data_4EB6 # _model_server_result.job_id xwGkrmT0jHtKBITdriVzlw _model_server_result.datetime_utc '2024-11-13 06:51:00' _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 4eb6 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"O","auth_seq_id":501}' # _entry.id 4EB6 # _exptl.entry_id 4EB6 _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 443.201 _entity.id 7 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description "GUANOSINE-5'-DIPHOSPHATE" _entity.pdbx_number_of_molecules 2 _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 4EB6 _cell.length_a 64.69 _cell.length_b 129.68 _cell.length_c 252.75 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 4EB6 _symmetry.cell_setting ? _symmetry.Int_Tables_number 19 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 21 21 21' # _pdbx_struct_assembly.method_details PISA _pdbx_struct_assembly.oligomeric_details pentameric _pdbx_struct_assembly.oligomeric_count 5 _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,J,K,L,M,N,O,P,Q,R,S,T,U,V _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 # loop_ _struct_asym.details _struct_asym.entity_id _struct_asym.id _struct_asym.pdbx_modified _struct_asym.pdbx_blank_PDB_chainid_flag ? 7 J N N ? 7 O 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 F O1B GTP . A GTP 501 1_555 G MG MG . A MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.945 ? metalc ? metalc2 F O2G GTP . A GTP 501 1_555 G MG MG . A MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.534 ? metalc ? metalc3 G MG MG . A MG 502 1_555 R O HOH . A HOH 601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.672 ? metalc ? metalc4 G MG MG . A MG 502 1_555 R O HOH . A HOH 602 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 3.051 ? metalc ? metalc5 G MG MG . A MG 502 1_555 R O HOH . A HOH 603 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.579 ? metalc ? metalc6 G MG MG . A MG 502 1_555 R O HOH . A HOH 604 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.081 ? metalc ? metalc7 L O1B GTP . C GTP 501 1_555 M MG MG . C MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.025 ? metalc ? metalc8 L O2G GTP . C GTP 501 1_555 M MG MG . C MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.274 ? metalc ? metalc9 M MG MG . C MG 502 1_555 T O HOH . C HOH 602 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.756 ? metalc ? metalc10 M MG MG . C MG 502 1_555 T O HOH . C HOH 603 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.405 ? metalc ? metalc11 M MG MG . C MG 502 1_555 T O HOH . C HOH 605 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.397 ? # _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 83 n n PB O2B GDP sing 84 n n PB O3B GDP sing 85 n n PB O3A GDP sing 86 n n O2B HOB2 GDP sing 87 n n O3B HOB3 GDP sing 88 n n O3A PA GDP sing 89 n n PA O1A GDP doub 90 n n PA O2A GDP sing 91 n n PA O5' GDP sing 92 n n O2A HOA2 GDP sing 93 n n O5' C5' GDP sing 94 n n C5' C4' GDP sing 95 n n C5' H5' GDP sing 96 n n C5' "H5''" GDP sing 97 n n C4' O4' GDP sing 98 n n C4' C3' GDP sing 99 n n C4' H4' GDP sing 100 n n O4' C1' GDP sing 101 n n C3' O3' GDP sing 102 n n C3' C2' GDP sing 103 n n C3' H3' GDP sing 104 n n O3' HO3' GDP sing 105 n n C2' O2' GDP sing 106 n n C2' C1' GDP sing 107 n n C2' H2' GDP sing 108 n n O2' HO2' GDP sing 109 n n C1' N9 GDP sing 110 n n C1' H1' GDP sing 111 n n N9 C8 GDP sing 112 n y N9 C4 GDP sing 113 n y C8 N7 GDP doub 114 n y C8 H8 GDP sing 115 n n N7 C5 GDP sing 116 n y C5 C6 GDP sing 117 n n C5 C4 GDP doub 118 n y C6 O6 GDP doub 119 n n C6 N1 GDP sing 120 n n N1 C2 GDP sing 121 n n N1 HN1 GDP sing 122 n n C2 N2 GDP sing 123 n n C2 N3 GDP doub 124 n n N2 HN21 GDP sing 125 n n N2 HN22 GDP sing 126 n n N3 C4 GDP sing 127 n n # _atom_sites.entry_id 4EB6 _atom_sites.fract_transf_matrix[1][1] 0.015458 _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] 0.007711 _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] 0.003956 _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 F 4 GTP A 1 501 501 GTP GTP . G 5 MG A 1 502 502 MG MG . H 6 SO4 A 1 503 503 SO4 SO4 . I 6 SO4 A 1 504 504 SO4 SO4 . J 7 GDP B 1 501 501 GDP GDP . K 6 SO4 B 1 502 502 SO4 SO4 . L 4 GTP C 1 501 501 GTP GTP . M 5 MG C 1 502 502 MG MG . N 8 VLB C 1 503 503 VLB VLB . O 7 GDP D 1 501 501 GDP GDP . P 6 SO4 D 1 502 502 SO4 SO4 . Q 6 SO4 D 1 503 503 SO4 SO4 . R 9 HOH A 1 601 601 HOH HOH . R 9 HOH A 2 602 602 HOH HOH . R 9 HOH A 3 603 603 HOH HOH . R 9 HOH A 4 604 604 HOH HOH . R 9 HOH A 5 605 605 HOH HOH . S 9 HOH B 1 601 601 HOH HOH . S 9 HOH B 2 602 602 HOH HOH . S 9 HOH B 3 603 603 HOH HOH . T 9 HOH C 1 601 601 HOH HOH . T 9 HOH C 2 602 602 HOH HOH . T 9 HOH C 3 603 603 HOH HOH . T 9 HOH C 4 604 604 HOH HOH . T 9 HOH C 5 605 605 HOH HOH . T 9 HOH C 6 606 606 HOH HOH . T 9 HOH C 7 607 607 HOH HOH . T 9 HOH C 8 608 608 HOH HOH . T 9 HOH C 9 609 609 HOH HOH . T 9 HOH C 10 610 610 HOH HOH . T 9 HOH C 11 611 611 HOH HOH . T 9 HOH C 12 612 612 HOH HOH . T 9 HOH C 13 613 613 HOH HOH . U 9 HOH D 1 601 601 HOH HOH . U 9 HOH D 2 602 602 HOH HOH . U 9 HOH D 3 603 603 HOH HOH . U 9 HOH D 4 604 604 HOH HOH . U 9 HOH D 5 605 605 HOH HOH . U 9 HOH D 6 606 606 HOH HOH . U 9 HOH D 7 607 607 HOH HOH . U 9 HOH D 8 608 608 HOH HOH . U 9 HOH D 9 609 609 HOH HOH . V 9 HOH E 1 201 201 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 . . . O 7 -38.005 157.721 116.757 1 125.96 ? PB GDP 501 D 1 HETATM 2 O O1B GDP . . . O 7 -37.314 158.76 115.936 1 130.76 ? O1B GDP 501 D 1 HETATM 3 O O2B GDP . . . O 7 -37.573 156.201 116.317 1 125.19 ? O2B GDP 501 D 1 HETATM 4 O O3B GDP . . . O 7 -39.595 157.921 116.512 1 130.82 ? O3B GDP 501 D 1 HETATM 5 O O3A GDP . . . O 7 -37.76 158.013 118.347 1 123.24 ? O3A GDP 501 D 1 HETATM 6 P PA GDP . . . O 7 -36.368 157.489 119.004 1 119.85 ? PA GDP 501 D 1 HETATM 7 O O1A GDP . . . O 7 -35.62 158.683 119.502 1 122.8 ? O1A GDP 501 D 1 HETATM 8 O O2A GDP . . . O 7 -35.473 156.749 117.87 1 121.46 ? O2A GDP 501 D 1 HETATM 9 O O5' GDP . . . O 7 -36.705 156.409 120.213 1 117.21 ? O5' GDP 501 D 1 HETATM 10 C C5' GDP . . . O 7 -36.864 156.94 121.556 1 116.81 ? C5' GDP 501 D 1 HETATM 11 C C4' GDP . . . O 7 -36.44 155.839 122.569 1 114.91 ? C4' GDP 501 D 1 HETATM 12 O O4' GDP . . . O 7 -35.09 155.326 122.373 1 113.32 ? O4' GDP 501 D 1 HETATM 13 C C3' GDP . . . O 7 -36.427 156.253 124.046 1 116.14 ? C3' GDP 501 D 1 HETATM 14 O O3' GDP . . . O 7 -36.462 155.082 124.822 1 118.08 ? O3' GDP 501 D 1 HETATM 15 C C2' GDP . . . O 7 -35.032 156.85 124.215 1 117.02 ? C2' GDP 501 D 1 HETATM 16 O O2' GDP . . . O 7 -34.491 156.728 125.512 1 119.11 ? O2' GDP 501 D 1 HETATM 17 C C1' GDP . . . O 7 -34.165 156.024 123.283 1 114.06 ? C1' GDP 501 D 1 HETATM 18 N N9 GDP . . . O 7 -33.278 156.921 122.554 1 114.88 ? N9 GDP 501 D 1 HETATM 19 C C8 GDP . . . O 7 -33.669 157.969 121.775 1 116.9 ? C8 GDP 501 D 1 HETATM 20 N N7 GDP . . . O 7 -32.659 158.558 121.236 1 118.97 ? N7 GDP 501 D 1 HETATM 21 C C5 GDP . . . O 7 -31.53 157.934 121.646 1 117.03 ? C5 GDP 501 D 1 HETATM 22 C C6 GDP . . . O 7 -30.125 158.099 121.37 1 119.91 ? C6 GDP 501 D 1 HETATM 23 O O6 GDP . . . O 7 -29.707 158.984 120.654 1 122.95 ? O6 GDP 501 D 1 HETATM 24 N N1 GDP . . . O 7 -29.246 157.255 121.972 1 118.46 ? N1 GDP 501 D 1 HETATM 25 C C2 GDP . . . O 7 -29.649 156.228 122.806 1 115.74 ? C2 GDP 501 D 1 HETATM 26 N N2 GDP . . . O 7 -28.671 155.42 123.369 1 117.19 ? N2 GDP 501 D 1 HETATM 27 N N3 GDP . . . O 7 -30.972 156.038 123.056 1 114.36 ? N3 GDP 501 D 1 HETATM 28 C C4 GDP . . . O 7 -31.927 156.857 122.501 1 114.91 ? C4 GDP 501 D 1 # _model_server_stats.io_time_ms 34 _model_server_stats.parse_time_ms 12 _model_server_stats.create_model_time_ms 30 _model_server_stats.query_time_ms 329 _model_server_stats.encode_time_ms 4 _model_server_stats.element_count 28 #