data_6V4L # _model_server_result.job_id h83VvtgDCC-S-o4QLOKIyg _model_server_result.datetime_utc '2025-04-18 03:36:07' _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":"E","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 . . . E 3 -8.139 -67.916 -16.22 1 112.46 ? PG AGS 501 C 1 HETATM 2 S S1G AGS . . . E 3 -7.499 -66.495 -17.372 1 80.99 ? S1G AGS 501 C 1 HETATM 3 O O2G AGS . . . E 3 -9.628 -68.216 -16.538 1 104.05 ? O2G AGS 501 C 1 HETATM 4 O O3G AGS . . . E 3 -7.282 -69.194 -16.441 1 79.47 ? O3G AGS 501 C 1 HETATM 5 P PB AGS . . . E 3 -7.273 -68.458 -13.761 1 118.67 ? PB AGS 501 C 1 HETATM 6 O O1B AGS . . . E 3 -8.123 -69.648 -13.562 1 91.27 ? O1B AGS 501 C 1 HETATM 7 O O2B AGS . . . E 3 -5.932 -68.795 -14.419 1 97.86 ? O2B AGS 501 C 1 HETATM 8 O O3B AGS . . . E 3 -7.983 -67.462 -14.746 1 110.75 ? O3B AGS 501 C 1 HETATM 9 P PA AGS . . . E 3 -5.424 -67.516 -11.977 1 129.31 ? PA AGS 501 C 1 HETATM 10 O O1A AGS . . . E 3 -5.001 -68.468 -10.926 1 111.83 ? O1A AGS 501 C 1 HETATM 11 O O2A AGS . . . E 3 -4.59 -67.561 -13.259 1 101.87 ? O2A AGS 501 C 1 HETATM 12 O O3A AGS . . . E 3 -6.932 -67.742 -12.395 1 119.64 ? O3A AGS 501 C 1 HETATM 13 O O5' AGS . . . E 3 -5.421 -66.067 -11.389 1 87.11 ? O5' AGS 501 C 1 HETATM 14 C C5' AGS . . . E 3 -4.244 -65.252 -11.41 1 74.57 ? C5' AGS 501 C 1 HETATM 15 C C4' AGS . . . E 3 -4.723 -63.865 -11.734 1 82.06 ? C4' AGS 501 C 1 HETATM 16 O O4' AGS . . . E 3 -5.763 -63.496 -10.809 1 72.12 ? O4' AGS 501 C 1 HETATM 17 C C3' AGS . . . E 3 -3.672 -62.766 -11.638 1 79.53 ? C3' AGS 501 C 1 HETATM 18 O O3' AGS . . . E 3 -3.909 -61.735 -12.592 1 68.05 ? O3' AGS 501 C 1 HETATM 19 C C2' AGS . . . E 3 -3.817 -62.265 -10.197 1 73.01 ? C2' AGS 501 C 1 HETATM 20 O O2' AGS . . . E 3 -3.671 -60.857 -10.074 1 75.82 ? O2' AGS 501 C 1 HETATM 21 C C1' AGS . . . E 3 -5.261 -62.601 -9.837 1 72.56 ? C1' AGS 501 C 1 HETATM 22 N N9 AGS . . . E 3 -5.393 -63.174 -8.507 1 74.22 ? N9 AGS 501 C 1 HETATM 23 C C8 AGS . . . E 3 -4.977 -64.406 -8.077 1 72.26 ? C8 AGS 501 C 1 HETATM 24 N N7 AGS . . . E 3 -5.198 -64.629 -6.804 1 67.98 ? N7 AGS 501 C 1 HETATM 25 C C5 AGS . . . E 3 -5.778 -63.45 -6.36 1 65.79 ? C5 AGS 501 C 1 HETATM 26 C C6 AGS . . . E 3 -6.25 -63.04 -5.098 1 67.81 ? C6 AGS 501 C 1 HETATM 27 N N6 AGS . . . E 3 -6.207 -63.808 -4.006 1 77.54 ? N6 AGS 501 C 1 HETATM 28 N N1 AGS . . . E 3 -6.772 -61.796 -4.997 1 67.62 ? N1 AGS 501 C 1 HETATM 29 C C2 AGS . . . E 3 -6.816 -61.026 -6.087 1 59.6 ? C2 AGS 501 C 1 HETATM 30 N N3 AGS . . . E 3 -6.404 -61.304 -7.326 1 59.33 ? N3 AGS 501 C 1 HETATM 31 C C4 AGS . . . E 3 -5.891 -62.54 -7.396 1 68.4 ? C4 AGS 501 C 1 # _model_server_stats.io_time_ms 25 _model_server_stats.parse_time_ms 17 _model_server_stats.create_model_time_ms 31 _model_server_stats.query_time_ms 293 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 31 #