data_8YRK # _model_server_result.job_id aNHqF1erG05fdIr0eO61QQ _model_server_result.datetime_utc '2025-04-27 10:07:40' _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 8yrk # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"X","auth_seq_id":401}' # _entry.id 8YRK # _exptl.entry_id 8YRK _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 505.208 _entity.id 14 _entity.src_method nat _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 8YRK _cell.length_a 104.097 _cell.length_b 158.982 _cell.length_c 179.057 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 8YRK _symmetry.cell_setting ? _symmetry.Int_Tables_number 19 _symmetry.space_group_name_Hall 'P 2ac 2ab' _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,T,U,V,W,X,Y,Z,AA,BA,CA _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 14 _struct_asym.id X _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 ? ? ? ? ? ? ? ? ? ? ? ? 2.672 ? metalc ? metalc2 A OD2 ASP 39 A ASP 39 1_555 I CA CA . A CA 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.273 ? metalc ? metalc3 A O THR 41 A THR 41 1_555 I CA CA . A CA 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.423 ? metalc ? metalc4 A O GLY 44 A GLY 44 1_555 I CA CA . A CA 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.367 ? metalc ? metalc5 A OE1 GLU 55 A GLU 55 1_555 I CA CA . A CA 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.657 ? metalc ? metalc6 A OE2 GLU 55 A GLU 55 1_555 I CA CA . A CA 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.391 ? metalc ? metalc7 G O1G GTP . A GTP 501 1_555 H MG MG . A MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.958 ? metalc ? metalc8 G O1B GTP . A GTP 501 1_555 H MG MG . A MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.138 ? metalc ? metalc9 H MG MG . A MG 502 1_555 Y O HOH . A HOH 601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.024 ? metalc ? metalc10 H MG MG . A MG 502 1_555 Y O HOH . A HOH 602 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.138 ? metalc ? metalc11 H MG MG . A MG 502 1_555 Y O HOH . A HOH 603 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.979 ? metalc ? metalc12 H MG MG . A MG 502 1_555 Y O HOH . A HOH 605 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.058 ? metalc ? metalc13 I CA CA . A CA 503 1_555 Y O HOH . A HOH 604 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.34 ? metalc ? metalc14 B OE1 GLN 11 B GLN 11 1_555 L MG MG . B MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.014 ? metalc ? metalc15 K O1A GDP . B GDP 501 1_555 L MG MG . B MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.08 ? metalc ? metalc16 L MG MG . B MG 502 1_555 Z O HOH . B HOH 602 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.869 ? metalc ? metalc17 L MG MG . B MG 502 1_555 Z O HOH . B HOH 604 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.464 ? metalc ? metalc18 L MG MG . B MG 502 1_555 Z O HOH . B HOH 605 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.055 ? metalc ? metalc19 L MG MG . B MG 502 1_555 Z O HOH . B HOH 606 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.537 ? metalc ? metalc20 C OD1 ASP 39 C ASP 39 1_555 R CA CA . C CA 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.853 ? metalc ? metalc21 C OD2 ASP 39 C ASP 39 1_555 R CA CA . C CA 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.299 ? metalc ? metalc22 C O THR 41 C THR 41 1_555 R CA CA . C CA 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.367 ? metalc ? metalc23 C OG1 THR 41 C THR 41 1_555 R CA CA . C CA 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.172 ? metalc ? metalc24 C O GLY 44 C GLY 44 1_555 R CA CA . C CA 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.894 ? metalc ? metalc25 C OE1 GLU 55 C GLU 55 1_555 R CA CA . C CA 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.306 ? metalc ? metalc26 C OE2 GLU 55 C GLU 55 1_555 R CA CA . C CA 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.433 ? metalc ? metalc27 Q O1G GTP . C GTP 501 1_555 T MG MG . D MG 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.728 ? metalc ? metalc28 Q O3G GTP . C GTP 501 1_555 T MG MG . D MG 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.328 ? metalc ? metalc29 Q O1B GTP . C GTP 501 1_555 T MG MG . D MG 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.419 ? metalc ? metalc30 R CA CA . C CA 502 1_555 AA O HOH . C HOH 605 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.569 ? metalc ? metalc31 AA O HOH . C HOH 602 1_555 T MG MG . D MG 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.218 ? metalc ? metalc32 AA O HOH . C HOH 603 1_555 T MG MG . D MG 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.065 ? metalc ? metalc33 AA O HOH . C HOH 604 1_555 T MG MG . D MG 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.4 ? metalc ? metalc34 AA O HOH . C HOH 607 1_555 T MG MG . D MG 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.09 ? metalc ? metalc35 U O1B GDP . D GDP 502 1_555 V MG MG . D MG 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.604 ? metalc ? metalc36 V MG MG . D MG 503 1_555 BA O HOH . D HOH 601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.665 ? metalc ? metalc37 V MG MG . D MG 503 1_555 BA O HOH . D HOH 603 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.3 ? metalc ? metalc38 V MG MG . D MG 503 1_555 BA O HOH . D HOH 604 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.383 ? # _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 50 n n PG O2G ACP sing 51 n n PG O3G ACP sing 52 n n PG C3B ACP sing 53 n n O2G HOG2 ACP sing 54 n n O3G HOG3 ACP sing 55 n n PB O1B ACP doub 56 n n PB O2B ACP sing 57 n n PB C3B ACP sing 58 n n PB O3A ACP sing 59 n n O2B HOB2 ACP sing 60 n n C3B H3B1 ACP sing 61 n n C3B H3B2 ACP sing 62 n n PA O1A ACP doub 63 n n PA O2A ACP sing 64 n n PA O3A ACP sing 65 n n PA O5' ACP sing 66 n n O2A HOA2 ACP sing 67 n n O5' C5' ACP sing 68 n n C5' C4' ACP sing 69 n n C5' "H5'1" ACP sing 70 n n C5' "H5'2" ACP sing 71 n n C4' O4' ACP sing 72 n n C4' C3' ACP sing 73 n n C4' H4' ACP sing 74 n n O4' C1' ACP sing 75 n n C3' O3' ACP sing 76 n n C3' C2' ACP sing 77 n n C3' H3' ACP sing 78 n n O3' HO3' ACP sing 79 n n C2' O2' ACP sing 80 n n C2' C1' ACP sing 81 n n C2' H2' ACP sing 82 n n O2' HO2' ACP sing 83 n n C1' N9 ACP sing 84 n n C1' H1' ACP sing 85 n n N9 C8 ACP sing 86 n y N9 C4 ACP sing 87 n y C8 N7 ACP doub 88 n y C8 H8 ACP sing 89 n n N7 C5 ACP sing 90 n y C5 C6 ACP sing 91 n y C5 C4 ACP doub 92 n y C6 N6 ACP sing 93 n n C6 N1 ACP doub 94 n y N6 HN61 ACP sing 95 n n N6 HN62 ACP sing 96 n n N1 C2 ACP sing 97 n y C2 N3 ACP doub 98 n y C2 H2 ACP sing 99 n n N3 C4 ACP sing 100 n y # _atom_sites.entry_id 8YRK _atom_sites.fract_transf_matrix[1][1] 0.009606 _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] 0.00629 _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] 0.005585 _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 CL A 1 504 504 CL CL . K 9 GDP B 1 501 501 GDP GDP . L 6 MG B 1 502 502 MG MG . M 10 MES B 1 503 503 MES MES . N 10 MES B 1 504 504 MES MES . O 11 GOL B 1 505 505 GOL GOL . P 12 A1D62 B 1 506 506 A1D62 LIG . Q 5 GTP C 1 501 501 GTP GTP . R 7 CA C 1 502 503 CA CA . S 13 EDO C 1 503 504 EDO EDO . T 6 MG D 1 501 502 MG MG . U 9 GDP D 1 502 501 GDP GDP . V 6 MG D 1 503 502 MG MG . W 12 A1D62 D 1 504 503 A1D62 LIG . X 14 ACP F 1 401 401 ACP ACP . Y 15 HOH A 1 601 2 HOH HOH . Y 15 HOH A 2 602 3 HOH HOH . Y 15 HOH A 3 603 4 HOH HOH . Y 15 HOH A 4 604 5 HOH HOH . Y 15 HOH A 5 605 1 HOH HOH . Z 15 HOH B 1 601 19 HOH HOH . Z 15 HOH B 2 602 8 HOH HOH . Z 15 HOH B 3 603 10 HOH HOH . Z 15 HOH B 4 604 6 HOH HOH . Z 15 HOH B 5 605 9 HOH HOH . Z 15 HOH B 6 606 7 HOH HOH . Z 15 HOH B 7 607 28 HOH HOH . Z 15 HOH B 8 608 29 HOH HOH . Z 15 HOH B 9 609 30 HOH HOH . AA 15 HOH C 1 601 26 HOH HOH . AA 15 HOH C 2 602 13 HOH HOH . AA 15 HOH C 3 603 12 HOH HOH . AA 15 HOH C 4 604 14 HOH HOH . AA 15 HOH C 5 605 15 HOH HOH . AA 15 HOH C 6 606 23 HOH HOH . AA 15 HOH C 7 607 11 HOH HOH . AA 15 HOH C 8 608 32 HOH HOH . AA 15 HOH C 9 609 27 HOH HOH . AA 15 HOH C 10 610 20 HOH HOH . AA 15 HOH C 11 611 21 HOH HOH . AA 15 HOH C 12 612 31 HOH HOH . BA 15 HOH D 1 601 16 HOH HOH . BA 15 HOH D 2 602 24 HOH HOH . BA 15 HOH D 3 603 17 HOH HOH . BA 15 HOH D 4 604 18 HOH HOH . BA 15 HOH D 5 605 33 HOH HOH . BA 15 HOH D 6 606 34 HOH HOH . CA 15 HOH E 1 201 22 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 . . . X 14 9.19 52.066 94.019 1 148 ? PG ACP 401 F 1 HETATM 2 O O1G ACP . . . X 14 10.474 52.812 94.2 1 129.31 ? O1G ACP 401 F 1 HETATM 3 O O2G ACP . . . X 14 7.986 53.016 93.828 1 131.69 ? O2G ACP 401 F 1 HETATM 4 O O3G ACP . . . X 14 9.227 51.104 92.81 1 115.97 ? O3G ACP 401 F 1 HETATM 5 P PB ACP . . . X 14 10.326 50.471 96.288 1 129.68 ? PB ACP 401 F 1 HETATM 6 O O1B ACP . . . X 14 11.398 50.319 95.237 1 126.43 ? O1B ACP 401 F 1 HETATM 7 O O2B ACP . . . X 14 10.046 49.082 96.932 1 120.35 ? O2B ACP 401 F 1 HETATM 8 C C3B ACP . . . X 14 8.806 51.068 95.462 1 128.31 ? C3B ACP 401 F 1 HETATM 9 P PA ACP . . . X 14 9.94 51.777 98.666 1 119.97 ? PA ACP 401 F 1 HETATM 10 O O1A ACP . . . X 14 10.582 52.715 99.601 1 97.71 ? O1A ACP 401 F 1 HETATM 11 O O2A ACP . . . X 14 8.588 52.288 98.165 1 112.17 ? O2A ACP 401 F 1 HETATM 12 O O3A ACP . . . X 14 10.896 51.518 97.39 1 122 ? O3A ACP 401 F 1 HETATM 13 O O5' ACP . . . X 14 9.757 50.362 99.343 1 123.66 ? O5' ACP 401 F 1 HETATM 14 C C5' ACP . . . X 14 8.45 49.766 99.498 1 116.93 ? C5' ACP 401 F 1 HETATM 15 C C4' ACP . . . X 14 8.097 49.633 100.96 1 101.17 ? C4' ACP 401 F 1 HETATM 16 O O4' ACP . . . X 14 8.996 50.425 101.758 1 91.15 ? O4' ACP 401 F 1 HETATM 17 C C3' ACP . . . X 14 6.713 50.153 101.325 1 100.23 ? C3' ACP 401 F 1 HETATM 18 O O3' ACP . . . X 14 5.729 49.145 101.125 1 105.72 ? O3' ACP 401 F 1 HETATM 19 C C2' ACP . . . X 14 6.856 50.52 102.809 1 90.86 ? C2' ACP 401 F 1 HETATM 20 O O2' ACP . . . X 14 6.359 49.491 103.656 1 101.73 ? O2' ACP 401 F 1 HETATM 21 C C1' ACP . . . X 14 8.371 50.697 102.997 1 87.93 ? C1' ACP 401 F 1 HETATM 22 N N9 ACP . . . X 14 8.764 52.033 103.438 1 93.59 ? N9 ACP 401 F 1 HETATM 23 C C8 ACP . . . X 14 9.579 52.92 102.783 1 96.62 ? C8 ACP 401 F 1 HETATM 24 N N7 ACP . . . X 14 9.764 54.05 103.422 1 98.88 ? N7 ACP 401 F 1 HETATM 25 C C5 ACP . . . X 14 9.02 53.895 104.584 1 98.7 ? C5 ACP 401 F 1 HETATM 26 C C6 ACP . . . X 14 8.797 54.739 105.69 1 95.91 ? C6 ACP 401 F 1 HETATM 27 N N6 ACP . . . X 14 9.326 55.961 105.814 1 95.18 ? N6 ACP 401 F 1 HETATM 28 N N1 ACP . . . X 14 8.001 54.279 106.681 1 95.92 ? N1 ACP 401 F 1 HETATM 29 C C2 ACP . . . X 14 7.469 53.059 106.565 1 95.17 ? C2 ACP 401 F 1 HETATM 30 N N3 ACP . . . X 14 7.607 52.177 105.573 1 91.66 ? N3 ACP 401 F 1 HETATM 31 C C4 ACP . . . X 14 8.398 52.657 104.607 1 96.29 ? C4 ACP 401 F 1 # _model_server_stats.io_time_ms 280 _model_server_stats.parse_time_ms 23 _model_server_stats.create_model_time_ms 20 _model_server_stats.query_time_ms 328 _model_server_stats.encode_time_ms 6 _model_server_stats.element_count 31 #