data_2GTP # _model_server_result.job_id jM2V6LRyfX8oK4E_3IiRzQ _model_server_result.datetime_utc '2024-11-28 15:51:58' _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 2gtp # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"G","auth_seq_id":402}' # _entry.id 2GTP # _exptl.entry_id 2GTP _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 2GTP _cell.length_a 90.451 _cell.length_b 102.904 _cell.length_c 128.761 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 2GTP _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 ? dimeric 2 author_defined_assembly 1 ? dimeric 2 author_defined_assembly 2 # loop_ _pdbx_struct_assembly_gen.asym_id_list _pdbx_struct_assembly_gen.assembly_id _pdbx_struct_assembly_gen.oper_expression A,D,E,F,G,K,N 1 1 B,C,H,I,J,L,M 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 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 N GLU 12 A GLU 43 1_555 E AL ALF . A ALF 355 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 3.553 ? metalc ? metalc2 A OG SER 16 A SER 47 1_555 F MG MG . A MG 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.998 ? metalc ? metalc3 A NH2 ARG 147 A ARG 178 1_555 E AL ALF . A ALF 355 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 3.644 ? metalc ? metalc4 A NH1 ARG 147 A ARG 178 1_555 E AL ALF . A ALF 355 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 3.649 ? metalc ? metalc5 A OG1 THR 150 A THR 181 1_555 F MG MG . A MG 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.203 ? metalc ? metalc6 E AL ALF . A ALF 355 1_555 F MG MG . A MG 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 3.565 ? metalc ? metalc7 E F1 ALF . A ALF 355 1_555 F MG MG . A MG 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.117 ? metalc ? metalc8 E AL ALF . A ALF 355 1_555 G O2B GDP . A GDP 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.947 ? metalc ? metalc9 E AL ALF . A ALF 355 1_555 K O HOH . A HOH 405 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.093 ? metalc ? metalc10 F MG MG . A MG 401 1_555 G O1B GDP . A GDP 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.814 ? metalc ? metalc11 F MG MG . A MG 401 1_555 K O HOH . A HOH 403 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.179 ? metalc ? metalc12 F MG MG . A MG 401 1_555 K O HOH . A HOH 404 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.996 ? metalc ? metalc13 B OG SER 16 B SER 47 1_555 I MG MG . B MG 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.494 ? metalc ? metalc14 B OG1 THR 150 B THR 181 1_555 I MG MG . B MG 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.333 ? metalc ? metalc15 H AL ALF . B ALF 355 1_555 I MG MG . B MG 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 3.29 ? metalc ? metalc16 H F3 ALF . B ALF 355 1_555 I MG MG . B MG 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.067 ? metalc ? metalc17 H AL ALF . B ALF 355 1_555 J O2B GDP . B GDP 403 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.881 ? metalc ? metalc18 H AL ALF . B ALF 355 1_555 L O HOH . B HOH 406 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.191 ? metalc ? metalc19 I MG MG . B MG 402 1_555 J O2B GDP . B GDP 403 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.856 ? metalc ? metalc20 I MG MG . B MG 402 1_555 J O1B GDP . B GDP 403 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.748 ? metalc ? metalc21 I MG MG . B MG 402 1_555 L O HOH . B HOH 404 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.083 ? metalc ? metalc22 I MG MG . B MG 402 1_555 L O HOH . B HOH 405 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.14 ? # _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 2GTP _atom_sites.fract_transf_matrix[1][1] 0.011056 _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] 0.009718 _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] 0.007766 _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 ALF A 1 355 1 ALF ALF . F 4 MG A 1 401 1 MG MG . G 5 GDP A 1 402 1 GDP GDP . H 3 ALF B 1 355 2 ALF ALF . I 4 MG B 1 402 2 MG MG . J 5 GDP B 1 403 2 GDP GDP . K 6 HOH A 1 403 1 HOH HOH . K 6 HOH A 2 404 2 HOH HOH . K 6 HOH A 3 405 5 HOH HOH . K 6 HOH A 4 406 7 HOH HOH . K 6 HOH A 5 407 8 HOH HOH . K 6 HOH A 6 408 11 HOH HOH . K 6 HOH A 7 409 12 HOH HOH . K 6 HOH A 8 410 13 HOH HOH . K 6 HOH A 9 411 17 HOH HOH . K 6 HOH A 10 412 18 HOH HOH . K 6 HOH A 11 413 19 HOH HOH . K 6 HOH A 12 414 22 HOH HOH . K 6 HOH A 13 415 23 HOH HOH . K 6 HOH A 14 416 24 HOH HOH . K 6 HOH A 15 417 25 HOH HOH . K 6 HOH A 16 418 31 HOH HOH . K 6 HOH A 17 419 32 HOH HOH . K 6 HOH A 18 420 34 HOH HOH . K 6 HOH A 19 421 35 HOH HOH . K 6 HOH A 20 422 37 HOH HOH . K 6 HOH A 21 423 42 HOH HOH . K 6 HOH A 22 424 43 HOH HOH . K 6 HOH A 23 425 45 HOH HOH . K 6 HOH A 24 426 50 HOH HOH . K 6 HOH A 25 427 51 HOH HOH . K 6 HOH A 26 428 57 HOH HOH . K 6 HOH A 27 429 62 HOH HOH . K 6 HOH A 28 430 63 HOH HOH . K 6 HOH A 29 431 67 HOH HOH . K 6 HOH A 30 432 70 HOH HOH . K 6 HOH A 31 433 75 HOH HOH . K 6 HOH A 32 434 79 HOH HOH . K 6 HOH A 33 435 84 HOH HOH . K 6 HOH A 34 436 85 HOH HOH . K 6 HOH A 35 437 87 HOH HOH . K 6 HOH A 36 438 88 HOH HOH . K 6 HOH A 37 439 91 HOH HOH . K 6 HOH A 38 440 100 HOH HOH . K 6 HOH A 39 441 102 HOH HOH . K 6 HOH A 40 442 104 HOH HOH . K 6 HOH A 41 443 107 HOH HOH . K 6 HOH A 42 444 108 HOH HOH . K 6 HOH A 43 445 109 HOH HOH . K 6 HOH A 44 446 110 HOH HOH . K 6 HOH A 45 447 111 HOH HOH . K 6 HOH A 46 448 113 HOH HOH . K 6 HOH A 47 449 116 HOH HOH . K 6 HOH A 48 450 118 HOH HOH . K 6 HOH A 49 451 120 HOH HOH . K 6 HOH A 50 452 126 HOH HOH . K 6 HOH A 51 453 131 HOH HOH . K 6 HOH A 52 454 133 HOH HOH . K 6 HOH A 53 455 136 HOH HOH . K 6 HOH A 54 456 139 HOH HOH . K 6 HOH A 55 457 140 HOH HOH . K 6 HOH A 56 458 141 HOH HOH . K 6 HOH A 57 459 144 HOH HOH . K 6 HOH A 58 460 145 HOH HOH . K 6 HOH A 59 461 148 HOH HOH . K 6 HOH A 60 462 149 HOH HOH . K 6 HOH A 61 463 150 HOH HOH . K 6 HOH A 62 464 154 HOH HOH . L 6 HOH B 1 404 3 HOH HOH . L 6 HOH B 2 405 4 HOH HOH . L 6 HOH B 3 406 6 HOH HOH . L 6 HOH B 4 407 9 HOH HOH . L 6 HOH B 5 408 10 HOH HOH . L 6 HOH B 6 409 16 HOH HOH . L 6 HOH B 7 410 20 HOH HOH . L 6 HOH B 8 411 21 HOH HOH . L 6 HOH B 9 412 27 HOH HOH . L 6 HOH B 10 413 28 HOH HOH . L 6 HOH B 11 414 30 HOH HOH . L 6 HOH B 12 415 33 HOH HOH . L 6 HOH B 13 416 36 HOH HOH . L 6 HOH B 14 417 38 HOH HOH . L 6 HOH B 15 418 40 HOH HOH . L 6 HOH B 16 419 41 HOH HOH . L 6 HOH B 17 420 46 HOH HOH . L 6 HOH B 18 421 49 HOH HOH . L 6 HOH B 19 422 52 HOH HOH . L 6 HOH B 20 423 54 HOH HOH . L 6 HOH B 21 424 58 HOH HOH . L 6 HOH B 22 425 59 HOH HOH . L 6 HOH B 23 426 60 HOH HOH . L 6 HOH B 24 427 61 HOH HOH . L 6 HOH B 25 428 65 HOH HOH . L 6 HOH B 26 429 66 HOH HOH . L 6 HOH B 27 430 71 HOH HOH . L 6 HOH B 28 431 72 HOH HOH . L 6 HOH B 29 432 73 HOH HOH . L 6 HOH B 30 433 76 HOH HOH . L 6 HOH B 31 434 77 HOH HOH . L 6 HOH B 32 435 78 HOH HOH . L 6 HOH B 33 436 80 HOH HOH . L 6 HOH B 34 437 81 HOH HOH . L 6 HOH B 35 438 89 HOH HOH . L 6 HOH B 36 439 90 HOH HOH . L 6 HOH B 37 440 93 HOH HOH . L 6 HOH B 38 441 98 HOH HOH . L 6 HOH B 39 442 112 HOH HOH . L 6 HOH B 40 443 121 HOH HOH . L 6 HOH B 41 444 122 HOH HOH . L 6 HOH B 42 445 124 HOH HOH . L 6 HOH B 43 446 129 HOH HOH . L 6 HOH B 44 447 132 HOH HOH . L 6 HOH B 45 448 134 HOH HOH . L 6 HOH B 46 449 135 HOH HOH . L 6 HOH B 47 450 137 HOH HOH . L 6 HOH B 48 451 146 HOH HOH . L 6 HOH B 49 452 147 HOH HOH . L 6 HOH B 50 453 153 HOH HOH . L 6 HOH B 51 454 155 HOH HOH . M 6 HOH C 1 193 53 HOH HOH . M 6 HOH C 2 194 55 HOH HOH . M 6 HOH C 3 195 64 HOH HOH . M 6 HOH C 4 196 68 HOH HOH . M 6 HOH C 5 197 69 HOH HOH . M 6 HOH C 6 198 74 HOH HOH . M 6 HOH C 7 199 82 HOH HOH . M 6 HOH C 8 200 86 HOH HOH . M 6 HOH C 9 201 94 HOH HOH . M 6 HOH C 10 202 115 HOH HOH . M 6 HOH C 11 203 117 HOH HOH . M 6 HOH C 12 204 130 HOH HOH . M 6 HOH C 13 205 142 HOH HOH . M 6 HOH C 14 206 152 HOH HOH . N 6 HOH D 1 193 29 HOH HOH . N 6 HOH D 2 194 39 HOH HOH . N 6 HOH D 3 195 95 HOH HOH . N 6 HOH D 4 196 97 HOH HOH . N 6 HOH D 5 197 105 HOH HOH . N 6 HOH D 6 198 114 HOH HOH . N 6 HOH D 7 199 125 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 . . . G 5 13.176 29.755 22.67 1 36.1 ? PB GDP 402 A 1 HETATM 2 O O1B GDP . . . G 5 12.025 30.753 22.716 1 32.02 ? O1B GDP 402 A 1 HETATM 3 O O2B GDP . . . G 5 13.456 29.196 21.284 1 35.72 ? O2B GDP 402 A 1 HETATM 4 O O3B GDP . . . G 5 14.474 30.344 23.206 1 33.06 ? O3B GDP 402 A 1 HETATM 5 O O3A GDP . . . G 5 12.853 28.524 23.685 1 37.46 ? O3A GDP 402 A 1 HETATM 6 P PA GDP . . . G 5 11.391 28.325 24.35 1 38.21 ? PA GDP 402 A 1 HETATM 7 O O1A GDP . . . G 5 10.372 28.278 23.255 1 37.31 ? O1A GDP 402 A 1 HETATM 8 O O2A GDP . . . G 5 11.019 29.388 25.369 1 36.49 ? O2A GDP 402 A 1 HETATM 9 O O5' GDP . . . G 5 11.536 26.927 25.112 1 38.34 ? O5' GDP 402 A 1 HETATM 10 C C5' GDP . . . G 5 11.687 25.693 24.432 1 39.36 ? C5' GDP 402 A 1 HETATM 11 C C4' GDP . . . G 5 11.036 24.596 25.254 1 39.01 ? C4' GDP 402 A 1 HETATM 12 O O4' GDP . . . G 5 11.835 24.318 26.387 1 37.35 ? O4' GDP 402 A 1 HETATM 13 C C3' GDP . . . G 5 9.649 24.981 25.767 1 40.14 ? C3' GDP 402 A 1 HETATM 14 O O3' GDP . . . G 5 8.761 23.856 25.679 1 39.83 ? O3' GDP 402 A 1 HETATM 15 C C2' GDP . . . G 5 9.864 25.34 27.212 1 41.39 ? C2' GDP 402 A 1 HETATM 16 O O2' GDP . . . G 5 8.741 24.979 28.015 1 44.73 ? O2' GDP 402 A 1 HETATM 17 C C1' GDP . . . G 5 11.083 24.52 27.59 1 39.48 ? C1' GDP 402 A 1 HETATM 18 N N9 GDP . . . G 5 11.952 25.182 28.586 1 38.95 ? N9 GDP 402 A 1 HETATM 19 C C8 GDP . . . G 5 12.51 26.397 28.503 1 39.2 ? C8 GDP 402 A 1 HETATM 20 N N7 GDP . . . G 5 13.287 26.66 29.597 1 38.9 ? N7 GDP 402 A 1 HETATM 21 C C5 GDP . . . G 5 13.223 25.59 30.393 1 39.16 ? C5 GDP 402 A 1 HETATM 22 C C6 GDP . . . G 5 13.792 25.184 31.692 1 39.79 ? C6 GDP 402 A 1 HETATM 23 O O6 GDP . . . G 5 14.55 25.957 32.336 1 39.76 ? O6 GDP 402 A 1 HETATM 24 N N1 GDP . . . G 5 13.466 23.978 32.173 1 39.15 ? N1 GDP 402 A 1 HETATM 25 C C2 GDP . . . G 5 12.672 23.132 31.506 1 39.05 ? C2 GDP 402 A 1 HETATM 26 N N2 GDP . . . G 5 12.396 21.919 32.033 1 39.34 ? N2 GDP 402 A 1 HETATM 27 N N3 GDP . . . G 5 12.118 23.44 30.323 1 39.34 ? N3 GDP 402 A 1 HETATM 28 C C4 GDP . . . G 5 12.355 24.622 29.72 1 39.65 ? C4 GDP 402 A 1 # _model_server_stats.io_time_ms 11 _model_server_stats.parse_time_ms 12 _model_server_stats.create_model_time_ms 24 _model_server_stats.query_time_ms 286 _model_server_stats.encode_time_ms 15 _model_server_stats.element_count 28 #