data_8HUH # _model_server_result.job_id x8ezXnQymrWB-bZM4t92jA _model_server_result.datetime_utc '2024-11-21 18:34:12' _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 8huh # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"S","auth_seq_id":401}' # _entry.id 8HUH # _exptl.entry_id 8HUH _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 505.208 _entity.id 11 _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 8HUH _cell.length_a 105.193 _cell.length_b 157.879 _cell.length_c 182.141 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 8HUH _symmetry.cell_setting ? _symmetry.Int_Tables_number 19 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 21 21 21' # _pdbx_struct_assembly.method_details ? _pdbx_struct_assembly.oligomeric_details hexameric _pdbx_struct_assembly.oligomeric_count 6 _pdbx_struct_assembly.details author_defined_assembly _pdbx_struct_assembly.id 1 # _pdbx_struct_assembly_gen.asym_id_list A,B,C,D,E,F,G,H,I,J,K,L,M,N,O,P,Q,R,S _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 11 _struct_asym.id S _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 OD1 ASP 39 A ASP 39 1_555 I CA CA . A CA 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.495 ? metalc ? metalc2 A OD2 ASP 39 A ASP 39 1_555 I CA CA . A CA 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.461 ? metalc ? metalc3 A O THR 41 A THR 41 1_555 I CA CA . A CA 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.459 ? metalc ? metalc4 A O GLY 44 A GLY 44 1_555 I CA CA . A CA 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.383 ? metalc ? metalc5 A OE1 GLU 55 A GLU 55 1_555 I CA CA . A CA 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.273 ? metalc ? metalc6 A OE2 GLU 55 A GLU 55 1_555 I CA CA . A CA 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.613 ? metalc ? metalc7 G O2G GTP . A GTP 501 1_555 H MG MG . A MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.105 ? metalc ? metalc8 G O2B GTP . A GTP 501 1_555 H MG MG . A MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.553 ? metalc ? metalc9 B OE1 GLN 11 B GLN 11 1_555 K MG MG . B MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.416 ? metalc ? metalc10 J O2A GDP . B GDP 501 1_555 K MG MG . B MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.471 ? metalc ? metalc11 C OD1 ASP 39 C ASP 39 1_555 Q CA CA . C CA 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.592 ? metalc ? metalc12 C OD2 ASP 39 C ASP 39 1_555 Q CA CA . C CA 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.579 ? metalc ? metalc13 C O THR 41 C THR 41 1_555 Q CA CA . C CA 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.856 ? metalc ? metalc14 C OG1 THR 41 C THR 41 1_555 Q CA CA . C CA 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.411 ? metalc ? metalc15 C O GLY 44 C GLY 44 1_555 Q CA CA . C CA 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.512 ? metalc ? metalc16 C OE1 GLU 55 C GLU 55 1_555 Q CA CA . C CA 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 3.04 ? metalc ? metalc17 C OE2 GLU 55 C GLU 55 1_555 Q CA CA . C CA 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.385 ? metalc ? metalc18 O O3G GTP . C GTP 501 1_555 P MG MG . C MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.378 ? metalc ? metalc19 O O2B GTP . C GTP 501 1_555 P MG MG . C MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.166 ? # _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 8HUH _atom_sites.fract_transf_matrix[1][1] 0.009506 _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] 0.006334 _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] 0.00549 _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 G 5 GTP A 1 501 501 GTP GTP . H 6 MG A 1 502 502 MG MG . I 7 CA A 1 503 503 CA CA . J 8 GDP B 1 501 501 GDP GDP . K 6 MG B 1 502 502 MG MG . L 9 MES B 1 503 503 MES MES . M 9 MES B 1 504 504 MES MES . N 10 MXV B 1 505 1 MXV AB1 . O 5 GTP C 1 501 501 GTP GTP . P 6 MG C 1 502 502 MG MG . Q 7 CA C 1 503 503 CA CA . R 8 GDP D 1 501 501 GDP GDP . S 11 ACP F 1 401 401 ACP ACP . # 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 . . . S 11 10.199 -49.003 -93.975 1 164.04 ? PG ACP 401 F 1 HETATM 2 O O1G ACP . . . S 11 9.566 -49.881 -92.936 1 144.46 ? O1G ACP 401 F 1 HETATM 3 O O2G ACP . . . S 11 11.448 -49.637 -94.632 1 144.03 ? O2G ACP 401 F 1 HETATM 4 O O3G ACP . . . S 11 10.608 -47.619 -93.42 1 156.53 ? O3G ACP 401 F 1 HETATM 5 P PB ACP . . . S 11 8.909 -50.038 -96.445 1 151.46 ? PB ACP 401 F 1 HETATM 6 O O1B ACP . . . S 11 7.948 -49.616 -97.527 1 154 ? O1B ACP 401 F 1 HETATM 7 O O2B ACP . . . S 11 8.107 -51.203 -95.808 1 145.01 ? O2B ACP 401 F 1 HETATM 8 C C3B ACP . . . S 11 9.046 -48.628 -95.296 1 152.17 ? C3B ACP 401 F 1 HETATM 9 P PA ACP . . . S 11 10.433 -51.171 -98.518 1 130.35 ? PA ACP 401 F 1 HETATM 10 O O1A ACP . . . S 11 9.276 -52.06 -98.787 1 126.71 ? O1A ACP 401 F 1 HETATM 11 O O2A ACP . . . S 11 11.754 -51.951 -98.604 1 125.23 ? O2A ACP 401 F 1 HETATM 12 O O3A ACP . . . S 11 10.376 -50.477 -97.026 1 137.03 ? O3A ACP 401 F 1 HETATM 13 O O5' ACP . . . S 11 10.611 -50.014 -99.584 1 131.45 ? O5' ACP 401 F 1 HETATM 14 C C5' ACP . . . S 11 9.796 -48.824 -99.569 1 131.65 ? C5' ACP 401 F 1 HETATM 15 C C4' ACP . . . S 11 8.939 -48.801 -100.809 1 125.03 ? C4' ACP 401 F 1 HETATM 16 O O4' ACP . . . S 11 9.527 -49.621 -101.83 1 110.16 ? O4' ACP 401 F 1 HETATM 17 C C3' ACP . . . S 11 7.542 -49.378 -100.624 1 119.7 ? C3' ACP 401 F 1 HETATM 18 O O3' ACP . . . S 11 6.623 -48.36 -100.253 1 117.03 ? O3' ACP 401 F 1 HETATM 19 C C2' ACP . . . S 11 7.187 -49.939 -102.01 1 102.06 ? C2' ACP 401 F 1 HETATM 20 O O2' ACP . . . S 11 6.235 -49.1 -102.652 1 102.77 ? O2' ACP 401 F 1 HETATM 21 C C1' ACP . . . S 11 8.523 -49.945 -102.761 1 93.13 ? C1' ACP 401 F 1 HETATM 22 N N9 ACP . . . S 11 8.881 -51.223 -103.351 1 96.82 ? N9 ACP 401 F 1 HETATM 23 C C8 ACP . . . S 11 9.747 -52.154 -102.839 1 103.16 ? C8 ACP 401 F 1 HETATM 24 N N7 ACP . . . S 11 9.896 -53.219 -103.589 1 100.29 ? N7 ACP 401 F 1 HETATM 25 C C5 ACP . . . S 11 9.062 -52.977 -104.666 1 95.99 ? C5 ACP 401 F 1 HETATM 26 C C6 ACP . . . S 11 8.762 -53.727 -105.817 1 94.32 ? C6 ACP 401 F 1 HETATM 27 N N6 ACP . . . S 11 9.296 -54.927 -106.083 1 95.17 ? N6 ACP 401 F 1 HETATM 28 N N1 ACP . . . S 11 7.883 -53.199 -106.692 1 99.46 ? N1 ACP 401 F 1 HETATM 29 C C2 ACP . . . S 11 7.345 -52.005 -106.428 1 98.6 ? C2 ACP 401 F 1 HETATM 30 N N3 ACP . . . S 11 7.551 -51.207 -105.38 1 99.53 ? N3 ACP 401 F 1 HETATM 31 C C4 ACP . . . S 11 8.424 -51.753 -104.532 1 98.86 ? C4 ACP 401 F 1 # _model_server_stats.io_time_ms 15 _model_server_stats.parse_time_ms 11 _model_server_stats.create_model_time_ms 36 _model_server_stats.query_time_ms 260 _model_server_stats.encode_time_ms 3 _model_server_stats.element_count 31 #