data_2GVD # _model_server_result.job_id ixDUvcQpDWSilLrKjC7bkw _model_server_result.datetime_utc '2024-10-27 00:30:34' _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 2gvd # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"G","auth_seq_id":584}' # _entry.id 2GVD # _exptl.entry_id 2GVD _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 718.27 _entity.id 6 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description "SPIRO(2,4,6-TRINITROBENZENE[1,2A]-2O',3O'-METHYLENE-ADENINE-TRIPHOSPHATE" _entity.pdbx_number_of_molecules 1 _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 2GVD _cell.length_a 118.2 _cell.length_b 133.4 _cell.length_c 70.6 _cell.Z_PDB 4 _cell.pdbx_unique_axis ? # _symmetry.entry_id 2GVD _symmetry.cell_setting ? _symmetry.Int_Tables_number 18 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 21 21 2' # _pdbx_struct_assembly.method_details ? _pdbx_struct_assembly.oligomeric_details trimeric _pdbx_struct_assembly.oligomeric_count 3 _pdbx_struct_assembly.details author_defined_assembly _pdbx_struct_assembly.id 1 # _pdbx_struct_assembly_gen.asym_id_list A,B,C,D,E,F,G,H,I,J,K,L,M _pdbx_struct_assembly_gen.assembly_id 1 _pdbx_struct_assembly_gen.oper_expression 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 # _struct_asym.details ? _struct_asym.entity_id 6 _struct_asym.id G _struct_asym.pdbx_modified N _struct_asym.pdbx_blank_PDB_chainid_flag 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 disulf ? disulf1 A SG CYS 77 A CYS 432 1_555 A SG CYS 89 A CYS 444 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.056 ? metalc ? metalc1 A OD2 ASP 41 A ASP 396 1_555 E MN MN . A MN 582 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.428 ? metalc ? metalc2 A OD1 ASP 41 A ASP 396 1_555 E MN MN . A MN 582 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.645 ? metalc ? metalc3 A O ILE 42 A ILE 397 1_555 E MN MN . A MN 582 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.441 ? metalc ? metalc4 A OD1 ASP 85 A ASP 440 1_555 D MN MN . A MN 581 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.361 ? metalc ? metalc5 A OD2 ASP 85 A ASP 440 1_555 E MN MN . A MN 582 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.194 ? metalc ? metalc6 E MN MN . A MN 582 1_555 G O2B 128 . A 128 584 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.263 ? metalc ? metalc7 E MN MN . A MN 582 1_555 G O3B 128 . A 128 584 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.552 ? metalc ? metalc8 C OG SER 54 C SER 54 1_555 H MN MN . C MN 396 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.344 ? metalc ? metalc9 C OG1 THR 204 C THR 204 1_555 H MN MN . C MN 396 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.325 ? metalc ? metalc10 J O2B GSP . C GSP 395 1_555 H MN MN . C MN 396 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.133 ? metalc ? metalc11 J O2G GSP . C GSP 395 1_555 H MN MN . C MN 396 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.272 ? # _chem_comp.formula 'C16 H17 N8 O19 P3' _chem_comp.formula_weight 718.27 _chem_comp.id 128 _chem_comp.mon_nstd_flag . _chem_comp.name "SPIRO(2,4,6-TRINITROBENZENE[1,2A]-2O',3O'-METHYLENE-ADENINE-TRIPHOSPHATE" _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 PG O1G 128 doub 1 n n PG O2G 128 sing 2 n n PG O3G 128 sing 3 n n PG O3B 128 sing 4 n n O2G HOG2 128 sing 5 n n O3G HOG3 128 sing 6 n n PB O1B 128 doub 7 n n PB O2B 128 sing 8 n n PB O3B 128 sing 9 n n PB O3A 128 sing 10 n n O2B HOB2 128 sing 11 n n PA O1A 128 doub 12 n n PA O2A 128 sing 13 n n PA O3A 128 sing 14 n n PA O5' 128 sing 15 n n O2A HOA2 128 sing 16 n n O5' C5' 128 sing 17 n n C5' C4' 128 sing 18 n n C5' H5' 128 sing 19 n n C5' "H5''" 128 sing 20 n n C4' O4' 128 sing 21 n n C4' C3' 128 sing 22 n n C4' H4' 128 sing 23 n n O4' C1' 128 sing 24 n n C3' O3' 128 sing 25 n n C3' C2' 128 sing 26 n n C3' H3' 128 sing 27 n n O3' C1F 128 sing 28 n n C2' O2' 128 sing 29 n n C2' C1' 128 sing 30 n n C2' H2' 128 sing 31 n n O2' C1F 128 sing 32 n n C1' N9 128 sing 33 n n C1' H1' 128 sing 34 n n N9 C8 128 sing 35 n y N9 C4 128 sing 36 n y C8 N7 128 doub 37 n y C8 H8 128 sing 38 n n N7 C5 128 sing 39 n y C5 C6 128 sing 40 n y C5 C4 128 doub 41 n y C6 N6 128 sing 42 n n C6 N1 128 doub 43 n y N6 HN61 128 sing 44 n n N6 HN62 128 sing 45 n n N1 C2 128 sing 46 n y C2 N3 128 doub 47 n y C2 H2 128 sing 48 n n N3 C4 128 sing 49 n y C1F C2F 128 sing 50 n n C1F C6F 128 sing 51 n n C2F C3F 128 doub 52 n n C2F N2F 128 sing 53 n n C3F C4F 128 sing 54 n n C3F H3F 128 sing 55 n n C4F C5F 128 sing 56 n n C4F N4F 128 doub 57 n n O4F H4F 128 sing 58 n n C5F C6F 128 doub 59 n n C5F H5F 128 sing 60 n n C6F N6F 128 sing 61 n n N2F O2F 128 doub 62 n n N2F O3F 128 sing 63 n n N4F O4F 128 sing 64 n n N4F O5F 128 sing 65 n n N6F O6F 128 doub 66 n n N6F O7F 128 sing 67 n n # _atom_sites.entry_id 2GVD _atom_sites.fract_transf_matrix[1][1] 0.00846 _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] 0.007496 _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] 0.014164 _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 D 4 MN A 1 581 502 MN MN . E 4 MN A 1 582 503 MN MN . F 5 FKP A 1 583 1 FKP FKP . G 6 128 A 1 584 10 128 128 . H 4 MN C 1 396 396 MN MN . I 7 CL C 1 397 397 CL CL . J 8 GSP C 1 395 395 GSP GSP . K 9 HOH A 1 1 1 HOH HOH . K 9 HOH A 2 11 11 HOH HOH . K 9 HOH A 3 19 19 HOH HOH . K 9 HOH A 4 21 21 HOH HOH . K 9 HOH A 5 23 23 HOH HOH . K 9 HOH A 6 31 31 HOH HOH . K 9 HOH A 7 42 42 HOH HOH . K 9 HOH A 8 45 45 HOH HOH . K 9 HOH A 9 56 56 HOH HOH . K 9 HOH A 10 63 63 HOH HOH . K 9 HOH A 11 68 68 HOH HOH . L 9 HOH B 1 2 2 HOH HOH . L 9 HOH B 2 4 4 HOH HOH . L 9 HOH B 3 5 5 HOH HOH . L 9 HOH B 4 7 7 HOH HOH . L 9 HOH B 5 9 9 HOH HOH . L 9 HOH B 6 10 10 HOH HOH . L 9 HOH B 7 12 12 HOH HOH . L 9 HOH B 8 13 13 HOH HOH . L 9 HOH B 9 15 15 HOH HOH . L 9 HOH B 10 16 16 HOH HOH . L 9 HOH B 11 18 18 HOH HOH . L 9 HOH B 12 28 28 HOH HOH . L 9 HOH B 13 36 36 HOH HOH . L 9 HOH B 14 41 41 HOH HOH . L 9 HOH B 15 57 57 HOH HOH . M 9 HOH C 1 398 3 HOH HOH . M 9 HOH C 2 399 6 HOH HOH . M 9 HOH C 3 400 8 HOH HOH . M 9 HOH C 4 401 14 HOH HOH . M 9 HOH C 5 402 17 HOH HOH . M 9 HOH C 6 403 20 HOH HOH . M 9 HOH C 7 404 22 HOH HOH . M 9 HOH C 8 405 24 HOH HOH . M 9 HOH C 9 406 25 HOH HOH . M 9 HOH C 10 407 26 HOH HOH . M 9 HOH C 11 408 29 HOH HOH . M 9 HOH C 12 409 30 HOH HOH . M 9 HOH C 13 410 38 HOH HOH . M 9 HOH C 14 411 39 HOH HOH . M 9 HOH C 15 412 40 HOH HOH . M 9 HOH C 16 413 43 HOH HOH . M 9 HOH C 17 414 44 HOH HOH . M 9 HOH C 18 415 47 HOH HOH . M 9 HOH C 19 416 48 HOH HOH . M 9 HOH C 20 417 50 HOH HOH . M 9 HOH C 21 418 54 HOH HOH . M 9 HOH C 22 419 59 HOH HOH . M 9 HOH C 23 420 64 HOH HOH . M 9 HOH C 24 421 65 HOH HOH . M 9 HOH C 25 422 67 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 PG 128 . . . G 6 57.87 -6.046 59.386 1 65.92 ? PG 128 584 A 1 HETATM 2 O O1G 128 . . . G 6 57.926 -5.598 57.852 1 70.23 ? O1G 128 584 A 1 HETATM 3 O O2G 128 . . . G 6 56.476 -5.519 59.959 1 66.36 ? O2G 128 584 A 1 HETATM 4 O O3G 128 . . . G 6 58.959 -5.353 60.053 1 69.78 ? O3G 128 584 A 1 HETATM 5 P PB 128 . . . G 6 59.173 -8.783 59.111 1 66.79 ? PB 128 584 A 1 HETATM 6 O O1B 128 . . . G 6 60.197 -8.408 59.611 1 60.17 ? O1B 128 584 A 1 HETATM 7 O O2B 128 . . . G 6 58.955 -9.774 59.32 1 69.27 ? O2B 128 584 A 1 HETATM 8 O O3B 128 . . . G 6 58.073 -7.706 59.487 1 66.04 ? O3B 128 584 A 1 HETATM 9 P PA 128 . . . G 6 59.274 -8.798 55.917 1 71.92 ? PA 128 584 A 1 HETATM 10 O O1A 128 . . . G 6 57.716 -8.687 55.648 1 64.51 ? O1A 128 584 A 1 HETATM 11 O O2A 128 . . . G 6 60.114 -7.738 55.234 1 76.27 ? O2A 128 584 A 1 HETATM 12 O O3A 128 . . . G 6 59.69 -8.619 57.484 1 68.53 ? O3A 128 584 A 1 HETATM 13 O O5' 128 . . . G 6 59.72 -10.386 55.681 1 72.15 ? O5' 128 584 A 1 HETATM 14 C C5' 128 . . . G 6 58.957 -11.488 56.245 1 70 ? C5' 128 584 A 1 HETATM 15 C C4' 128 . . . G 6 59.642 -12.908 55.876 1 69.43 ? C4' 128 584 A 1 HETATM 16 O O4' 128 . . . G 6 58.728 -13.492 54.865 1 70.54 ? O4' 128 584 A 1 HETATM 17 C C3' 128 . . . G 6 60.885 -13 55.135 1 69.84 ? C3' 128 584 A 1 HETATM 18 O O3' 128 . . . G 6 61.788 -13.874 55.868 1 71.85 ? O3' 128 584 A 1 HETATM 19 C C2' 128 . . . G 6 60.622 -13.644 53.702 1 70.08 ? C2' 128 584 A 1 HETATM 20 O O2' 128 . . . G 6 61.382 -14.875 53.524 1 74.37 ? O2' 128 584 A 1 HETATM 21 C C1' 128 . . . G 6 59.098 -13.952 53.6 1 69.29 ? C1' 128 584 A 1 HETATM 22 N N9 128 . . . G 6 58.321 -13.151 52.589 1 66.11 ? N9 128 584 A 1 HETATM 23 C C8 128 . . . G 6 58.193 -11.813 52.385 1 67.35 ? C8 128 584 A 1 HETATM 24 N N7 128 . . . G 6 57.423 -11.467 51.4 1 68.76 ? N7 128 584 A 1 HETATM 25 C C5 128 . . . G 6 56.993 -12.628 50.899 1 65.42 ? C5 128 584 A 1 HETATM 26 C C6 128 . . . G 6 56.117 -12.854 49.776 1 66.18 ? C6 128 584 A 1 HETATM 27 N N6 128 . . . G 6 55.6 -11.798 49.114 1 69.46 ? N6 128 584 A 1 HETATM 28 N N1 128 . . . G 6 55.778 -14.192 49.393 1 64.67 ? N1 128 584 A 1 HETATM 29 C C2 128 . . . G 6 56.337 -15.226 50.111 1 63.53 ? C2 128 584 A 1 HETATM 30 N N3 128 . . . G 6 57.172 -14.982 51.18 1 62.16 ? N3 128 584 A 1 HETATM 31 C C4 128 . . . G 6 57.55 -13.699 51.6 1 63.62 ? C4 128 584 A 1 HETATM 32 C C1F 128 . . . G 6 62.096 -15.003 54.885 1 78.27 ? C1F 128 584 A 1 HETATM 33 C C2F 128 . . . G 6 63.608 -15.067 54.501 1 81.63 ? C2F 128 584 A 1 HETATM 34 C C3F 128 . . . G 6 64.415 -16.164 54.886 1 85.05 ? C3F 128 584 A 1 HETATM 35 C C4F 128 . . . G 6 64.034 -17.29 55.614 1 86.27 ? C4F 128 584 A 1 HETATM 36 C C5F 128 . . . G 6 62.669 -17.327 56.016 1 83.97 ? C5F 128 584 A 1 HETATM 37 C C6F 128 . . . G 6 61.64 -16.262 55.711 1 82.21 ? C6F 128 584 A 1 HETATM 38 N N2F 128 . . . G 6 64.281 -14.026 53.739 1 82.72 ? N2F 128 584 A 1 HETATM 39 N N4F 128 . . . G 6 64.831 -18.318 55.954 1 88.97 ? N4F 128 584 A 1 HETATM 40 N N6F 128 . . . G 6 60.31 -16.589 56.254 1 85.12 ? N6F 128 584 A 1 HETATM 41 O O2F 128 . . . G 6 63.744 -13.036 53.338 1 85.4 ? O2F 128 584 A 1 HETATM 42 O O3F 128 . . . G 6 65.468 -14.095 53.451 1 82.71 ? O3F 128 584 A 1 HETATM 43 O O4F 128 . . . G 6 64.457 -19.296 56.593 1 92.67 ? O4F 128 584 A 1 HETATM 44 O O5F 128 . . . G 6 66.002 -18.347 55.639 1 90.96 ? O5F 128 584 A 1 HETATM 45 O O6F 128 . . . G 6 60.129 -17.647 56.893 1 84.41 ? O6F 128 584 A 1 HETATM 46 O O7F 128 . . . G 6 59.33 -15.937 56.154 1 87.77 ? O7F 128 584 A 1 # _model_server_stats.io_time_ms 9 _model_server_stats.parse_time_ms 9 _model_server_stats.create_model_time_ms 7 _model_server_stats.query_time_ms 301 _model_server_stats.encode_time_ms 5 _model_server_stats.element_count 46 #