sing 75 n n PB O3A GDP sing 76 n n O2B HOB2 GDP sing 77 n n O3B HOB3 GDP sing 78 n n O3A PA GDP sing 79 n n PA O1A GDP doub 80 n n PA O2A GDP sing 81 n n PA O5' GDP sing 82 n n O2A HOA2 GDP sing 83 n n O5' C5' GDP sing 84 n n C5' C4' GDP sing 85 n n C5' H5' GDP sing 86 n n C5' "H5''" GDP sing 87 n n C4' O4' GDP sing 88 n n C4' C3' GDP sing 89 n n C4' H4' GDP sing 90 n n O4' C1' GDP sing 91 n n C3' O3' GDP sing 92 n n C3' C2' GDP sing 93 n n C3' H3' GDP sing 94 n n O3' HO3' GDP sing 95 n n C2' O2' GDP sing 96 n n C2' C1' GDP sing 97 n n C2' H2' GDP sing 98 n n O2' HO2' GDP sing 99 n n C1' N9 GDP sing 100 n n C1' H1' GDP sing 101 n n N9 C8 GDP sing 102 n y N9 C4 GDP sing 103 n y C8 N7 GDP doub 104 n y C8 H8 GDP sing 105 n n N7 C5 GDP sing 106 n y C5 C6 GDP sing 107 n n C5 C4 GDP doub 108 n y C6 O6 GDP doub 109 n n C6 N1 GDP sing 110 n n N1 C2 GDP sing 111 n n N1 HN1 GDP sing 112 n n C2 N2 GDP sing 113 n n C2 N3 GDP doub 114 n n N2 HN21 GDP sing 115 n n N2 HN22 GDP sing 116 n n N3 C4 GDP sing 117 n n # _atom_sites.entry_id 7OHL _atom_sites.fract_transf_matrix[1][1] 0.013885 _atom_sites.fract_transf_matrix[1][2] 0 _atom_sites.fract_transf_matrix[1][3] 0.00528 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.019421 _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] 0.012155 _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 BEF A 1 402 1 BEF BEF . D 4 MN A 1 403 1 MN MN . E 5 K A 1 404 1 K K . F 6 HOH A 1 501 65 HOH HOH . F 6 HOH A 2 502 115 HOH HOH . F 6 HOH A 3 503 101 HOH HOH . F 6 HOH A 4 504 42 HOH HOH . F 6 HOH A 5 505 47 HOH HOH . F 6 HOH A 6 506 17 HOH HOH . F 6 HOH A 7 507 62 HOH HOH . F 6 HOH A 8 508 100 HOH HOH . F 6 HOH A 9 509 37 HOH HOH . F 6 HOH A 10 510 86 HOH HOH . F 6 HOH A 11 511 64 HOH HOH . F 6 HOH A 12 512 21 HOH HOH . F 6 HOH A 13 513 30 HOH HOH . F 6 HOH A 14 514 24 HOH HOH . F 6 HOH A 15 515 18 HOH HOH . F 6 HOH A 16 516 48 HOH HOH . F 6 HOH A 17 517 19 HOH HOH . F 6 HOH A 18 518 80 HOH HOH . F 6 HOH A 19 519 92 HOH HOH . F 6 HOH A 20 520 87 HOH HOH . F 6 HOH A 21 521 102 HOH HOH . F 6 HOH A 22 522 10 HOH HOH . F 6 HOH A 23 523 31 HOH HOH . F 6 HOH A 24 524 68 HOH HOH . F 6 HOH A 25 525 95 HOH HOH . F 6 HOH A 26 526 11 HOH HOH . F 6 HOH A 27 527 57 HOH HOH . F 6 HOH A 28 528 40 HOH HOH . F 6 HOH A 29 529 22 HOH HOH . F 6 HOH A 30 530 26 HOH HOH . F 6 HOH A 31 531 58 HOH HOH . F 6 HOH A 32 532 13 HOH HOH . F 6 HOH A 33 533 56 HOH HOH . F 6 HOH A 34 534 23 HOH HOH . F 6 HOH A 35 535 76 HOH HOH . F 6 HOH A 36 536 55 HOH HOH . F 6 HOH A 37 537 9 HOH HOH . F 6 HOH A 38 538 79 HOH HOH . F 6 HOH A 39 539 70 HOH HOH . F 6 HOH A 40 540 43 HOH HOH . F 6 HOH A 41 541 52 HOH HOH . F 6 HOH A 42 542 28 HOH HOH . F 6 HOH A 43 543 82 HOH HOH . F 6 HOH A 44 544 15 HOH HOH . F 6 HOH A 45 545 94 HOH HOH . F 6 HOH A 46 546 46 HOH HOH . F 6 HOH A 47 547 74 HOH HOH . F 6 HOH A 48 548 6 HOH HOH . F 6 HOH A 49 549 60 HOH HOH . F 6 HOH A 50 550 12 HOH HOH . F 6 HOH A 51 551 1 HOH HOH . F 6 HOH A 52 552 14 HOH HOH . F 6 HOH A 53 553 25 HOH HOH . F 6 HOH A 54 554 78 HOH HOH . F 6 HOH A 55 555 49 HOH HOH . F 6 HOH A 56 556 91 HOH HOH . F 6 HOH A 57 557 105 HOH HOH . F 6 HOH A 58 558 114 HOH HOH . F 6 HOH A 59 559 35 HOH HOH . F 6 HOH A 60 560 2 HOH HOH . F 6 HOH A 61 561 93 HOH HOH . F 6 HOH A 62 562 8 HOH HOH . F 6 HOH A 63 563 61 HOH HOH . F 6 HOH A 64 564 96 HOH HOH . F 6 HOH A 65 565 5 HOH HOH . F 6 HOH A 66 566 98 HOH HOH . F 6 HOH A 67 567 4 HOH HOH . F 6 HOH A 68 568 3 HOH HOH . F 6 HOH A 69 569 39 HOH HOH . F 6 HOH A 70 570 20 HOH HOH . F 6 HOH A 71 571 108 HOH HOH . F 6 HOH A 72 572 75 HOH HOH . F 6 HOH A 73 573 113 HOH HOH . F 6 HOH A 74 574 32 HOH HOH . F 6 HOH A 75 575 53 HOH HOH . F 6 HOH A 76 576 81 HOH HOH . F 6 HOH A 77 577 84 HOH HOH . F 6 HOH A 78 578 27 HOH HOH . F 6 HOH A 79 579 33 HOH HOH . F 6 HOH A 80 580 16 HOH HOH . F 6 HOH A 81 581 67 HOH HOH . F 6 HOH A 82 582 36 HOH HOH . F 6 HOH A 83 583 7 HOH HOH . F 6 HOH A 84 584 44 HOH HOH . F 6 HOH A 85 585 99 HOH HOH . F 6 HOH A 86 586 97 HOH HOH . F 6 HOH A 87 587 51 HOH HOH . F 6 HOH A 88 588 103 HOH HOH . F 6 HOH A 89 589 107 HOH HOH . F 6 HOH A 90 590 85 HOH HOH . F 6 HOH A 91 591 41 HOH HOH . F 6 HOH A 92 592 59 HOH HOH . F 6 HOH A 93 593 69 HOH HOH . F 6 HOH A 94 594 29 HOH HOH . F 6 HOH A 95 595 89 HOH HOH . F 6 HOH A 96 596 71 HOH HOH . F 6 HOH A 97 597 111 HOH HOH . F 6 HOH A 98 598 66 HOH HOH . F 6 HOH A 99 599 34 HOH HOH . F 6 HOH A 100 600 54 HOH HOH . F 6 HOH A 101 601 72 HOH HOH . F 6 HOH A 102 602 63 HOH HOH . F 6 HOH A 103 603 109 HOH HOH . F 6 HOH A 104 604 110 HOH HOH . F 6 HOH A 105 605 83 HOH HOH . F 6 HOH A 106 606 104 HOH HOH . F 6 HOH A 107 607 112 HOH HOH . F 6 HOH A 108 608 50 HOH HOH . F 6 HOH A 109 609 45 HOH HOH . F 6 HOH A 110 610 38 HOH HOH . F 6 HOH A 111 611 90 HOH HOH . F 6 HOH A 112 612 117 HOH HOH . F 6 HOH A 113 613 106 HOH HOH . F 6 HOH A 114 614 73 HOH HOH . F 6 HOH A 115 615 116 HOH HOH . F 6 HOH A 116 616 88 HOH HOH . F 6 HOH A 117 617 77 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 5.584 -10.159 26.968 1 30.01 ? PB GDP 401 A 1 HETATM 2 O O1B GDP . . . B 2 6.575 -9.006 27.014 1 26.35 ? O1B GDP 401 A 1 HETATM 3 O O2B GDP . . . B 2 4.195 -9.667 27.405 1 26.36 ? O2B GDP 401 A 1 HETATM 4 O O3B GDP . . . B 2 5.895 -11.365 27.811 1 28.05 ? O3B GDP 401 A 1 HETATM 5 O O3A GDP . . . B 2 5.369 -10.702 25.426 1 28.93 ? O3A GDP 401 A 1 HETATM 6 P PA GDP . . . B 2 5.284 -9.72 24.079 1 31.31 ? PA GDP 401 A 1 HETATM 7 O O1A GDP . . . B 2 6.628 -9.334 23.666 1 32.44 ? O1A GDP 401 A 1 HETATM 8 O O2A GDP . . . B 2 4.328 -8.55 24.503 1 29.21 ? O2A GDP 401 A 1 HETATM 9 O O5' GDP . . . B 2 4.732 -10.851 22.996 1 30.4 ? O5' GDP 401 A 1 HETATM 10 C C5' GDP . . . B 2 3.429 -11.252 23.186 1 31.71 ? C5' GDP 401 A 1 HETATM 11 C C4' GDP . . . B 2 2.749 -11.219 21.755 1 31.91 ? C4' GDP 401 A 1 HETATM 12 O O4' GDP . . . B 2 2.537 -9.851 21.227 1 29.28 ? O4' GDP 401 A 1 HETATM 13 C C3' GDP . . . B 2 3.677 -11.902 20.7 1 33.36 ? C3' GDP 401 A 1 HETATM 14 O O3' GDP . . . B 2 3.417 -13.278 20.677 1 30.35 ? O3' GDP 401 A 1 HETATM 15 C C2' GDP . . . B 2 3.303 -11.14 19.412 1 29.86 ? C2' GDP 401 A 1 HETATM 16 O O2' GDP . . . B 2 2.064 -11.721 18.843 1 32.6 ? O2' GDP 401 A 1 HETATM 17 C C1' GDP . . . B 2 2.849 -9.798 19.731 1 31.03 ? C1' GDP 401 A 1 HETATM 18 N N9 GDP . . . B 2 3.585 -8.595 19.684 1 30.42 ? N9 GDP 401 A 1 HETATM 19 C C8 GDP . . . B 2 4.736 -8.295 20.459 1 32.63 ? C8 GDP 401 A 1 HETATM 20 N N7 GDP . . . B 2 5.016 -6.973 20.235 1 27.18 ? N7 GDP 401 A 1 HETATM 21 C C5 GDP . . . B 2 4.096 -6.55 19.24 1 27.06 ? C5 GDP 401 A 1 HETATM 22 C C6 GDP . . . B 2 3.928 -5.281 18.634 1 31.85 ? C6 GDP 401 A 1 HETATM 23 O O6 GDP . . . B 2 4.709 -4.333 18.933 1 33.97 ? O6 GDP 401 A 1 HETATM 24 N N1 GDP . . . B 2 2.804 -5.131 17.835 1 33 ? N1 GDP 401 A 1 HETATM 25 C C2 GDP . . . B 2 2.038 -6.187 17.556 1 31.36 ? C2 GDP 401 A 1 HETATM 26 N N2 GDP . . . B 2 0.982 -6.021 16.693 1 30.61 ? N2 GDP 401 A 1 HETATM 27 N N3 GDP . . . B 2 2.163 -7.424 18.116 1 25.21 ? N3 GDP 401 A 1 HETATM 28 C C4 GDP . . . B 2 3.204 -7.572 18.977 1 29.11 ? C4 GDP 401 A 1 HETATM 29 H H4' GDP . . . B 2 1.783 -11.724 21.894 1 38.28 ? H4' GDP 401 A 1 HETATM 30 H H3' GDP . . . B 2 4.759 -11.852 20.886 1 40.03 ? H3' GDP 401 A 1 HETATM 31 H HO3' GDP . . . B 2 3.164 -13.544 19.782 1 36.42 ? HO3' GDP 401 A 1 HETATM 32 H H2' GDP . . . B 2 4.183 -11.179 18.754 1 35.83 ? H2' GDP 401 A 1 HETATM 33 H HO2' GDP . . . B 2 2.191 -11.889 17.899 1 39.11 ? HO2' GDP 401 A 1 HETATM 34 H H1' GDP . . . B 2 2.137 -9.691 18.9 1 37.23 ? H1' GDP 401 A 1 HETATM 35 H H8 GDP . . . B 2 5.283 -8.976 21.1 1 39.15 ? H8 GDP 401 A 1 HETATM 36 H HN1 GDP . . . B 2 2.559 -4.195 17.452 1 39.59 ? HN1 GDP 401 A 1 HETATM 37 H HN21 GDP . . . B 2 0.344 -6.729 16.564 1 36.73 ? HN21 GDP 401 A 1 HETATM 38 H HN22 GDP . . . B 2 0.816 -5.099 16.263 1 36.73 ? HN22 GDP 401 A 1 # _model_server_stats.io_time_ms 24 _model_server_stats.parse_time_ms 31 _model_server_stats.create_model_time_ms 19 _model_server_stats.query_time_ms 912 _model_server_stats.encode_time_ms 8 _model_server_stats.element_count 38 #