data_6XER # _model_server_result.job_id BSp4UYQ1b8BdGyGQdvMwmA _model_server_result.datetime_utc '2024-11-17 14:17:47' _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 6xer # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"I","auth_seq_id":501}' # _entry.id 6XER # _exptl.entry_id 6XER _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 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 6XER _cell.length_a 65.717 _cell.length_b 127.025 _cell.length_c 254.208 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 6XER _symmetry.cell_setting ? _symmetry.Int_Tables_number 19 _symmetry.space_group_name_Hall 'P 2ac 2ab' _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 _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 7 _struct_asym.id I _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 F O2G GTP . A GTP 501 1_555 G MG MG . A MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.022 ? metalc ? metalc2 F O2B GTP . A GTP 501 1_555 G MG MG . A MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.419 ? metalc ? metalc3 G MG MG . A MG 502 1_555 Q O HOH . A HOH 601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.145 ? metalc ? metalc4 G MG MG . A MG 502 1_555 Q O HOH . A HOH 602 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.06 ? metalc ? metalc5 G MG MG . A MG 502 1_555 Q O HOH . A HOH 603 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.177 ? metalc ? metalc6 G MG MG . A MG 502 1_555 Q O HOH . A HOH 604 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.363 ? metalc ? metalc7 L O3G GTP . C GTP 501 1_555 M MG MG . C MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.129 ? metalc ? metalc8 L O2B GTP . C GTP 501 1_555 M MG MG . C MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.221 ? metalc ? metalc9 M MG MG . C MG 502 1_555 S O HOH . C HOH 601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.952 ? metalc ? metalc10 M MG MG . C MG 502 1_555 S O HOH . C HOH 603 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.057 ? metalc ? metalc11 M MG MG . C MG 502 1_555 S O HOH . C HOH 604 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.087 ? metalc ? metalc12 M MG MG . C MG 502 1_555 S O HOH . C HOH 606 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.179 ? # _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 6XER _atom_sites.fract_transf_matrix[1][1] 0.015217 _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] 0.007872 _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] 0.003934 _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 1 SO4 SO4 . I 7 GDP B 1 501 501 GDP GDP . J 8 LOC B 1 502 502 LOC LOC . K 6 SO4 B 1 503 2 SO4 SO4 . L 4 GTP C 1 501 501 GTP GTP . M 5 MG C 1 502 502 MG MG . N 4 GTP D 1 501 501 GTP GTP . O 8 LOC D 1 502 502 LOC LOC . P 6 SO4 D 1 503 3 SO4 SO4 . Q 9 HOH A 1 601 4 HOH HOH . Q 9 HOH A 2 602 6 HOH HOH . Q 9 HOH A 3 603 3 HOH HOH . Q 9 HOH A 4 604 5 HOH HOH . Q 9 HOH A 5 605 11 HOH HOH . Q 9 HOH A 6 606 13 HOH HOH . Q 9 HOH A 7 607 14 HOH HOH . Q 9 HOH A 8 608 12 HOH HOH . Q 9 HOH A 9 609 32 HOH HOH . R 9 HOH B 1 601 17 HOH HOH . R 9 HOH B 2 602 15 HOH HOH . R 9 HOH B 3 603 16 HOH HOH . S 9 HOH C 1 601 8 HOH HOH . S 9 HOH C 2 602 33 HOH HOH . S 9 HOH C 3 603 10 HOH HOH . S 9 HOH C 4 604 7 HOH HOH . S 9 HOH C 5 605 28 HOH HOH . S 9 HOH C 6 606 9 HOH HOH . S 9 HOH C 7 607 18 HOH HOH . S 9 HOH C 8 608 19 HOH HOH . S 9 HOH C 9 609 21 HOH HOH . S 9 HOH C 10 610 22 HOH HOH . S 9 HOH C 11 611 26 HOH HOH . S 9 HOH C 12 612 25 HOH HOH . S 9 HOH C 13 613 23 HOH HOH . T 9 HOH D 1 601 30 HOH HOH . T 9 HOH D 2 602 31 HOH HOH . T 9 HOH D 3 603 29 HOH HOH . U 9 HOH E 1 201 20 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 . . . I 7 3.134 21.188 34.281 1 62 ? PB GDP 501 B 1 HETATM 2 O O1B GDP . . . I 7 4.59 21.608 34.32 1 54.39 ? O1B GDP 501 B 1 HETATM 3 O O2B GDP . . . I 7 2.252 22.02 35.183 1 58.14 ? O2B GDP 501 B 1 HETATM 4 O O3B GDP . . . I 7 3.047 19.722 34.686 1 72.66 ? O3B GDP 501 B 1 HETATM 5 O O3A GDP . . . I 7 2.653 21.375 32.767 1 62.56 ? O3A GDP 501 B 1 HETATM 6 P PA GDP . . . I 7 1.266 20.795 32.2 1 67.85 ? PA GDP 501 B 1 HETATM 7 O O1A GDP . . . I 7 0.458 21.968 31.69 1 68.53 ? O1A GDP 501 B 1 HETATM 8 O O2A GDP . . . I 7 0.514 19.964 33.21 1 62.76 ? O2A GDP 501 B 1 HETATM 9 O O5' GDP . . . I 7 1.845 19.852 31.024 1 71.08 ? O5' GDP 501 B 1 HETATM 10 C C5' GDP . . . I 7 1.558 20.004 29.637 1 69.33 ? C5' GDP 501 B 1 HETATM 11 C C4' GDP . . . I 7 1.177 18.652 29.05 1 68.41 ? C4' GDP 501 B 1 HETATM 12 O O4' GDP . . . I 7 0.001 18.183 29.729 1 63.59 ? O4' GDP 501 B 1 HETATM 13 C C3' GDP . . . I 7 0.765 18.793 27.607 1 69.28 ? C3' GDP 501 B 1 HETATM 14 O O3' GDP . . . I 7 0.788 17.491 27.016 1 76.49 ? O3' GDP 501 B 1 HETATM 15 C C2' GDP . . . I 7 -0.681 19.181 27.775 1 70.09 ? C2' GDP 501 B 1 HETATM 16 O O2' GDP . . . I 7 -1.496 19.03 26.612 1 72.22 ? O2' GDP 501 B 1 HETATM 17 C C1' GDP . . . I 7 -1.111 18.192 28.835 1 63.21 ? C1' GDP 501 B 1 HETATM 18 N N9 GDP . . . I 7 -2.304 18.692 29.552 1 62.83 ? N9 GDP 501 B 1 HETATM 19 C C8 GDP . . . I 7 -2.4 19.87 30.211 1 60.61 ? C8 GDP 501 B 1 HETATM 20 N N7 GDP . . . I 7 -3.63 20.019 30.779 1 56.09 ? N7 GDP 501 B 1 HETATM 21 C C5 GDP . . . I 7 -4.335 18.912 30.487 1 60.04 ? C5 GDP 501 B 1 HETATM 22 C C6 GDP . . . I 7 -5.697 18.402 30.774 1 61.72 ? C6 GDP 501 B 1 HETATM 23 O O6 GDP . . . I 7 -6.504 19.073 31.445 1 59.39 ? O6 GDP 501 B 1 HETATM 24 N N1 GDP . . . I 7 -6.037 17.193 30.286 1 62.81 ? N1 GDP 501 B 1 HETATM 25 C C2 GDP . . . I 7 -5.189 16.45 29.557 1 59.98 ? C2 GDP 501 B 1 HETATM 26 N N2 GDP . . . I 7 -5.614 15.25 29.111 1 60.34 ? N2 GDP 501 B 1 HETATM 27 N N3 GDP . . . I 7 -3.929 16.851 29.247 1 60.2 ? N3 GDP 501 B 1 HETATM 28 C C4 GDP . . . I 7 -3.459 18.045 29.674 1 60.57 ? C4 GDP 501 B 1 # _model_server_stats.io_time_ms 122 _model_server_stats.parse_time_ms 22 _model_server_stats.create_model_time_ms 47 _model_server_stats.query_time_ms 238 _model_server_stats.encode_time_ms 5 _model_server_stats.element_count 28 #