data_6V4L # _model_server_result.job_id 5_P13huvCJ8ISkK51Iexqg _model_server_result.datetime_utc '2025-04-18 01:51:59' _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 6v4l # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"G","auth_seq_id":501}' # _entry.id 6V4L # _exptl.entry_id 6V4L _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 523.247 _entity.id 3 _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 90 _cell.angle_gamma 90 _cell.entry_id 6V4L _cell.length_a 164.271 _cell.length_b 164.271 _cell.length_c 123.388 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 6V4L _symmetry.cell_setting ? _symmetry.Int_Tables_number 77 _symmetry.space_group_name_Hall 'P 4c' _symmetry.space_group_name_H-M 'P 42' # _pdbx_struct_assembly.method_details ? _pdbx_struct_assembly.oligomeric_details octameric _pdbx_struct_assembly.oligomeric_count 8 _pdbx_struct_assembly.details author_defined_assembly _pdbx_struct_assembly.id 1 # loop_ _pdbx_struct_assembly_gen.asym_id_list _pdbx_struct_assembly_gen.assembly_id _pdbx_struct_assembly_gen.oper_expression A,B,C,D,E,F,G,H 1 1 A,B,C,D,E,F,G,H 1 2 # loop_ _pdbx_struct_oper_list.id _pdbx_struct_oper_list.type _pdbx_struct_oper_list.name _pdbx_struct_oper_list.symmetry_operation _pdbx_struct_oper_list.matrix[1][1] _pdbx_struct_oper_list.matrix[1][2] _pdbx_struct_oper_list.matrix[1][3] _pdbx_struct_oper_list.matrix[2][1] _pdbx_struct_oper_list.matrix[2][2] _pdbx_struct_oper_list.matrix[2][3] _pdbx_struct_oper_list.matrix[3][1] _pdbx_struct_oper_list.matrix[3][2] _pdbx_struct_oper_list.matrix[3][3] _pdbx_struct_oper_list.vector[1] _pdbx_struct_oper_list.vector[2] _pdbx_struct_oper_list.vector[3] 1 'identity operation' 1_555 x,y,z 1 0 0 0 1 0 0 0 1 0 0 0 2 'crystal symmetry operation' 2_545 -x,-y-1,z -1 0 0 0 -1 0 0 0 1 0 -164.271 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 F N N ? 3 G N N ? 3 H N N # _struct_conn.conn_type_id disulf _struct_conn.details ? _struct_conn.id disulf1 _struct_conn.ptnr1_label_asym_id B _struct_conn.ptnr1_label_atom_id SG _struct_conn.ptnr1_label_comp_id CYS _struct_conn.ptnr1_label_seq_id 251 _struct_conn.ptnr1_auth_asym_id B _struct_conn.ptnr1_auth_comp_id CYS _struct_conn.ptnr1_auth_seq_id 251 _struct_conn.ptnr1_symmetry 1_555 _struct_conn.ptnr2_label_asym_id B _struct_conn.ptnr2_label_atom_id SG _struct_conn.ptnr2_label_comp_id CYS _struct_conn.ptnr2_label_seq_id 348 _struct_conn.ptnr2_auth_asym_id B _struct_conn.ptnr2_auth_comp_id CYS _struct_conn.ptnr2_auth_seq_id 348 _struct_conn.ptnr2_symmetry 1_555 _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 2.038 _struct_conn.pdbx_value_order ? # _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 6V4L _atom_sites.fract_transf_matrix[1][1] 0.006088 _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] 0.006088 _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] 0.008105 _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 AGS C 1 501 1 AGS AGS . F 3 AGS C 1 502 4 AGS AGS . G 3 AGS D 1 501 2 AGS AGS . H 3 AGS D 1 502 3 AGS AGS . # 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 . . . G 3 2.818 -95.482 17.266 1 157.84 ? PG AGS 501 D 1 HETATM 2 S S1G AGS . . . G 3 3.621 -93.899 18.062 1 86.68 ? S1G AGS 501 D 1 HETATM 3 O O2G AGS . . . G 3 1.329 -95.544 17.709 1 79.73 ? O2G AGS 501 D 1 HETATM 4 O O3G AGS . . . G 3 3.558 -96.776 17.69 1 77.43 ? O3G AGS 501 D 1 HETATM 5 P PB AGS . . . G 3 1.606 -94.832 15.039 1 111.54 ? PB AGS 501 D 1 HETATM 6 O O1B AGS . . . G 3 0.435 -95.385 15.748 1 82.86 ? O1B AGS 501 D 1 HETATM 7 O O2B AGS . . . G 3 1.736 -93.31 15.132 1 116.91 ? O2B AGS 501 D 1 HETATM 8 O O3B AGS . . . G 3 2.882 -95.419 15.719 1 104.87 ? O3B AGS 501 D 1 HETATM 9 P PA AGS . . . G 3 0.504 -94.236 12.71 1 105.2 ? PA AGS 501 D 1 HETATM 10 O O1A AGS . . . G 3 0.889 -92.818 12.84 1 96.97 ? O1A AGS 501 D 1 HETATM 11 O O2A AGS . . . G 3 0.327 -94.798 11.296 1 78.6 ? O2A AGS 501 D 1 HETATM 12 O O3A AGS . . . G 3 1.516 -95.155 13.494 1 87.49 ? O3A AGS 501 D 1 HETATM 13 O O5' AGS . . . G 3 -0.754 -94.431 13.64 1 103.02 ? O5' AGS 501 D 1 HETATM 14 C C5' AGS . . . G 3 -1.673 -93.378 13.955 1 87.21 ? C5' AGS 501 D 1 HETATM 15 C C4' AGS . . . G 3 -3.029 -94.005 14.071 1 73.59 ? C4' AGS 501 D 1 HETATM 16 O O4' AGS . . . G 3 -3.585 -93.798 15.392 1 64.37 ? O4' AGS 501 D 1 HETATM 17 C C3' AGS . . . G 3 -4.098 -93.476 13.131 1 63.68 ? C3' AGS 501 D 1 HETATM 18 O O3' AGS . . . G 3 -3.952 -94.001 11.816 1 71.15 ? O3' AGS 501 D 1 HETATM 19 C C2' AGS . . . G 3 -5.35 -93.986 13.824 1 62.46 ? C2' AGS 501 D 1 HETATM 20 O O2' AGS . . . G 3 -5.324 -95.394 13.661 1 64.09 ? O2' AGS 501 D 1 HETATM 21 C C1' AGS . . . G 3 -4.999 -93.719 15.29 1 63.75 ? C1' AGS 501 D 1 HETATM 22 N N9 AGS . . . G 3 -5.445 -92.42 15.786 1 72.93 ? N9 AGS 501 D 1 HETATM 23 C C8 AGS . . . G 3 -4.947 -91.191 15.438 1 81.37 ? C8 AGS 501 D 1 HETATM 24 N N7 AGS . . . G 3 -5.552 -90.184 16.021 1 81.33 ? N7 AGS 501 D 1 HETATM 25 C C5 AGS . . . G 3 -6.537 -90.791 16.786 1 75.9 ? C5 AGS 501 D 1 HETATM 26 C C6 AGS . . . G 3 -7.532 -90.271 17.638 1 73.24 ? C6 AGS 501 D 1 HETATM 27 N N6 AGS . . . G 3 -7.7 -88.967 17.872 1 78.07 ? N6 AGS 501 D 1 HETATM 28 N N1 AGS . . . G 3 -8.358 -91.152 18.25 1 51.14 ? N1 AGS 501 D 1 HETATM 29 C C2 AGS . . . G 3 -8.192 -92.457 18.016 1 51.89 ? C2 AGS 501 D 1 HETATM 30 N N3 AGS . . . G 3 -7.294 -93.062 17.234 1 59.95 ? N3 AGS 501 D 1 HETATM 31 C C4 AGS . . . G 3 -6.492 -92.168 16.641 1 69.3 ? C4 AGS 501 D 1 # _model_server_stats.io_time_ms 26 _model_server_stats.parse_time_ms 13 _model_server_stats.create_model_time_ms 20 _model_server_stats.query_time_ms 280 _model_server_stats.encode_time_ms 4 _model_server_stats.element_count 31 #