data_7MNT # _model_server_result.job_id IAbVj3OtAsCoG81cyfAoow _model_server_result.datetime_utc '2024-11-19 09:40:05' _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 7mnt # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"H","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 . . . H 3 39.22 34.736 34.731 1 89.98 ? PB GDP 301 C 1 HETATM 2 O O1B GDP . . . H 3 38.112 35.335 33.89 1 101.81 ? O1B GDP 301 C 1 HETATM 3 O O2B GDP . . . H 3 40.539 35.011 34.046 1 113.38 ? O2B GDP 301 C 1 HETATM 4 O O3B GDP . . . H 3 39.202 35.326 36.124 1 64.02 ? O3B GDP 301 C 1 HETATM 5 O O3A GDP . . . H 3 39.009 33.122 34.813 1 79.34 ? O3A GDP 301 C 1 HETATM 6 P PA GDP . . . H 3 38.281 32.304 33.589 1 97.15 ? PA GDP 301 C 1 HETATM 7 O O1A GDP . . . H 3 38.611 32.937 32.242 1 80.17 ? O1A GDP 301 C 1 HETATM 8 O O2A GDP . . . H 3 36.789 32.323 33.84 1 103.51 ? O2A GDP 301 C 1 HETATM 9 O O5' GDP . . . H 3 38.797 30.715 33.579 1 111.13 ? O5' GDP 301 C 1 HETATM 10 C C5' GDP . . . H 3 40.097 30.422 33.15 1 108.53 ? C5' GDP 301 C 1 HETATM 11 C C4' GDP . . . H 3 40.297 28.862 33.354 1 84.64 ? C4' GDP 301 C 1 HETATM 12 O O4' GDP . . . H 3 39.846 28.543 34.817 1 94.49 ? O4' GDP 301 C 1 HETATM 13 C C3' GDP . . . H 3 39.564 28.204 32.564 1 109.38 ? C3' GDP 301 C 1 HETATM 14 O O3' GDP . . . H 3 40.39 27.275 31.746 1 86.13 ? O3' GDP 301 C 1 HETATM 15 C C2' GDP . . . H 3 38.495 27.311 33.476 1 106.69 ? C2' GDP 301 C 1 HETATM 16 O O2' GDP . . . H 3 38.441 25.955 32.949 1 114.75 ? O2' GDP 301 C 1 HETATM 17 C C1' GDP . . . H 3 38.966 27.29 34.659 1 110.86 ? C1' GDP 301 C 1 HETATM 18 N N9 GDP . . . H 3 37.89 27.239 35.713 1 110.53 ? N9 GDP 301 C 1 HETATM 19 C C8 GDP . . . H 3 37.285 28.453 35.813 1 111.7 ? C8 GDP 301 C 1 HETATM 20 N N7 GDP . . . H 3 36.333 28.348 36.765 1 116.72 ? N7 GDP 301 C 1 HETATM 21 C C5 GDP . . . H 3 36.358 27.104 37.248 1 122.63 ? C5 GDP 301 C 1 HETATM 22 C C6 GDP . . . H 3 35.544 26.376 38.323 1 118.45 ? C6 GDP 301 C 1 HETATM 23 O O6 GDP . . . H 3 34.684 26.958 38.918 1 128.14 ? O6 GDP 301 C 1 HETATM 24 N N1 GDP . . . H 3 35.827 25.005 38.617 1 132 ? N1 GDP 301 C 1 HETATM 25 C C2 GDP . . . H 3 36.868 24.327 37.893 1 125.36 ? C2 GDP 301 C 1 HETATM 26 N N2 GDP . . . H 3 37.216 22.928 38.129 1 134.05 ? N2 GDP 301 C 1 HETATM 27 N N3 GDP . . . H 3 37.631 25.028 36.871 1 124.61 ? N3 GDP 301 C 1 HETATM 28 C C4 GDP . . . H 3 37.332 26.434 36.582 1 116.26 ? C4 GDP 301 C 1 HETATM 29 H H5' GDP . . . H 3 40.204 30.659 32.215 1 131.04 ? H5' GDP 301 C 1 HETATM 30 H "H5''" GDP . . . H 3 40.739 30.909 33.69 1 131.04 ? "H5''" GDP 301 C 1 HETATM 31 H H4' GDP . . . H 3 41.218 28.609 33.223 1 102.37 ? H4' GDP 301 C 1 HETATM 32 H H3' GDP . . . H 3 39.072 28.807 31.985 1 132.05 ? H3' GDP 301 C 1 HETATM 33 H HO3' GDP . . . H 3 40.229 27.405 30.922 1 104.16 ? HO3' GDP 301 C 1 HETATM 34 H H2' GDP . . . H 3 37.616 27.715 33.435 1 128.82 ? H2' GDP 301 C 1 HETATM 35 H HO2' GDP . . . H 3 39.104 25.826 32.433 1 138.5 ? HO2' GDP 301 C 1 HETATM 36 H H1' GDP . . . H 3 39.53 26.506 34.75 1 133.83 ? H1' GDP 301 C 1 HETATM 37 H H8 GDP . . . H 3 37.479 29.21 35.308 1 134.84 ? H8 GDP 301 C 1 HETATM 38 H HN1 GDP . . . H 3 35.376 24.589 39.22 1 159.2 ? HN1 GDP 301 C 1 HETATM 39 H HN21 GDP . . . H 3 36.796 22.472 38.718 1 161.66 ? HN21 GDP 301 C 1 HETATM 40 H HN22 GDP . . . H 3 37.845 22.56 37.672 1 161.66 ? HN22 GDP 301 C 1 # _model_server_stats.io_time_ms 17 _model_server_stats.parse_time_ms 23 _model_server_stats.create_model_time_ms 9 _model_server_stats.query_time_ms 282 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 40 #