data_4JSP # _model_server_result.job_id pb5rUD27swlZksbBZbaoeA _model_server_result.datetime_utc '2024-11-20 04:28:27' _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 4jsp # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"E","auth_seq_id":3000}' # _entry.id 4JSP # _exptl.entry_id 4JSP _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 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 4JSP _cell.length_a 139.4 _cell.length_b 163.2 _cell.length_c 207.8 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 4JSP _symmetry.cell_setting ? _symmetry.Int_Tables_number 18 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 2 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,B,E,F,G 1 1 C,D,H,I,J 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 ? 3 E N N ? 3 H 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 OD1 ASN 968 B ASN 2343 1_555 F MG MG . B MG 3001 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.932 ? metalc ? metalc2 E O2G AGS . B AGS 3000 1_555 F MG MG . B MG 3001 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.214 ? metalc ? metalc3 E O1A AGS . B AGS 3000 1_555 F MG MG . B MG 3001 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.773 ? metalc ? metalc4 E O3G AGS . B AGS 3000 1_555 G MG MG . B MG 3002 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.215 ? metalc ? metalc5 H O2G AGS . A AGS 3000 1_555 I MG MG . A MG 3001 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.848 ? metalc ? metalc6 H O1A AGS . A AGS 3000 1_555 I MG MG . A MG 3001 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.837 ? metalc ? metalc7 H O3G AGS . A AGS 3000 1_555 J MG MG . A MG 3002 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.534 ? metalc ? metalc8 H O1B AGS . A AGS 3000 1_555 J MG MG . A MG 3002 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.859 ? # _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 4JSP _atom_sites.fract_transf_matrix[1][1] 0.007174 _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] 0.006127 _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] 0.004812 _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 B 1 3000 3000 AGS AGS . F 4 MG B 1 3001 3001 MG MG . G 4 MG B 1 3002 3002 MG MG . H 3 AGS A 1 3000 3000 AGS AGS . I 4 MG A 1 3001 3001 MG MG . J 4 MG A 1 3002 3002 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 . . . E 3 -19.231 -29.725 -63.681 1 82.13 ? PG AGS 3000 B 1 HETATM 2 S S1G AGS . . . E 3 -20.836 -29.086 -64.865 1 84.45 ? S1G AGS 3000 B 1 HETATM 3 O O2G AGS . . . E 3 -18.443 -28.435 -63.083 1 74.86 ? O2G AGS 3000 B 1 HETATM 4 O O3G AGS . . . E 3 -18.261 -30.531 -64.485 1 77.19 ? O3G AGS 3000 B 1 HETATM 5 P PB AGS . . . E 3 -20.49 -32.094 -62.663 1 78.75 ? PB AGS 3000 B 1 HETATM 6 O O1B AGS . . . E 3 -19.553 -32.937 -63.506 1 78.98 ? O1B AGS 3000 B 1 HETATM 7 O O2B AGS . . . E 3 -21.929 -31.925 -63.107 1 79.33 ? O2B AGS 3000 B 1 HETATM 8 O O3B AGS . . . E 3 -19.83 -30.621 -62.456 1 76.4 ? O3B AGS 3000 B 1 HETATM 9 P PA AGS . . . E 3 -19.838 -32.079 -59.889 1 71.34 ? PA AGS 3000 B 1 HETATM 10 O O1A AGS . . . E 3 -18.59 -31.325 -60.31 1 68.52 ? O1A AGS 3000 B 1 HETATM 11 O O2A AGS . . . E 3 -19.691 -33.121 -58.815 1 70.74 ? O2A AGS 3000 B 1 HETATM 12 O O3A AGS . . . E 3 -20.517 -32.757 -61.187 1 74.71 ? O3A AGS 3000 B 1 HETATM 13 O O5' AGS . . . E 3 -21.019 -31.074 -59.442 1 67.07 ? O5' AGS 3000 B 1 HETATM 14 C C5' AGS . . . E 3 -22.295 -31.575 -59.049 1 61.43 ? C5' AGS 3000 B 1 HETATM 15 C C4' AGS . . . E 3 -22.601 -31.142 -57.622 1 57.9 ? C4' AGS 3000 B 1 HETATM 16 O O4' AGS . . . E 3 -22.352 -32.225 -56.74 1 56.75 ? O4' AGS 3000 B 1 HETATM 17 C C3' AGS . . . E 3 -21.723 -30.008 -57.12 1 56.99 ? C3' AGS 3000 B 1 HETATM 18 O O3' AGS . . . E 3 -22.374 -28.756 -57.315 1 57.97 ? O3' AGS 3000 B 1 HETATM 19 C C2' AGS . . . E 3 -21.503 -30.292 -55.647 1 56.12 ? C2' AGS 3000 B 1 HETATM 20 O O2' AGS . . . E 3 -22.451 -29.636 -54.798 1 56.78 ? O2' AGS 3000 B 1 HETATM 21 C C1' AGS . . . E 3 -21.762 -31.772 -55.512 1 55.31 ? C1' AGS 3000 B 1 HETATM 22 N N9 AGS . . . E 3 -20.489 -32.478 -55.206 1 53.44 ? N9 AGS 3000 B 1 HETATM 23 C C8 AGS . . . E 3 -19.534 -32.85 -56.08 1 52.87 ? C8 AGS 3000 B 1 HETATM 24 N N7 AGS . . . E 3 -18.511 -33.491 -55.467 1 51.35 ? N7 AGS 3000 B 1 HETATM 25 C C5 AGS . . . E 3 -18.81 -33.526 -54.166 1 50.89 ? C5 AGS 3000 B 1 HETATM 26 C C6 AGS . . . E 3 -18.161 -34.05 -52.953 1 51.01 ? C6 AGS 3000 B 1 HETATM 27 N N6 AGS . . . E 3 -16.957 -34.676 -53.024 1 50.73 ? N6 AGS 3000 B 1 HETATM 28 N N1 AGS . . . E 3 -18.817 -33.881 -51.778 1 50.77 ? N1 AGS 3000 B 1 HETATM 29 C C2 AGS . . . E 3 -20.014 -33.261 -51.703 1 50.67 ? C2 AGS 3000 B 1 HETATM 30 N N3 AGS . . . E 3 -20.655 -32.759 -52.769 1 50.74 ? N3 AGS 3000 B 1 HETATM 31 C C4 AGS . . . E 3 -20.109 -32.862 -53.997 1 51.45 ? C4 AGS 3000 B 1 # _model_server_stats.io_time_ms 16 _model_server_stats.parse_time_ms 10 _model_server_stats.create_model_time_ms 58 _model_server_stats.query_time_ms 280 _model_server_stats.encode_time_ms 3 _model_server_stats.element_count 31 #