data_6QV1 # _model_server_result.job_id LOjqK2YHzEzlhliTeWiy0w _model_server_result.datetime_utc '2024-11-22 18:17:56' _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 6qv1 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"I","auth_seq_id":600}' # _entry.id 6QV1 # _exptl.entry_id 6QV1 _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 523.247 _entity.id 4 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description 'PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER' _entity.pdbx_number_of_molecules 4 _entity.pdbx_parent_entity_id . _entity.pdbx_mutation ? _entity.pdbx_fragment ? _entity.pdbx_ec ? # _cell.angle_alpha 90 _cell.angle_beta 91.26 _cell.angle_gamma 90 _cell.entry_id 6QV1 _cell.length_a 90.75 _cell.length_b 199.26 _cell.length_c 113.16 _cell.Z_PDB 4 _cell.pdbx_unique_axis ? # _symmetry.entry_id 6QV1 _symmetry.cell_setting ? _symmetry.Int_Tables_number 4 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 1 21 1' # 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 trimeric 3 author_and_software_defined_assembly 1 PISA trimeric 3 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,G,H,I,J 1 1 C,D,F,K,L,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 ? 4 G N N ? 4 I N N ? 4 K N N ? 4 M 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 disulf ? disulf1 E SG CYS 25 E CYS 22 1_555 E SG CYS 98 E CYS 95 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.033 ? disulf ? disulf2 F SG CYS 25 F CYS 22 1_555 F SG CYS 98 F CYS 95 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.035 ? metalc ? metalc1 A OG SER 383 A SER 373 1_555 H MG MG . A MG 601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.285 ? metalc ? metalc2 A OE1 GLN 424 A GLN 414 1_555 H MG MG . A MG 601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.047 ? metalc ? metalc3 G O2G AGS . A AGS 600 1_555 H MG MG . A MG 601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.947 ? metalc ? metalc4 G O2B AGS . A AGS 600 1_555 H MG MG . A MG 601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.948 ? metalc ? metalc5 B OG1 THR 395 B THR 395 1_555 J MG MG . B MG 601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.941 ? metalc ? metalc6 B OE1 GLN 436 B GLN 436 1_555 J MG MG . B MG 601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.204 ? metalc ? metalc7 I O3G AGS . B AGS 600 1_555 J MG MG . B MG 601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.584 ? metalc ? metalc8 I O2B AGS . B AGS 600 1_555 J MG MG . B MG 601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.078 ? metalc ? metalc9 C OG SER 383 C SER 373 1_555 L MG MG . C MG 601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.949 ? metalc ? metalc10 C OE1 GLN 424 C GLN 414 1_555 L MG MG . C MG 601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.943 ? metalc ? metalc11 K O2G AGS . C AGS 600 1_555 L MG MG . C MG 601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.17 ? metalc ? metalc12 K O2B AGS . C AGS 600 1_555 L MG MG . C MG 601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.064 ? metalc ? metalc13 D OG1 THR 395 D THR 395 1_555 N MG MG . D MG 601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.948 ? metalc ? metalc14 D OE1 GLN 436 D GLN 436 1_555 N MG MG . D MG 601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.344 ? metalc ? metalc15 M O3G AGS . D AGS 600 1_555 N MG MG . D MG 601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.166 ? metalc ? metalc16 M O2B AGS . D AGS 600 1_555 N MG MG . D MG 601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.943 ? # _chem_comp.formula 'C10 H16 N5 O12 P3 S' _chem_comp.formula_weight 523.247 _chem_comp.id AGS _chem_comp.mon_nstd_flag . _chem_comp.name 'PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER' _chem_comp.type non-polymer _chem_comp.pdbx_synonyms "ATP-GAMMA-S;ADENOSINE 5'-(3-THIOTRIPHOSPHATE);ADENOSINE 5'-(GAMMA-THIOTRIPHOSPHATE);ADENOSINE-5'-DIPHOSPHATE MONOTHIOPHOSPHATE" # 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 S1G AGS doub 1 n n PG O2G AGS sing 2 n n PG O3G AGS sing 3 n n PG O3B AGS sing 4 n n PB O1B AGS doub 5 n n PB O2B AGS sing 6 n n PB O3B AGS sing 7 n n PB O3A AGS sing 8 n n PA O1A AGS doub 9 n n PA O2A AGS sing 10 n n PA O3A AGS sing 11 n n PA O5' AGS sing 12 n n O5' C5' AGS sing 13 n n C5' C4' AGS sing 14 n n C4' O4' AGS sing 15 n n C4' C3' AGS sing 16 n n O4' C1' AGS sing 17 n n C3' O3' AGS sing 18 n n C3' C2' AGS sing 19 n n C2' O2' AGS sing 20 n n C2' C1' AGS sing 21 n n C1' N9 AGS sing 22 n n N9 C8 AGS sing 23 n y N9 C4 AGS sing 24 n y C8 N7 AGS doub 25 n y N7 C5 AGS sing 26 n y C5 C6 AGS sing 27 n y C5 C4 AGS doub 28 n y C6 N6 AGS sing 29 n n C6 N1 AGS doub 30 n y N1 C2 AGS sing 31 n y C2 N3 AGS doub 32 n y N3 C4 AGS sing 33 n y O2G HOG2 AGS sing 34 n n O3G H21 AGS sing 35 n n O2B HOB2 AGS sing 36 n n O2A HOA2 AGS sing 37 n n C5' "H5'1" AGS sing 38 n n C5' "H5'2" AGS sing 39 n n C4' H4' AGS sing 40 n n C3' H3' AGS sing 41 n n O3' HO3' AGS sing 42 n n C2' H2' AGS sing 43 n n O2' HO2' AGS sing 44 n n C1' H1' AGS sing 45 n n C8 H8 AGS sing 46 n n N6 HN61 AGS sing 47 n n N6 HN62 AGS sing 48 n n C2 H2 AGS sing 49 n n # _atom_sites.entry_id 6QV1 _atom_sites.fract_transf_matrix[1][1] 0.011019 _atom_sites.fract_transf_matrix[1][2] 0 _atom_sites.fract_transf_matrix[1][3] 0.000242 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.005019 _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] 0.008839 _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 G 4 AGS A 1 600 600 AGS AGS . H 5 MG A 1 601 601 MG MG . I 4 AGS B 1 600 600 AGS AGS . J 5 MG B 1 601 601 MG MG . K 4 AGS C 1 600 600 AGS AGS . L 5 MG C 1 601 601 MG MG . M 4 AGS D 1 600 600 AGS AGS . N 5 MG D 1 601 601 MG MG . # 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 AGS . . . I 4 8.41 32.559 26.681 1 100.62 ? PG AGS 600 B 1 HETATM 2 S S1G AGS . . . I 4 7.537 30.89 26.915 1 102.25 ? S1G AGS 600 B 1 HETATM 3 O O2G AGS . . . I 4 9.207 33.073 27.915 1 100.34 ? O2G AGS 600 B 1 HETATM 4 O O3G AGS . . . I 4 7.612 33.851 26.344 1 101.1 ? O3G AGS 600 B 1 HETATM 5 P PB AGS . . . I 4 9.332 32.569 23.971 1 99.29 ? PB AGS 600 B 1 HETATM 6 O O1B AGS . . . I 4 9.68 31.336 23.237 1 100.28 -1 O1B AGS 600 B 1 HETATM 7 O O2B AGS . . . I 4 7.952 33.144 23.691 1 99.17 ? O2B AGS 600 B 1 HETATM 8 O O3B AGS . . . I 4 9.447 32.377 25.544 1 99.82 ? O3B AGS 600 B 1 HETATM 9 P PA AGS . . . I 4 10.523 34.986 22.783 1 96.77 ? PA AGS 600 B 1 HETATM 10 O O1A AGS . . . I 4 10.293 34.623 21.373 1 97.32 -1 O1A AGS 600 B 1 HETATM 11 O O2A AGS . . . I 4 9.615 36.07 23.364 1 97.45 ? O2A AGS 600 B 1 HETATM 12 O O3A AGS . . . I 4 10.404 33.721 23.739 1 97.69 ? O3A AGS 600 B 1 HETATM 13 O O5' AGS . . . I 4 12.028 35.426 22.998 1 95.4 ? O5' AGS 600 B 1 HETATM 14 C C5' AGS . . . I 4 13.111 34.511 22.745 1 95.92 ? C5' AGS 600 B 1 HETATM 15 C C4' AGS . . . I 4 14.421 35.173 23.088 1 96.27 ? C4' AGS 600 B 1 HETATM 16 O O4' AGS . . . I 4 14.493 36.472 22.466 1 96.75 ? O4' AGS 600 B 1 HETATM 17 C C3' AGS . . . I 4 14.723 35.377 24.571 1 96.31 ? C3' AGS 600 B 1 HETATM 18 O O3' AGS . . . I 4 16.074 35.03 24.851 1 96 ? O3' AGS 600 B 1 HETATM 19 C C2' AGS . . . I 4 14.393 36.857 24.803 1 97.15 ? C2' AGS 600 B 1 HETATM 20 O O2' AGS . . . I 4 15.214 37.437 25.812 1 97.74 ? O2' AGS 600 B 1 HETATM 21 C C1' AGS . . . I 4 14.697 37.48 23.437 1 97.34 ? C1' AGS 600 B 1 HETATM 22 N N9 AGS . . . I 4 13.865 38.629 23.082 1 97.42 ? N9 AGS 600 B 1 HETATM 23 C C8 AGS . . . I 4 12.528 38.623 22.777 1 97.07 ? C8 AGS 600 B 1 HETATM 24 N N7 AGS . . . I 4 12.063 39.783 22.38 1 96.74 ? N7 AGS 600 B 1 HETATM 25 C C5 AGS . . . I 4 13.17 40.617 22.436 1 96.46 ? C5 AGS 600 B 1 HETATM 26 C C6 AGS . . . I 4 13.35 41.981 22.129 1 95.94 ? C6 AGS 600 B 1 HETATM 27 N N6 AGS . . . I 4 12.392 42.756 21.608 1 94.96 ? N6 AGS 600 B 1 HETATM 28 N N1 AGS . . . I 4 14.58 42.513 22.322 1 97.04 ? N1 AGS 600 B 1 HETATM 29 C C2 AGS . . . I 4 15.562 41.723 22.776 1 97.37 ? C2 AGS 600 B 1 HETATM 30 N N3 AGS . . . I 4 15.517 40.42 23.073 1 97.11 ? N3 AGS 600 B 1 HETATM 31 C C4 AGS . . . I 4 14.286 39.921 22.88 1 97.13 ? C4 AGS 600 B 1 # _model_server_stats.io_time_ms 48 _model_server_stats.parse_time_ms 14 _model_server_stats.create_model_time_ms 36 _model_server_stats.query_time_ms 258 _model_server_stats.encode_time_ms 5 _model_server_stats.element_count 31 #