data_1XPO # _model_server_result.job_id D634D7Y0AN2QGMbjoelK3A _model_server_result.datetime_utc '2025-08-31 14:59:00' _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 1xpo # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"V","auth_seq_id":4600}' # _entry.id 1XPO # _exptl.entry_id 1XPO _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 6 _entity.pdbx_parent_entity_id . _entity.pdbx_mutation ? _entity.pdbx_fragment ? _entity.pdbx_ec ? # _cell.angle_alpha 90 _cell.angle_beta 108.79 _cell.angle_gamma 90 _cell.entry_id 1XPO _cell.length_a 211.933 _cell.length_b 111.37 _cell.length_c 161.033 _cell.Z_PDB 24 _cell.pdbx_unique_axis ? # _symmetry.entry_id 1XPO _symmetry.cell_setting monoclinic _symmetry.Int_Tables_number 5 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'C 1 2 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 ? dimeric 2 author_defined_assembly 1 ? dimeric 2 author_defined_assembly 2 ? dimeric 2 author_defined_assembly 3 ? dimeric 2 author_defined_assembly 4 ? dimeric 2 author_defined_assembly 5 ? dimeric 2 author_defined_assembly 6 # loop_ _pdbx_struct_assembly_gen.asym_id_list _pdbx_struct_assembly_gen.assembly_id _pdbx_struct_assembly_gen.oper_expression A,G,M,N 1 1 B,H,O,P,Q 2 1 C,I,R,S,T 3 1 D,J,U,V,W 4 1 E,K,X,Y,Z 5 1 F,L,AA,BA,CA 6 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 N N N ? 4 P N N ? 4 S N N ? 4 V N N ? 4 Y N N ? 4 BA 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 G OG1 THR 185 A THR 185 1_555 M MG MG . A MG 1601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.814 ? metalc ? metalc2 G NH2 ARG 212 A ARG 212 1_555 M MG MG . A MG 1601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.518 ? metalc ? metalc3 G OE2 GLU 215 A GLU 215 1_555 M MG MG . A MG 1601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.287 ? metalc ? metalc4 N O2G AGS . A AGS 1600 1_555 M MG MG . A MG 1601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.951 ? metalc ? metalc5 H OG1 THR 185 B THR 185 1_555 O MG MG . B MG 2601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.704 ? metalc ? metalc6 P O2G AGS . B AGS 2600 1_555 O MG MG . B MG 2601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.494 ? metalc ? metalc7 P O2B AGS . B AGS 2600 1_555 O MG MG . B MG 2601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.829 ? metalc ? metalc8 O MG MG . B MG 2601 1_555 Q O2A BCM . B BCM 2701 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.703 ? metalc ? metalc9 I OG1 THR 185 C THR 185 1_555 R MG MG . C MG 3601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.309 ? metalc ? metalc10 S O2G AGS . C AGS 3600 1_555 R MG MG . C MG 3601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 3.016 ? metalc ? metalc11 S O2B AGS . C AGS 3600 1_555 R MG MG . C MG 3601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.476 ? metalc ? metalc12 R MG MG . C MG 3601 1_555 T O9 BCM . C BCM 3701 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.872 ? metalc ? metalc13 J OG1 THR 185 D THR 185 1_555 U MG MG . D MG 4601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.2 ? metalc ? metalc14 J NH2 ARG 366 D ARG 366 1_555 X MG MG . E MG 5601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.574 ? metalc ? metalc15 V O2B AGS . D AGS 4600 1_555 U MG MG . D MG 4601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.804 ? metalc ? metalc16 V O2G AGS . D AGS 4600 1_555 U MG MG . D MG 4601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.448 ? metalc ? metalc17 K OG1 THR 185 E THR 185 1_555 X MG MG . E MG 5601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.403 ? metalc ? metalc18 K NH2 ARG 212 E ARG 212 1_555 X MG MG . E MG 5601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.739 ? metalc ? metalc19 Y O2G AGS . E AGS 5600 1_555 X MG MG . E MG 5601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.491 ? metalc ? metalc20 X MG MG . E MG 5601 1_555 Z O2A BCM . E BCM 5701 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.823 ? metalc ? metalc21 L OG1 THR 185 F THR 185 1_555 AA MG MG . F MG 6601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.366 ? metalc ? metalc22 L OE1 GLU 215 F GLU 215 1_555 AA MG MG . F MG 6601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 3.028 ? metalc ? metalc23 BA O2G AGS . F AGS 6600 1_555 AA MG MG . F MG 6601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.305 ? metalc ? metalc24 BA O2B AGS . F AGS 6600 1_555 AA MG MG . F MG 6601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 3.016 ? # _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 1XPO _atom_sites.fract_transf_matrix[1][1] 0.004718 _atom_sites.fract_transf_matrix[1][2] 0 _atom_sites.fract_transf_matrix[1][3] 0.001605 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.008979 _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] 0.006559 _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 M 3 MG A 1 1601 1601 MG MG . N 4 AGS A 1 1600 1600 AGS AGS . O 3 MG B 1 2601 2601 MG MG . P 4 AGS B 1 2600 2600 AGS AGS . Q 5 BCM B 1 2701 2701 BCM BCM . R 3 MG C 1 3601 3601 MG MG . S 4 AGS C 1 3600 3600 AGS AGS . T 5 BCM C 1 3701 3701 BCM BCM . U 3 MG D 1 4601 4601 MG MG . V 4 AGS D 1 4600 4600 AGS AGS . W 5 BCM D 1 4701 4701 BCM BCM . X 3 MG E 1 5601 5601 MG MG . Y 4 AGS E 1 5600 5600 AGS AGS . Z 5 BCM E 1 5701 5701 BCM BCM . AA 3 MG F 1 6601 6601 MG MG . BA 4 AGS F 1 6600 6600 AGS AGS . CA 5 BCM F 1 6701 6701 BCM BCM . # 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 . . . V 4 27.745 27.445 45.991 1 103.79 ? PG AGS 4600 D 1 HETATM 2 S S1G AGS . . . V 4 26.372 28.66 45.035 1 104.04 ? S1G AGS 4600 D 1 HETATM 3 O O2G AGS . . . V 4 28.746 26.898 44.88 1 103.97 ? O2G AGS 4600 D 1 HETATM 4 O O3G AGS . . . V 4 27.007 26.218 46.683 1 103.95 ? O3G AGS 4600 D 1 HETATM 5 P PB AGS . . . V 4 30.112 28.156 47.331 1 102.13 ? PB AGS 4600 D 1 HETATM 6 O O1B AGS . . . V 4 30.433 26.876 48.219 1 102.2 ? O1B AGS 4600 D 1 HETATM 7 O O2B AGS . . . V 4 30.89 28.092 45.954 1 102.19 ? O2B AGS 4600 D 1 HETATM 8 O O3B AGS . . . V 4 28.527 28.318 47.102 1 103.08 ? O3B AGS 4600 D 1 HETATM 9 P PA AGS . . . V 4 30.068 30.961 47.881 1 99.7 ? PA AGS 4600 D 1 HETATM 10 O O1A AGS . . . V 4 29.173 31.074 46.567 1 99.8 ? O1A AGS 4600 D 1 HETATM 11 O O2A AGS . . . V 4 31.275 31.993 47.848 1 99.81 ? O2A AGS 4600 D 1 HETATM 12 O O3A AGS . . . V 4 30.594 29.462 48.146 1 100.96 ? O3A AGS 4600 D 1 HETATM 13 O O5' AGS . . . V 4 29.152 31.225 49.175 1 98.74 ? O5' AGS 4600 D 1 HETATM 14 C C5' AGS . . . V 4 29.417 30.544 50.406 1 97.12 ? C5' AGS 4600 D 1 HETATM 15 C C4' AGS . . . V 4 29.129 31.394 51.64 1 95.9 ? C4' AGS 4600 D 1 HETATM 16 O O4' AGS . . . V 4 30.194 31.195 52.567 1 95.36 ? O4' AGS 4600 D 1 HETATM 17 C C3' AGS . . . V 4 29.068 32.88 51.315 1 95.41 ? C3' AGS 4600 D 1 HETATM 18 O O3' AGS . . . V 4 27.794 33.399 51.666 1 95.43 ? O3' AGS 4600 D 1 HETATM 19 C C2' AGS . . . V 4 30.175 33.546 52.112 1 95.07 ? C2' AGS 4600 D 1 HETATM 20 O O2' AGS . . . V 4 29.643 34.497 53.022 1 95.07 ? O2' AGS 4600 D 1 HETATM 21 C C1' AGS . . . V 4 30.853 32.428 52.887 1 94.74 ? C1' AGS 4600 D 1 HETATM 22 N N9 AGS . . . V 4 32.308 32.315 52.594 1 93.96 ? N9 AGS 4600 D 1 HETATM 23 C C8 AGS . . . V 4 32.928 31.397 51.8 1 93.69 ? C8 AGS 4600 D 1 HETATM 24 N N7 AGS . . . V 4 34.293 31.567 51.761 1 93.52 ? N7 AGS 4600 D 1 HETATM 25 C C5 AGS . . . V 4 34.561 32.619 52.553 1 93.36 ? C5 AGS 4600 D 1 HETATM 26 C C6 AGS . . . V 4 35.733 33.402 53.017 1 93.18 ? C6 AGS 4600 D 1 HETATM 27 N N6 AGS . . . V 4 36.979 33.075 52.598 1 93.15 ? N6 AGS 4600 D 1 HETATM 28 N N1 AGS . . . V 4 35.544 34.448 53.867 1 93.16 ? N1 AGS 4600 D 1 HETATM 29 C C2 AGS . . . V 4 34.326 34.822 54.321 1 93.2 ? C2 AGS 4600 D 1 HETATM 30 N N3 AGS . . . V 4 33.192 34.19 53.97 1 93.29 ? N3 AGS 4600 D 1 HETATM 31 C C4 AGS . . . V 4 33.287 33.067 53.07 1 93.51 ? C4 AGS 4600 D 1 # _model_server_stats.io_time_ms 13 _model_server_stats.parse_time_ms 9 _model_server_stats.create_model_time_ms 23 _model_server_stats.query_time_ms 654 _model_server_stats.encode_time_ms 69 _model_server_stats.element_count 31 #