data_6P8Y # _model_server_result.job_id KWaQVLsNjg7Q0bp5Xop0rA _model_server_result.datetime_utc '2024-11-22 05:25:18' _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 6p8y # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"D","auth_seq_id":302}' # _entry.id 6P8Y # _exptl.entry_id 6P8Y _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 443.201 _entity.id 3 _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 93.9 _cell.angle_gamma 90 _cell.entry_id 6P8Y _cell.length_a 33.756 _cell.length_b 106.045 _cell.length_c 39.9 _cell.Z_PDB 4 _cell.pdbx_unique_axis ? # _symmetry.entry_id 6P8Y _symmetry.cell_setting ? _symmetry.Int_Tables_number 4 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 1 21 1' # 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 monomeric 1 author_and_software_defined_assembly 1 PISA monomeric 1 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,C,D,E,I 1 1 B,F,G,H,J 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 ? 3 D N N ? 3 G 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 covale ? covale1 A SG CYS 26 A CYS 12 1_555 E C01 O5Y . A O5Y 303 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.81 ? covale ? covale2 B SG CYS 26 B CYS 12 1_555 H C01 O5Y . B O5Y 303 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.807 ? metalc ? metalc1 A OG SER 31 A SER 17 1_555 C MG MG . A MG 301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.171 ? metalc ? metalc2 C MG MG . A MG 301 1_555 D O2B GDP . A GDP 302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.176 ? metalc ? metalc3 C MG MG . A MG 301 1_555 I O HOH . A HOH 407 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.178 ? metalc ? metalc4 C MG MG . A MG 301 1_555 I O HOH . A HOH 411 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.176 ? metalc ? metalc5 C MG MG . A MG 301 1_555 I O HOH . A HOH 414 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.178 ? metalc ? metalc6 C MG MG . A MG 301 1_555 I O HOH . A HOH 416 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.179 ? metalc ? metalc7 B OG SER 31 B SER 17 1_555 F MG MG . B MG 301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.174 ? metalc ? metalc8 F MG MG . B MG 301 1_555 G O1B GDP . B GDP 302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.177 ? metalc ? metalc9 F MG MG . B MG 301 1_555 J O HOH . B HOH 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.179 ? metalc ? metalc10 F MG MG . B MG 301 1_555 J O HOH . B HOH 404 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.175 ? metalc ? metalc11 F MG MG . B MG 301 1_555 J O HOH . B HOH 408 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.175 ? metalc ? metalc12 F MG MG . B MG 301 1_555 J O HOH . B HOH 409 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.18 ? # _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 6P8Y _atom_sites.fract_transf_matrix[1][1] 0.029624 _atom_sites.fract_transf_matrix[1][2] 0 _atom_sites.fract_transf_matrix[1][3] 0.00202 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.00943 _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] 0.025121 _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 C 2 MG A 1 301 301 MG MG . D 3 GDP A 1 302 501 GDP GDP . E 4 O5Y A 1 303 701 O5Y UNL . F 2 MG B 1 301 301 MG MG . G 3 GDP B 1 302 501 GDP GDP . H 4 O5Y B 1 303 701 O5Y UNL . I 5 HOH A 1 401 21 HOH HOH . I 5 HOH A 2 402 1 HOH HOH . I 5 HOH A 3 403 9 HOH HOH . I 5 HOH A 4 404 10 HOH HOH . I 5 HOH A 5 405 7 HOH HOH . I 5 HOH A 6 406 6 HOH HOH . I 5 HOH A 7 407 401 HOH HOH . I 5 HOH A 8 408 19 HOH HOH . I 5 HOH A 9 409 11 HOH HOH . I 5 HOH A 10 410 3 HOH HOH . I 5 HOH A 11 411 404 HOH HOH . I 5 HOH A 12 412 22 HOH HOH . I 5 HOH A 13 413 2 HOH HOH . I 5 HOH A 14 414 403 HOH HOH . I 5 HOH A 15 415 18 HOH HOH . I 5 HOH A 16 416 402 HOH HOH . I 5 HOH A 17 417 20 HOH HOH . I 5 HOH A 18 418 4 HOH HOH . I 5 HOH A 19 419 12 HOH HOH . I 5 HOH A 20 420 5 HOH HOH . J 5 HOH B 1 401 401 HOH HOH . J 5 HOH B 2 402 15 HOH HOH . J 5 HOH B 3 403 16 HOH HOH . J 5 HOH B 4 404 403 HOH HOH . J 5 HOH B 5 405 13 HOH HOH . J 5 HOH B 6 406 8 HOH HOH . J 5 HOH B 7 407 14 HOH HOH . J 5 HOH B 8 408 404 HOH HOH . J 5 HOH B 9 409 402 HOH HOH . J 5 HOH B 10 410 17 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 . . . D 3 0.881 -8.473 -8.515 1 37.95 ? PB GDP 302 A 1 HETATM 2 O O1B GDP . . . D 3 -0.208 -9.094 -9.348 1 38.19 ? O1B GDP 302 A 1 HETATM 3 O O2B GDP . . . D 3 1.556 -9.41 -7.542 1 38.24 ? O2B GDP 302 A 1 HETATM 4 O O3B GDP . . . D 3 0.467 -7.169 -7.879 1 38.55 ? O3B GDP 302 A 1 HETATM 5 O O3A GDP . . . D 3 2.014 -8.044 -9.583 1 37.32 ? O3A GDP 302 A 1 HETATM 6 P PA GDP . . . D 3 3.368 -8.88 -9.857 1 37.03 ? PA GDP 302 A 1 HETATM 7 O O1A GDP . . . D 3 2.992 -10.224 -10.424 1 37.85 ? O1A GDP 302 A 1 HETATM 8 O O2A GDP . . . D 3 4.252 -8.793 -8.639 1 37.65 ? O2A GDP 302 A 1 HETATM 9 O O5' GDP . . . D 3 4.045 -8.053 -11.058 1 37.51 ? O5' GDP 302 A 1 HETATM 10 C C5' GDP . . . D 3 3.253 -7.755 -12.208 1 38.05 ? C5' GDP 302 A 1 HETATM 11 C C4' GDP . . . D 3 4.114 -7.42 -13.418 1 38.42 ? C4' GDP 302 A 1 HETATM 12 O O4' GDP . . . D 3 4.758 -6.156 -13.215 1 38.03 ? O4' GDP 302 A 1 HETATM 13 C C3' GDP . . . D 3 5.2 -8.453 -13.668 1 38.23 ? C3' GDP 302 A 1 HETATM 14 O O3' GDP . . . D 3 5.26 -8.765 -15.064 1 38.43 ? O3' GDP 302 A 1 HETATM 15 C C2' GDP . . . D 3 6.476 -7.788 -13.196 1 37.98 ? C2' GDP 302 A 1 HETATM 16 O O2' GDP . . . D 3 7.576 -8.123 -14.042 1 39.06 ? O2' GDP 302 A 1 HETATM 17 C C1' GDP . . . D 3 6.18 -6.297 -13.255 1 37.51 ? C1' GDP 302 A 1 HETATM 18 N N9 GDP . . . D 3 6.779 -5.527 -12.136 1 37.16 ? N9 GDP 302 A 1 HETATM 19 C C8 GDP . . . D 3 6.541 -5.681 -10.816 1 37.29 ? C8 GDP 302 A 1 HETATM 20 N N7 GDP . . . D 3 7.259 -4.787 -10.085 1 36.19 ? N7 GDP 302 A 1 HETATM 21 C C5 GDP . . . D 3 7.97 -4.039 -10.943 1 36.42 ? C5 GDP 302 A 1 HETATM 22 C C6 GDP . . . D 3 8.935 -2.913 -10.851 1 36.27 ? C6 GDP 302 A 1 HETATM 23 O O6 GDP . . . D 3 9.268 -2.427 -9.747 1 36.14 ? O6 GDP 302 A 1 HETATM 24 N N1 GDP . . . D 3 9.438 -2.42 -11.991 1 36 ? N1 GDP 302 A 1 HETATM 25 C C2 GDP . . . D 3 9.103 -2.917 -13.2 1 36.09 ? C2 GDP 302 A 1 HETATM 26 N N2 GDP . . . D 3 9.651 -2.377 -14.312 1 37.16 ? N2 GDP 302 A 1 HETATM 27 N N3 GDP . . . D 3 8.23 -3.942 -13.361 1 36.49 ? N3 GDP 302 A 1 HETATM 28 C C4 GDP . . . D 3 7.644 -4.529 -12.292 1 36.8 ? C4 GDP 302 A 1 # _model_server_stats.io_time_ms 9 _model_server_stats.parse_time_ms 12 _model_server_stats.create_model_time_ms 28 _model_server_stats.query_time_ms 280 _model_server_stats.encode_time_ms 6 _model_server_stats.element_count 28 #