data_4H1W # _model_server_result.job_id d5cSJ8jP-EERCJJNmYFfcA _model_server_result.datetime_utc '2025-03-31 07:21:41' _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 4h1w # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"G","auth_seq_id":1005}' # _entry.id 4H1W # _exptl.entry_id 4H1W _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 505.208 _entity.id 5 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description 'PHOSPHOMETHYLPHOSPHONIC ACID ADENYLATE ESTER' _entity.pdbx_number_of_molecules 1 _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 4H1W _cell.length_a 85.87 _cell.length_b 139.54 _cell.length_c 141.56 _cell.Z_PDB 4 _cell.pdbx_unique_axis ? # _symmetry.entry_id 4H1W _symmetry.cell_setting ? _symmetry.Int_Tables_number 18 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 21 2 21' # _pdbx_struct_assembly.method_details PISA _pdbx_struct_assembly.oligomeric_details dimeric _pdbx_struct_assembly.oligomeric_count 2 _pdbx_struct_assembly.details author_and_software_defined_assembly _pdbx_struct_assembly.id 1 # _pdbx_struct_assembly_gen.asym_id_list A,B,C,D,E,F,G,H _pdbx_struct_assembly_gen.assembly_id 1 _pdbx_struct_assembly_gen.oper_expression 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 # _struct_asym.details ? _struct_asym.entity_id 5 _struct_asym.id G _struct_asym.pdbx_modified N _struct_asym.pdbx_blank_PDB_chainid_flag 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 O VAL 304 A VAL 304 1_555 E MG MG . A MG 1003 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.322 ? metalc ? metalc2 A OE1 GLU 309 A GLU 309 1_555 E MG MG . A MG 1003 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.113 ? metalc ? metalc3 A O LEU 711 A LEU 711 1_555 C K K . A K 1001 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.6 ? metalc ? metalc4 A O LYS 712 A LYS 712 1_555 C K K . A K 1001 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.614 ? metalc ? metalc5 A O ALA 714 A ALA 714 1_555 C K K . A K 1001 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.743 ? metalc ? metalc6 A OE1 GLU 732 A GLU 732 1_555 C K K . A K 1001 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.7 ? metalc ? metalc7 A OD1 ASN 796 A ASN 796 1_555 F MG MG . A MG 1004 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.29 ? metalc ? metalc8 A OD1 ASP 800 A ASP 800 1_555 F MG MG . A MG 1004 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.157 ? metalc ? metalc9 A OD2 ASP 800 A ASP 800 1_555 F MG MG . A MG 1004 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.301 ? metalc ? metalc10 C K K . A K 1001 1_555 H O HOH . A HOH 1101 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.996 ? metalc ? metalc11 C K K . A K 1001 1_555 H O HOH . A HOH 1108 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.708 ? metalc ? metalc12 D MG MG . A MG 1002 1_555 G O3G ACP . A ACP 1005 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.156 ? metalc ? metalc13 D MG MG . A MG 1002 1_555 H O HOH . A HOH 1102 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.081 ? metalc ? metalc14 D MG MG . A MG 1002 1_555 H O HOH . A HOH 1103 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.07 ? metalc ? metalc15 D MG MG . A MG 1002 1_555 H O HOH . A HOH 1104 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.083 ? metalc ? metalc16 E MG MG . A MG 1003 1_555 H O HOH . A HOH 1105 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.088 ? metalc ? metalc17 F MG MG . A MG 1004 1_555 H O HOH . A HOH 1106 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.046 ? metalc ? metalc18 F MG MG . A MG 1004 1_555 H O HOH . A HOH 1107 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.094 ? # _chem_comp.formula 'C11 H18 N5 O12 P3' _chem_comp.formula_weight 505.208 _chem_comp.id ACP _chem_comp.mon_nstd_flag . _chem_comp.name 'PHOSPHOMETHYLPHOSPHONIC ACID ADENYLATE ESTER' _chem_comp.type non-polymer _chem_comp.pdbx_synonyms "ADENOSINE-5'-[BETA, GAMMA-METHYLENE]TRIPHOSPHATE" # 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 O1G ACP doub 1 n n PG O2G ACP sing 2 n n PG O3G ACP sing 3 n n PG C3B ACP sing 4 n n O2G HOG2 ACP sing 5 n n O3G HOG3 ACP sing 6 n n PB O1B ACP doub 7 n n PB O2B ACP sing 8 n n PB C3B ACP sing 9 n n PB O3A ACP sing 10 n n O2B HOB2 ACP sing 11 n n C3B H3B1 ACP sing 12 n n C3B H3B2 ACP sing 13 n n PA O1A ACP doub 14 n n PA O2A ACP sing 15 n n PA O3A ACP sing 16 n n PA O5' ACP sing 17 n n O2A HOA2 ACP sing 18 n n O5' C5' ACP sing 19 n n C5' C4' ACP sing 20 n n C5' "H5'1" ACP sing 21 n n C5' "H5'2" ACP sing 22 n n C4' O4' ACP sing 23 n n C4' C3' ACP sing 24 n n C4' H4' ACP sing 25 n n O4' C1' ACP sing 26 n n C3' O3' ACP sing 27 n n C3' C2' ACP sing 28 n n C3' H3' ACP sing 29 n n O3' HO3' ACP sing 30 n n C2' O2' ACP sing 31 n n C2' C1' ACP sing 32 n n C2' H2' ACP sing 33 n n O2' HO2' ACP sing 34 n n C1' N9 ACP sing 35 n n C1' H1' ACP sing 36 n n N9 C8 ACP sing 37 n y N9 C4 ACP sing 38 n y C8 N7 ACP doub 39 n y C8 H8 ACP sing 40 n n N7 C5 ACP sing 41 n y C5 C6 ACP sing 42 n y C5 C4 ACP doub 43 n y C6 N6 ACP sing 44 n n C6 N1 ACP doub 45 n y N6 HN61 ACP sing 46 n n N6 HN62 ACP sing 47 n n N1 C2 ACP sing 48 n y C2 N3 ACP doub 49 n y C2 H2 ACP sing 50 n n N3 C4 ACP sing 51 n y # _atom_sites.entry_id 4H1W _atom_sites.fract_transf_matrix[1][1] 0.011646 _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] 0.007166 _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] 0.007064 _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 C 3 K A 1 1001 995 K K . D 4 MG A 1 1002 996 MG MG . E 4 MG A 1 1003 997 MG MG . F 4 MG A 1 1004 1000 MG MG . G 5 ACP A 1 1005 1001 ACP ACP . H 6 HOH A 1 1101 1 HOH HOH . H 6 HOH A 2 1102 2 HOH HOH . H 6 HOH A 3 1103 3 HOH HOH . H 6 HOH A 4 1104 4 HOH HOH . H 6 HOH A 5 1105 5 HOH HOH . H 6 HOH A 6 1106 6 HOH HOH . H 6 HOH A 7 1107 7 HOH HOH . H 6 HOH A 8 1108 8 HOH HOH . # 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 ACP . . . G 5 27.557 55.302 185.927 1 222.54 ? PG ACP 1005 A 1 HETATM 2 O O1G ACP . . . G 5 27.571 54.026 186.862 1 80.8 ? O1G ACP 1005 A 1 HETATM 3 O O2G ACP . . . G 5 28.884 55.08 185.101 1 113.18 ? O2G ACP 1005 A 1 HETATM 4 O O3G ACP . . . G 5 26.526 55.312 184.863 1 221.69 ? O3G ACP 1005 A 1 HETATM 5 P PB ACP . . . G 5 26.73 58.1 186.599 1 122.73 ? PB ACP 1005 A 1 HETATM 6 O O1B ACP . . . G 5 25.212 57.911 186.978 1 189.26 ? O1B ACP 1005 A 1 HETATM 7 O O2B ACP . . . G 5 26.879 58.815 185.312 1 116.72 ? O2B ACP 1005 A 1 HETATM 8 C C3B ACP . . . G 5 27.625 56.697 186.797 1 41.72 ? C3B ACP 1005 A 1 HETATM 9 O O3A ACP . . . G 5 27.267 58.969 187.807 0.25 170.68 ? O3A ACP 1005 A 1 # _model_server_stats.io_time_ms 21 _model_server_stats.parse_time_ms 9 _model_server_stats.create_model_time_ms 7 _model_server_stats.query_time_ms 306 _model_server_stats.encode_time_ms 1 _model_server_stats.element_count 9 #