data_6S6D # _model_server_result.job_id hwIhP2oaehtNkayZgUO0nQ _model_server_result.datetime_utc '2024-10-11 07:25:05' _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 6s6d # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"L","auth_seq_id":401}' # _entry.id 6S6D # _exptl.entry_id 6S6D _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 443.201 _entity.id 5 _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 6S6D _cell.length_a 71.504 _cell.length_b 81.439 _cell.length_c 246.033 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 6S6D _symmetry.cell_setting ? _symmetry.Int_Tables_number 19 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 21 21 21' # loop_ _pdbx_struct_assembly.method_details _pdbx_struct_assembly.oligomeric_details _pdbx_struct_assembly.oligomeric_count _pdbx_struct_assembly.details _pdbx_struct_assembly.id PISA dimeric 2 author_and_software_defined_assembly 1 PISA dimeric 2 author_and_software_defined_assembly 2 # loop_ _pdbx_struct_assembly_gen.asym_id_list _pdbx_struct_assembly_gen.assembly_id _pdbx_struct_assembly_gen.oper_expression A,B,E,F,G,M,N 1 1 C,D,H,I,J,K,L,O,P 2 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 ? 5 G N N ? 5 L 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 A OG1 THR 21 A THR 21 1_555 F MG MG . A MG 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.02 ? metalc ? metalc2 A OG1 THR 42 A THR 42 1_555 F MG MG . A MG 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.964 ? metalc ? metalc3 E O1G GTP . A GTP 401 1_555 F MG MG . A MG 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.149 ? metalc ? metalc4 E O1B GTP . A GTP 401 1_555 F MG MG . A MG 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.076 ? metalc ? metalc5 F MG MG . A MG 402 1_555 M O HOH . A HOH 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.283 ? metalc ? metalc6 F MG MG . A MG 402 1_555 M O HOH . A HOH 507 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.059 ? metalc ? metalc7 C OG1 THR 21 B THR 21 1_555 I MG MG . B MG 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.989 ? metalc ? metalc8 C OG1 THR 42 B THR 42 1_555 I MG MG . B MG 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.472 ? metalc ? metalc9 H O1G GTP . B GTP 401 1_555 I MG MG . B MG 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.295 ? metalc ? metalc10 H O1B GTP . B GTP 401 1_555 I MG MG . B MG 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.454 ? metalc ? metalc11 I MG MG . B MG 402 1_555 O O HOH . B HOH 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.448 ? metalc ? metalc12 I MG MG . B MG 402 1_555 O O HOH . B HOH 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.225 ? # _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 101 n n PB O2B GDP sing 102 n n PB O3B GDP sing 103 n n PB O3A GDP sing 104 n n O2B HOB2 GDP sing 105 n n O3B HOB3 GDP sing 106 n n O3A PA GDP sing 107 n n PA O1A GDP doub 108 n n PA O2A GDP sing 109 n n PA O5' GDP sing 110 n n O2A HOA2 GDP sing 111 n n O5' C5' GDP sing 112 n n C5' C4' GDP sing 113 n n C5' H5' GDP sing 114 n n C5' "H5''" GDP sing 115 n n C4' O4' GDP sing 116 n n C4' C3' GDP sing 117 n n C4' H4' GDP sing 118 n n O4' C1' GDP sing 119 n n C3' O3' GDP sing 120 n n C3' C2' GDP sing 121 n n C3' H3' GDP sing 122 n n O3' HO3' GDP sing 123 n n C2' O2' GDP sing 124 n n C2' C1' GDP sing 125 n n C2' H2' GDP sing 126 n n O2' HO2' GDP sing 127 n n C1' N9 GDP sing 128 n n C1' H1' GDP sing 129 n n N9 C8 GDP sing 130 n y N9 C4 GDP sing 131 n y C8 N7 GDP doub 132 n y C8 H8 GDP sing 133 n n N7 C5 GDP sing 134 n y C5 C6 GDP sing 135 n n C5 C4 GDP doub 136 n y C6 O6 GDP doub 137 n n C6 N1 GDP sing 138 n n N1 C2 GDP sing 139 n n N1 HN1 GDP sing 140 n n C2 N2 GDP sing 141 n n C2 N3 GDP doub 142 n n N2 HN21 GDP sing 143 n n N2 HN22 GDP sing 144 n n N3 C4 GDP sing 145 n n # _atom_sites.entry_id 6S6D _atom_sites.fract_transf_matrix[1][1] 0.013985 _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] 0.012279 _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] 0.004064 _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 E 3 GTP A 1 401 1 GTP GTP . F 4 MG A 1 402 1 MG MG . G 5 GDP C 1 401 3 GDP GDP . H 3 GTP B 1 401 2 GTP GTP . I 4 MG B 1 402 2 MG MG . J 6 9JE B 1 403 1 9JE PEN . K 6 9JE B 1 404 2 9JE PEN . L 5 GDP D 1 401 4 GDP GDP . M 7 HOH A 1 501 113 HOH HOH . M 7 HOH A 2 502 117 HOH HOH . M 7 HOH A 3 503 119 HOH HOH . M 7 HOH A 4 504 112 HOH HOH . M 7 HOH A 5 505 111 HOH HOH . M 7 HOH A 6 506 19 HOH HOH . M 7 HOH A 7 507 118 HOH HOH . M 7 HOH A 8 508 72 HOH HOH . M 7 HOH A 9 509 102 HOH HOH . M 7 HOH A 10 510 88 HOH HOH . M 7 HOH A 11 511 21 HOH HOH . M 7 HOH A 12 512 17 HOH HOH . M 7 HOH A 13 513 28 HOH HOH . M 7 HOH A 14 514 12 HOH HOH . N 7 HOH C 1 501 25 HOH HOH . N 7 HOH C 2 502 116 HOH HOH . N 7 HOH C 3 503 9 HOH HOH . N 7 HOH C 4 504 110 HOH HOH . N 7 HOH C 5 505 53 HOH HOH . N 7 HOH C 6 506 68 HOH HOH . N 7 HOH C 7 507 64 HOH HOH . N 7 HOH C 8 508 20 HOH HOH . N 7 HOH C 9 509 24 HOH HOH . N 7 HOH C 10 510 37 HOH HOH . N 7 HOH C 11 511 49 HOH HOH . N 7 HOH C 12 512 115 HOH HOH . N 7 HOH C 13 513 1 HOH HOH . N 7 HOH C 14 514 114 HOH HOH . N 7 HOH C 15 515 40 HOH HOH . O 7 HOH B 1 501 2 HOH HOH . O 7 HOH B 2 502 3 HOH HOH . O 7 HOH B 3 503 43 HOH HOH . O 7 HOH B 4 504 4 HOH HOH . O 7 HOH B 5 505 41 HOH HOH . O 7 HOH B 6 506 78 HOH HOH . O 7 HOH B 7 507 27 HOH HOH . O 7 HOH B 8 508 50 HOH HOH . O 7 HOH B 9 509 60 HOH HOH . O 7 HOH B 10 510 18 HOH HOH . O 7 HOH B 11 511 101 HOH HOH . O 7 HOH B 12 512 42 HOH HOH . O 7 HOH B 13 513 16 HOH HOH . O 7 HOH B 14 514 31 HOH HOH . O 7 HOH B 15 515 23 HOH HOH . O 7 HOH B 16 516 104 HOH HOH . O 7 HOH B 17 517 22 HOH HOH . O 7 HOH B 18 518 6 HOH HOH . P 7 HOH D 1 501 26 HOH HOH . P 7 HOH D 2 502 65 HOH HOH . P 7 HOH D 3 503 5 HOH HOH . P 7 HOH D 4 504 30 HOH HOH . P 7 HOH D 5 505 8 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 . . . L 5 -21.208 22.549 -68.622 1 121.19 ? PB GDP 401 D 1 HETATM 2 O O1B GDP . . . L 5 -21.584 21.886 -69.926 1 105.11 ? O1B GDP 401 D 1 HETATM 3 O O2B GDP . . . L 5 -21.006 24.061 -68.727 1 102.38 -1 O2B GDP 401 D 1 HETATM 4 O O3B GDP . . . L 5 -20.099 21.86 -67.87 1 123.39 ? O3B GDP 401 D 1 HETATM 5 O O3A GDP . . . L 5 -22.52 22.228 -67.71 1 102.48 ? O3A GDP 401 D 1 HETATM 6 P PA GDP . . . L 5 -22.446 21.639 -66.207 1 107.02 ? PA GDP 401 D 1 HETATM 7 O O1A GDP . . . L 5 -21.852 20.242 -66.275 1 90.88 ? O1A GDP 401 D 1 HETATM 8 O O2A GDP . . . L 5 -21.825 22.743 -65.349 1 99.88 -1 O2A GDP 401 D 1 HETATM 9 O O5' GDP . . . L 5 -23.978 21.453 -65.746 1 90.23 ? O5' GDP 401 D 1 HETATM 10 C C5' GDP . . . L 5 -24.829 22.571 -65.882 1 91.22 ? C5' GDP 401 D 1 HETATM 11 C C4' GDP . . . L 5 -26.111 22.299 -65.135 1 97.38 ? C4' GDP 401 D 1 HETATM 12 O O4' GDP . . . L 5 -26.755 21.234 -65.826 1 93.74 ? O4' GDP 401 D 1 HETATM 13 C C3' GDP . . . L 5 -25.923 21.882 -63.666 1 97.23 ? C3' GDP 401 D 1 HETATM 14 O O3' GDP . . . L 5 -26.735 22.686 -62.781 1 87.34 ? O3' GDP 401 D 1 HETATM 15 C C2' GDP . . . L 5 -26.368 20.429 -63.616 1 93.69 ? C2' GDP 401 D 1 HETATM 16 O O2' GDP . . . L 5 -27.143 20.08 -62.455 1 85.36 ? O2' GDP 401 D 1 HETATM 17 C C1' GDP . . . L 5 -27.271 20.359 -64.833 1 95.7 ? C1' GDP 401 D 1 HETATM 18 N N9 GDP . . . L 5 -27.379 18.989 -65.339 1 90.25 ? N9 GDP 401 D 1 HETATM 19 C C8 GDP . . . L 5 -26.419 18.222 -65.869 1 91.65 ? C8 GDP 401 D 1 HETATM 20 N N7 GDP . . . L 5 -26.939 17.01 -66.223 1 88.1 ? N7 GDP 401 D 1 HETATM 21 C C5 GDP . . . L 5 -28.235 17.015 -65.897 1 79.52 ? C5 GDP 401 D 1 HETATM 22 C C6 GDP . . . L 5 -29.349 16.073 -65.991 1 88.63 ? C6 GDP 401 D 1 HETATM 23 O O6 GDP . . . L 5 -29.168 14.938 -66.496 1 92.88 ? O6 GDP 401 D 1 HETATM 24 N N1 GDP . . . L 5 -30.54 16.478 -65.526 1 93.99 ? N1 GDP 401 D 1 HETATM 25 C C2 GDP . . . L 5 -30.742 17.704 -64.999 1 100.29 ? C2 GDP 401 D 1 HETATM 26 N N2 GDP . . . L 5 -31.965 18.056 -64.555 1 105.28 ? N2 GDP 401 D 1 HETATM 27 N N3 GDP . . . L 5 -29.764 18.628 -64.89 1 96.2 ? N3 GDP 401 D 1 HETATM 28 C C4 GDP . . . L 5 -28.517 18.321 -65.311 1 90.26 ? C4 GDP 401 D 1 # _model_server_stats.io_time_ms 11 _model_server_stats.parse_time_ms 12 _model_server_stats.create_model_time_ms 26 _model_server_stats.query_time_ms 351 _model_server_stats.encode_time_ms 8 _model_server_stats.element_count 28 #