data_7MNT # _model_server_result.job_id 59nDuG8RxkWYfJ2VCZZCNQ _model_server_result.datetime_utc '2024-11-19 09:33:21' _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 7mnt # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"E","auth_seq_id":301}' # _entry.id 7MNT # _exptl.entry_id 7MNT _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 90 _cell.angle_gamma 90 _cell.entry_id 7MNT _cell.length_a 53.02 _cell.length_b 94.27 _cell.length_c 108.16 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 7MNT _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,K,L 1 1 C,D,H,I,J,M,N 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 E N N ? 3 H 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 44 A THR 24 1_555 F MG MG . A MG 302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.132 ? metalc ? metalc2 E O3B GDP . A GDP 301 1_555 F MG MG . A MG 302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.958 ? metalc ? metalc3 F MG MG . A MG 302 1_555 K O HOH . A HOH 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.123 ? metalc ? metalc4 F MG MG . A MG 302 1_555 K O HOH . A HOH 403 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.103 ? metalc ? metalc5 F MG MG . A MG 302 1_555 K O HOH . A HOH 405 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.229 ? metalc ? metalc6 F MG MG . A MG 302 1_555 K O HOH . A HOH 409 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.141 ? metalc ? metalc7 B SG CYS 21 B CYS 1612 1_555 G ZN ZN . B ZN 1701 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.294 ? metalc ? metalc8 B SG CYS 24 B CYS 1615 1_555 G ZN ZN . B ZN 1701 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.385 ? metalc ? metalc9 B SG CYS 35 B CYS 1626 1_555 G ZN ZN . B ZN 1701 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.433 ? metalc ? metalc10 B SG CYS 38 B CYS 1629 1_555 G ZN ZN . B ZN 1701 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.357 ? metalc ? metalc11 C OG1 THR 44 C THR 24 1_555 I MG MG . C MG 302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.105 ? metalc ? metalc12 H O1B GDP . C GDP 301 1_555 I MG MG . C MG 302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.989 ? metalc ? metalc13 I MG MG . C MG 302 1_555 M O HOH . C HOH 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.09 ? metalc ? metalc14 I MG MG . C MG 302 1_555 M O HOH . C HOH 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.1 ? metalc ? metalc15 I MG MG . C MG 302 1_555 M O HOH . C HOH 404 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.16 ? metalc ? metalc16 I MG MG . C MG 302 1_555 M O HOH . C HOH 405 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.157 ? metalc ? metalc17 D SG CYS 21 D CYS 1612 1_555 J ZN ZN . D ZN 1701 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.442 ? metalc ? metalc18 D SG CYS 24 D CYS 1615 1_555 J ZN ZN . D ZN 1701 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.329 ? metalc ? metalc19 D SG CYS 35 D CYS 1626 1_555 J ZN ZN . D ZN 1701 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.317 ? metalc ? metalc20 D SG CYS 38 D CYS 1629 1_555 J ZN ZN . D ZN 1701 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.334 ? # _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 7MNT _atom_sites.fract_transf_matrix[1][1] 0.018861 _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] 0.010608 _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] 0.009246 _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 GDP A 1 301 301 GDP GDP . F 4 MG A 1 302 401 MG MG . G 5 ZN B 1 1701 1701 ZN ZN . H 3 GDP C 1 301 301 GDP GDP . I 4 MG C 1 302 401 MG MG . J 5 ZN D 1 1701 1701 ZN ZN . K 6 HOH A 1 401 513 HOH HOH . K 6 HOH A 2 402 503 HOH HOH . K 6 HOH A 3 403 502 HOH HOH . K 6 HOH A 4 404 505 HOH HOH . K 6 HOH A 5 405 501 HOH HOH . K 6 HOH A 6 406 515 HOH HOH . K 6 HOH A 7 407 506 HOH HOH . K 6 HOH A 8 408 508 HOH HOH . K 6 HOH A 9 409 504 HOH HOH . K 6 HOH A 10 410 517 HOH HOH . K 6 HOH A 11 411 516 HOH HOH . K 6 HOH A 12 412 509 HOH HOH . K 6 HOH A 13 413 518 HOH HOH . K 6 HOH A 14 414 514 HOH HOH . K 6 HOH A 15 415 512 HOH HOH . L 6 HOH B 1 1801 519 HOH HOH . L 6 HOH B 2 1802 507 HOH HOH . L 6 HOH B 3 1803 520 HOH HOH . L 6 HOH B 4 1804 510 HOH HOH . L 6 HOH B 5 1805 523 HOH HOH . M 6 HOH C 1 401 503 HOH HOH . M 6 HOH C 2 402 501 HOH HOH . M 6 HOH C 3 403 521 HOH HOH . M 6 HOH C 4 404 502 HOH HOH . M 6 HOH C 5 405 504 HOH HOH . M 6 HOH C 6 406 511 HOH HOH . N 6 HOH D 1 1801 522 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 . . . E 3 -7.357 31.579 28.186 1 57.91 ? PB GDP 301 A 1 HETATM 2 O O1B GDP . . . E 3 -7.068 30.753 26.956 1 62.2 ? O1B GDP 301 A 1 HETATM 3 O O2B GDP . . . E 3 -8.748 32.165 28.131 1 74.5 ? O2B GDP 301 A 1 HETATM 4 O O3B GDP . . . E 3 -6.326 32.679 28.352 1 69.61 ? O3B GDP 301 A 1 HETATM 5 O O3A GDP . . . E 3 -7.27 30.602 29.478 1 63.65 ? O3A GDP 301 A 1 HETATM 6 P PA GDP . . . E 3 -6.722 31.168 30.907 1 76.49 ? PA GDP 301 A 1 HETATM 7 O O1A GDP . . . E 3 -5.212 31.219 30.875 1 53.72 ? O1A GDP 301 A 1 HETATM 8 O O2A GDP . . . E 3 -7.314 32.54 31.186 1 57.01 ? O2A GDP 301 A 1 HETATM 9 O O5' GDP . . . E 3 -7.216 30.089 32.08 1 75.42 ? O5' GDP 301 A 1 HETATM 10 C C5' GDP . . . E 3 -8.592 29.833 32.128 1 74.03 ? C5' GDP 301 A 1 HETATM 11 C C4' GDP . . . E 3 -8.885 28.883 33.359 1 63.03 ? C4' GDP 301 A 1 HETATM 12 O O4' GDP . . . E 3 -8.194 27.52 33.052 1 54.31 ? O4' GDP 301 A 1 HETATM 13 C C3' GDP . . . E 3 -8.368 29.33 34.421 1 58.41 ? C3' GDP 301 A 1 HETATM 14 O O3' GDP . . . E 3 -9.18 28.964 35.612 1 66.02 ? O3' GDP 301 A 1 HETATM 15 C C2' GDP . . . E 3 -6.894 28.58 34.558 1 60.07 ? C2' GDP 301 A 1 HETATM 16 O O2' GDP . . . E 3 -6.472 28.659 35.944 1 62.99 ? O2' GDP 301 A 1 HETATM 17 C C1' GDP . . . E 3 -7.206 27.389 34.233 1 60.32 ? C1' GDP 301 A 1 HETATM 18 N N9 GDP . . . E 3 -6.108 26.442 33.837 1 55.64 ? N9 GDP 301 A 1 HETATM 19 C C8 GDP . . . E 3 -5.335 26.977 32.856 1 57.98 ? C8 GDP 301 A 1 HETATM 20 N N7 GDP . . . E 3 -4.381 26.07 32.559 1 57.54 ? N7 GDP 301 A 1 HETATM 21 C C5 GDP . . . E 3 -4.578 24.995 33.328 1 56.77 ? C5 GDP 301 A 1 HETATM 22 C C6 GDP . . . E 3 -3.848 23.662 33.46 1 50.65 ? C6 GDP 301 A 1 HETATM 23 O O6 GDP . . . E 3 -2.893 23.44 32.774 1 51.87 ? O6 GDP 301 A 1 HETATM 24 N N1 GDP . . . E 3 -4.312 22.693 34.401 1 70.21 ? N1 GDP 301 A 1 HETATM 25 C C2 GDP . . . E 3 -5.458 22.99 35.21 1 53.72 ? C2 GDP 301 A 1 HETATM 26 N N2 GDP . . . E 3 -5.981 22.044 36.187 1 67.46 ? N2 GDP 301 A 1 HETATM 27 N N3 GDP . . . E 3 -6.149 24.261 35.078 1 57.55 ? N3 GDP 301 A 1 HETATM 28 C C4 GDP . . . E 3 -5.657 25.243 34.107 1 70.01 ? C4 GDP 301 A 1 HETATM 29 H H5' GDP . . . E 3 -9.078 30.666 32.231 1 89.63 ? H5' GDP 301 A 1 HETATM 30 H "H5''" GDP . . . E 3 -8.866 29.392 31.31 1 89.63 ? "H5''" GDP 301 A 1 HETATM 31 H H4' GDP . . . E 3 -9.832 28.756 33.483 1 76.43 ? H4' GDP 301 A 1 HETATM 32 H H3' GDP . . . E 3 -8.255 30.292 34.364 1 70.89 ? H3' GDP 301 A 1 HETATM 33 H HO3' GDP . . . E 3 -9.413 29.671 36.023 1 80.03 ? HO3' GDP 301 A 1 HETATM 34 H H2' GDP . . . E 3 -6.252 28.999 33.967 1 72.89 ? H2' GDP 301 A 1 HETATM 35 H HO2' GDP . . . E 3 -5.901 29.283 36.031 1 76.39 ? HO2' GDP 301 A 1 HETATM 36 H H1' GDP . . . E 3 -7.685 26.997 34.98 1 73.19 ? H1' GDP 301 A 1 HETATM 37 H H8 GDP . . . E 3 -5.432 27.819 32.473 1 70.38 ? H8 GDP 301 A 1 HETATM 38 H HN1 GDP . . . E 3 -3.909 21.938 34.479 1 85.06 ? HN1 GDP 301 A 1 HETATM 39 H HN21 GDP . . . E 3 -6.67 22.25 36.659 1 81.75 ? HN21 GDP 301 A 1 HETATM 40 H HN22 GDP . . . E 3 -5.601 21.28 36.293 1 81.75 ? HN22 GDP 301 A 1 # _model_server_stats.io_time_ms 24 _model_server_stats.parse_time_ms 29 _model_server_stats.create_model_time_ms 16 _model_server_stats.query_time_ms 313 _model_server_stats.encode_time_ms 3 _model_server_stats.element_count 40 #