data_4GNK # _model_server_result.job_id M2Q98CuHWQ5QgRVVZTuxVw _model_server_result.datetime_utc '2024-11-01 07:17:36' _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 4gnk # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"F","auth_seq_id":401}' # _entry.id 4GNK # _exptl.entry_id 4GNK _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 443.201 _entity.id 4 _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 4GNK _cell.length_a 91.423 _cell.length_b 188.845 _cell.length_c 293.857 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 4GNK _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 PISA monomeric 1 author_and_software_defined_assembly 3 # loop_ _pdbx_struct_assembly_gen.asym_id_list _pdbx_struct_assembly_gen.assembly_id _pdbx_struct_assembly_gen.oper_expression A,B,F,G,H,I,N 1 1 C,D,J,K,L,M,O 2 1 E 3 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 ? 4 F N N ? 4 J 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 OG SER 47 A SER 53 1_555 H MG MG . A MG 403 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.18 ? metalc ? metalc2 A OG1 THR 180 A THR 186 1_555 H MG MG . A MG 403 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.181 ? metalc ? metalc3 F O2B GDP . A GDP 401 1_555 H MG MG . A MG 403 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.173 ? metalc ? metalc4 F O3B GDP . A GDP 401 1_555 H MG MG . A MG 403 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.674 ? metalc ? metalc5 H MG MG . A MG 403 1_555 N O HOH . A HOH 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.066 ? metalc ? metalc6 H MG MG . A MG 403 1_555 N O HOH . A HOH 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.065 ? metalc ? metalc7 B OD1 ASN 334 B ASN 333 1_555 I CA CA . B CA 1301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.422 ? metalc ? metalc8 B OE1 GLU 363 B GLU 362 1_555 I CA CA . B CA 1301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.208 ? metalc ? metalc9 B OD2 ASP 365 B ASP 364 1_555 I CA CA . B CA 1301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.773 ? metalc ? metalc10 B OE1 GLU 414 B GLU 413 1_555 I CA CA . B CA 1301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.773 ? metalc ? metalc11 C OG SER 47 C SER 53 1_555 L MG MG . C MG 403 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.027 ? metalc ? metalc12 C OG1 THR 180 C THR 186 1_555 L MG MG . C MG 403 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.188 ? metalc ? metalc13 J O2B GDP . C GDP 401 1_555 L MG MG . C MG 403 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.823 ? metalc ? metalc14 L MG MG . C MG 403 1_555 O O HOH . C HOH 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.065 ? metalc ? metalc15 L MG MG . C MG 403 1_555 O O HOH . C HOH 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.068 ? metalc ? metalc16 D OD1 ASN 334 D ASN 333 1_555 M CA CA . D CA 1301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.419 ? metalc ? metalc17 D OE1 GLU 363 D GLU 362 1_555 M CA CA . D CA 1301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.318 ? metalc ? metalc18 D OD2 ASP 365 D ASP 364 1_555 M CA CA . D CA 1301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.737 ? metalc ? metalc19 D OE1 GLU 414 D GLU 413 1_555 M CA CA . D CA 1301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.833 ? # _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 87 n n PB O2B GDP sing 88 n n PB O3B GDP sing 89 n n PB O3A GDP sing 90 n n O2B HOB2 GDP sing 91 n n O3B HOB3 GDP sing 92 n n O3A PA GDP sing 93 n n PA O1A GDP doub 94 n n PA O2A GDP sing 95 n n PA O5' GDP sing 96 n n O2A HOA2 GDP sing 97 n n O5' C5' GDP sing 98 n n C5' C4' GDP sing 99 n n C5' H5' GDP sing 100 n n C5' "H5''" GDP sing 101 n n C4' O4' GDP sing 102 n n C4' C3' GDP sing 103 n n C4' H4' GDP sing 104 n n O4' C1' GDP sing 105 n n C3' O3' GDP sing 106 n n C3' C2' GDP sing 107 n n C3' H3' GDP sing 108 n n O3' HO3' GDP sing 109 n n C2' O2' GDP sing 110 n n C2' C1' GDP sing 111 n n C2' H2' GDP sing 112 n n O2' HO2' GDP sing 113 n n C1' N9 GDP sing 114 n n C1' H1' GDP sing 115 n n N9 C8 GDP sing 116 n y N9 C4 GDP sing 117 n y C8 N7 GDP doub 118 n y C8 H8 GDP sing 119 n n N7 C5 GDP sing 120 n y C5 C6 GDP sing 121 n n C5 C4 GDP doub 122 n y C6 O6 GDP doub 123 n n C6 N1 GDP sing 124 n n N1 C2 GDP sing 125 n n N1 HN1 GDP sing 126 n n C2 N2 GDP sing 127 n n C2 N3 GDP doub 128 n n N2 HN21 GDP sing 129 n n N2 HN22 GDP sing 130 n n N3 C4 GDP sing 131 n n # _atom_sites.entry_id 4GNK _atom_sites.fract_transf_matrix[1][1] 0.010938 _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] 0.005295 _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] 0.003403 _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 GDP A 1 401 360 GDP GDP . G 5 ALF A 1 402 361 ALF AMF . H 6 MG A 1 403 361 MG AMF . I 7 CA B 1 1301 900 CA CA . J 4 GDP C 1 401 360 GDP GDP . K 5 ALF C 1 402 361 ALF AMF . L 6 MG C 1 403 361 MG AMF . M 7 CA D 1 1301 900 CA CA . N 8 HOH A 1 501 361 HOH AMF . N 8 HOH A 2 502 361 HOH AMF . N 8 HOH A 3 503 361 HOH AMF . O 8 HOH C 1 501 361 HOH AMF . O 8 HOH C 2 502 361 HOH AMF . O 8 HOH C 3 503 361 HOH AMF . # 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 . . . F 4 -25.752 32.801 -53.53 1 94.12 ? PB GDP 401 A 1 HETATM 2 O O1B GDP . . . F 4 -24.739 32.541 -54.619 1 94.25 ? O1B GDP 401 A 1 HETATM 3 O O2B GDP . . . F 4 -27.181 32.893 -54.006 1 93.44 ? O2B GDP 401 A 1 HETATM 4 O O3B GDP . . . F 4 -25.544 31.964 -52.294 1 94.14 ? O3B GDP 401 A 1 HETATM 5 O O3A GDP . . . F 4 -25.391 34.296 -53.07 1 94.79 ? O3A GDP 401 A 1 HETATM 6 P PA GDP . . . F 4 -26.461 35.244 -52.337 1 95.81 ? PA GDP 401 A 1 HETATM 7 O O1A GDP . . . F 4 -27.657 35.427 -53.242 1 97.05 ? O1A GDP 401 A 1 HETATM 8 O O2A GDP . . . F 4 -26.629 34.747 -50.925 1 94.15 ? O2A GDP 401 A 1 HETATM 9 O O5' GDP . . . F 4 -25.658 36.637 -52.261 1 98.55 ? O5' GDP 401 A 1 HETATM 10 C C5' GDP . . . F 4 -24.311 36.64 -51.786 1 98.49 ? C5' GDP 401 A 1 HETATM 11 C C4' GDP . . . F 4 -23.998 37.895 -50.98 1 98.03 ? C4' GDP 401 A 1 HETATM 12 O O4' GDP . . . F 4 -23.583 38.928 -51.876 1 97.57 ? O4' GDP 401 A 1 HETATM 13 C C3' GDP . . . F 4 -25.188 38.412 -50.184 1 97.62 ? C3' GDP 401 A 1 HETATM 14 O O3' GDP . . . F 4 -24.798 38.655 -48.831 1 97.64 ? O3' GDP 401 A 1 HETATM 15 C C2' GDP . . . F 4 -25.604 39.688 -50.88 1 98.35 ? C2' GDP 401 A 1 HETATM 16 O O2' GDP . . . F 4 -25.946 40.709 -49.944 1 99.28 ? O2' GDP 401 A 1 HETATM 17 C C1' GDP . . . F 4 -24.393 40.088 -51.708 1 100.52 ? C1' GDP 401 A 1 HETATM 18 N N9 GDP . . . F 4 -24.791 40.606 -53.034 1 104.37 ? N9 GDP 401 A 1 HETATM 19 C C8 GDP . . . F 4 -25.559 39.971 -53.938 1 105.54 ? C8 GDP 401 A 1 HETATM 20 N N7 GDP . . . F 4 -25.72 40.74 -55.045 1 108.21 ? N7 GDP 401 A 1 HETATM 21 C C5 GDP . . . F 4 -25.045 41.887 -54.856 1 109.71 ? C5 GDP 401 A 1 HETATM 22 C C6 GDP . . . F 4 -24.796 43.132 -55.626 1 112.52 ? C6 GDP 401 A 1 HETATM 23 O O6 GDP . . . F 4 -25.281 43.29 -56.766 1 114.08 ? O6 GDP 401 A 1 HETATM 24 N N1 GDP . . . F 4 -24.033 44.086 -55.069 1 114.67 ? N1 GDP 401 A 1 HETATM 25 C C2 GDP . . . F 4 -23.492 43.943 -53.839 1 114.16 ? C2 GDP 401 A 1 HETATM 26 N N2 GDP . . . F 4 -22.73 44.948 -53.336 1 115.61 ? N2 GDP 401 A 1 HETATM 27 N N3 GDP . . . F 4 -23.681 42.829 -53.08 1 112.2 ? N3 GDP 401 A 1 HETATM 28 C C4 GDP . . . F 4 -24.431 41.79 -53.527 1 108.75 ? C4 GDP 401 A 1 # _model_server_stats.io_time_ms 119 _model_server_stats.parse_time_ms 14 _model_server_stats.create_model_time_ms 48 _model_server_stats.query_time_ms 302 _model_server_stats.encode_time_ms 4 _model_server_stats.element_count 28 #