data_8CLD # _model_server_result.job_id HK2yRKe4O0NQ7z7aCWpDwg _model_server_result.datetime_utc '2025-07-09 18:49:20' _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 8cld # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"Q","auth_seq_id":401}' # _entry.id 8CLD # _exptl.entry_id 8CLD _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 505.208 _entity.id 10 _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 8CLD _cell.length_a 106.06 _cell.length_b 159.61 _cell.length_c 180.61 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 8CLD _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 PISA _pdbx_struct_assembly.oligomeric_details hexameric _pdbx_struct_assembly.oligomeric_count 6 _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,I,J,K,L,M,N,O,P,Q,R,S,T _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 10 _struct_asym.id Q _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 ? ? ? ? ? ? ? ? ? ? ? ? 2.496 ? metalc ? metalc2 A OD2 ASP 39 A ASP 39 1_555 I CA CA . A CA 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.426 ? metalc ? metalc3 A O THR 41 A THR 41 1_555 I CA CA . A CA 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 3.17 ? metalc ? metalc4 A OG1 THR 41 A THR 41 1_555 I CA CA . A CA 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.369 ? metalc ? metalc5 A O GLY 44 A GLY 44 1_555 I CA CA . A CA 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.599 ? metalc ? metalc6 A OE2 GLU 55 A GLU 55 1_555 I CA CA . A CA 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.557 ? metalc ? metalc7 G O1G GTP . A GTP 501 1_555 H MG MG . A MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.712 ? metalc ? metalc8 G O2G GTP . A GTP 501 1_555 H MG MG . A MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.855 ? metalc ? metalc9 G O1B GTP . A GTP 501 1_555 H MG MG . A MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.818 ? metalc ? metalc10 J O1A GDP . B GDP 501 1_555 K MG MG . B MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.503 ? metalc ? metalc11 C OD1 ASP 39 C ASP 39 1_555 N CA CA . C CA 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.223 ? metalc ? metalc12 C OD2 ASP 39 C ASP 39 1_555 N CA CA . C CA 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.297 ? metalc ? metalc13 C O THR 41 C THR 41 1_555 N CA CA . C CA 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.588 ? metalc ? metalc14 C OG1 THR 41 C THR 41 1_555 N CA CA . C CA 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.321 ? metalc ? metalc15 C O GLY 44 C GLY 44 1_555 N CA CA . C CA 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.99 ? metalc ? metalc16 C OE1 GLU 55 C GLU 55 1_555 N CA CA . C CA 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.704 ? metalc ? metalc17 C OE2 GLU 55 C GLU 55 1_555 N CA CA . C CA 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.282 ? metalc ? metalc18 C OE1 GLU 71 C GLU 71 1_555 M MG MG . C MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.868 ? metalc ? metalc19 L O1G GTP . C GTP 501 1_555 M MG MG . C MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.538 ? metalc ? metalc20 L O1B GTP . C GTP 501 1_555 M MG MG . C MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.943 ? # _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 8CLD _atom_sites.fract_transf_matrix[1][1] 0.009429 _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] 0.006265 _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] 0.005537 _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 1 501 504 GDP GDP . K 6 MG B 1 502 505 MG MG . L 5 GTP C 1 501 506 GTP GTP . M 6 MG C 1 502 507 MG MG . N 7 CA C 1 503 508 CA CA . O 8 GDP D 1 501 509 GDP GTP . P 9 BKF D 1 502 510 BKF ANS . Q 10 ACP F 1 401 511 ACP ACP . R 11 HOH A 1 601 5 HOH HOH . S 11 HOH C 1 601 3 HOH HOH . T 11 HOH E 1 201 6 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 . . . Q 10 8.259 50.928 94.307 1 119.27 ? PG ACP 401 F 1 HETATM 2 O O1G ACP . . . Q 10 7.411 52.106 94.672 1 90.11 ? O1G ACP 401 F 1 HETATM 3 O O2G ACP . . . Q 10 9.257 51.244 93.171 1 106.93 ? O2G ACP 401 F 1 HETATM 4 O O3G ACP . . . Q 10 7.413 49.713 93.861 1 101.2 ? O3G ACP 401 F 1 HETATM 5 P PB ACP . . . Q 10 10.935 51.045 95.646 1 120.13 ? PB ACP 401 F 1 HETATM 6 O O1B ACP . . . Q 10 11.011 52.233 94.718 1 108.3 ? O1B ACP 401 F 1 HETATM 7 O O2B ACP . . . Q 10 11.887 49.917 95.143 1 105.34 ? O2B ACP 401 F 1 HETATM 8 C C3B ACP . . . Q 10 9.235 50.376 95.711 1 113.92 ? C3B ACP 401 F 1 HETATM 9 P PA ACP . . . Q 10 10.415 52.639 97.685 1 107.07 ? PA ACP 401 F 1 HETATM 10 O O1A ACP . . . Q 10 9.615 53.271 96.616 1 103.27 ? O1A ACP 401 F 1 HETATM 11 O O2A ACP . . . Q 10 11.266 53.609 98.509 1 81.25 ? O2A ACP 401 F 1 HETATM 12 O O3A ACP . . . Q 10 11.401 51.504 97.125 1 113.19 ? O3A ACP 401 F 1 HETATM 13 O O5' ACP . . . Q 10 9.481 51.836 98.673 1 105.45 ? O5' ACP 401 F 1 HETATM 14 C C5' ACP . . . Q 10 10.028 51.085 99.779 1 104.46 ? C5' ACP 401 F 1 HETATM 15 C C4' ACP . . . Q 10 8.914 50.673 100.708 1 93.59 ? C4' ACP 401 F 1 HETATM 16 O O4' ACP . . . Q 10 9.409 50.862 102.049 1 96.9 ? O4' ACP 401 F 1 HETATM 17 C C3' ACP . . . Q 10 7.754 51.651 100.622 1 95.52 ? C3' ACP 401 F 1 HETATM 18 O O3' ACP . . . Q 10 6.796 51.037 99.767 1 91.67 ? O3' ACP 401 F 1 HETATM 19 C C2' ACP . . . Q 10 7.169 51.556 102.025 1 96.15 ? C2' ACP 401 F 1 HETATM 20 O O2' ACP . . . Q 10 6.643 50.239 102.126 1 100.22 ? O2' ACP 401 F 1 HETATM 21 C C1' ACP . . . Q 10 8.449 51.519 102.856 1 98.6 ? C1' ACP 401 F 1 HETATM 22 N N9 ACP . . . Q 10 8.967 52.861 103.109 1 89.12 ? N9 ACP 401 F 1 HETATM 23 C C8 ACP . . . Q 10 9.782 53.601 102.291 1 86.4 ? C8 ACP 401 F 1 HETATM 24 N N7 ACP . . . Q 10 10.102 54.776 102.776 1 87.94 ? N7 ACP 401 F 1 HETATM 25 C C5 ACP . . . Q 10 9.456 54.812 104.003 1 91.21 ? C5 ACP 401 F 1 HETATM 26 C C6 ACP . . . Q 10 9.393 55.789 105.016 1 94.19 ? C6 ACP 401 F 1 HETATM 27 N N6 ACP . . . Q 10 10.015 56.971 104.951 1 89.16 ? N6 ACP 401 F 1 HETATM 28 N N1 ACP . . . Q 10 8.659 55.507 106.115 1 95.01 ? N1 ACP 401 F 1 HETATM 29 C C2 ACP . . . Q 10 8.035 54.329 106.187 1 93.1 ? C2 ACP 401 F 1 HETATM 30 N N3 ACP . . . Q 10 8.021 53.333 105.298 1 90.95 ? N3 ACP 401 F 1 HETATM 31 C C4 ACP . . . Q 10 8.755 53.637 104.222 1 88.96 ? C4 ACP 401 F 1 # _model_server_stats.io_time_ms 40 _model_server_stats.parse_time_ms 22 _model_server_stats.create_model_time_ms 57 _model_server_stats.query_time_ms 314 _model_server_stats.encode_time_ms 5 _model_server_stats.element_count 31 #