data_8WD0 # _model_server_result.job_id 4iOhZTmULlAwsbyYct0FTw _model_server_result.datetime_utc '2024-10-11 02:18:50' _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 8wd0 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"U","auth_seq_id":401}' # _entry.id 8WD0 # _exptl.entry_id 8WD0 _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 505.208 _entity.id 12 _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 8WD0 _cell.length_a 156.56 _cell.length_b 181.54 _cell.length_c 104.74 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 8WD0 _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 _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 12 _struct_asym.id U _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 ? ? ? ? ? ? ? ? ? ? ? ? 2.615 ? metalc ? metalc2 A OD2 ASP 39 A ASP 39 1_555 I CA CA . A CA 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.266 ? metalc ? metalc3 A O THR 41 A THR 41 1_555 I CA CA . A CA 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.465 ? metalc ? metalc4 A OG1 THR 41 A THR 41 1_555 I CA CA . A CA 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.412 ? metalc ? metalc5 A O GLY 44 A GLY 44 1_555 I CA CA . A CA 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.296 ? metalc ? metalc6 A OE1 GLU 55 A GLU 55 1_555 I CA CA . A CA 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.595 ? metalc ? metalc7 A OE2 GLU 55 A GLU 55 1_555 I CA CA . A CA 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.596 ? metalc ? metalc8 G O1G GTP . A GTP 501 1_555 H MG MG . A MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.018 ? metalc ? metalc9 G O1B GTP . A GTP 501 1_555 H MG MG . A MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.211 ? metalc ? metalc10 K MG MG . B MG 501 1_555 N O1A GDP . B GDP 504 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.002 ? metalc ? metalc11 C OD1 ASP 39 C ASP 39 1_555 Q CA CA . C CA 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.497 ? metalc ? metalc12 C OD2 ASP 39 C ASP 39 1_555 Q CA CA . C CA 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.274 ? metalc ? metalc13 C O THR 41 C THR 41 1_555 Q CA CA . C CA 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.444 ? metalc ? metalc14 C OG1 THR 41 C THR 41 1_555 Q CA CA . C CA 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.363 ? metalc ? metalc15 C O GLY 44 C GLY 44 1_555 Q CA CA . C CA 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.277 ? metalc ? metalc16 C OE1 GLU 55 C GLU 55 1_555 Q CA CA . C CA 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.387 ? metalc ? metalc17 C OE2 GLU 55 C GLU 55 1_555 Q CA CA . C CA 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.428 ? metalc ? metalc18 O O1G GTP . C GTP 501 1_555 P MG MG . C MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.202 ? metalc ? metalc19 O O1B GTP . C GTP 501 1_555 P MG MG . C MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.231 ? metalc ? metalc20 R O1G GTP . D GTP 501 1_555 S MG MG . D MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.939 ? metalc ? metalc21 R O2G GTP . D GTP 501 1_555 S MG MG . D MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.104 ? metalc ? metalc22 R O1B GTP . D GTP 501 1_555 S MG MG . D MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.34 ? # _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 8WD0 _atom_sites.fract_transf_matrix[1][1] 0.006387 _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] 0.005508 _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] 0.009547 _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 GOL A 1 504 504 GOL GOL . K 6 MG B 1 501 502 MG MG . L 9 MES B 1 502 503 MES MES . M 10 W4F B 1 503 601 W4F LIG . N 11 GDP B 1 504 501 GDP GDP . 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 5 GTP D 1 501 501 GTP GTP . S 6 MG D 1 502 502 MG MG . T 10 W4F D 1 503 601 W4F LIG . U 12 ACP F 1 401 401 ACP ACP . V 13 HOH A 1 601 7 HOH HOH . V 13 HOH A 2 602 9 HOH HOH . V 13 HOH A 3 603 54 HOH HOH . V 13 HOH A 4 604 57 HOH HOH . V 13 HOH A 5 605 72 HOH HOH . V 13 HOH A 6 606 49 HOH HOH . V 13 HOH A 7 607 74 HOH HOH . V 13 HOH A 8 608 59 HOH HOH . V 13 HOH A 9 609 37 HOH HOH . V 13 HOH A 10 610 69 HOH HOH . V 13 HOH A 11 611 56 HOH HOH . W 13 HOH B 1 601 33 HOH HOH . W 13 HOH B 2 602 48 HOH HOH . W 13 HOH B 3 603 36 HOH HOH . W 13 HOH B 4 604 19 HOH HOH . W 13 HOH B 5 605 75 HOH HOH . W 13 HOH B 6 606 44 HOH HOH . W 13 HOH B 7 607 38 HOH HOH . W 13 HOH B 8 608 14 HOH HOH . W 13 HOH B 9 609 2 HOH HOH . W 13 HOH B 10 610 40 HOH HOH . W 13 HOH B 11 611 18 HOH HOH . W 13 HOH B 12 612 13 HOH HOH . W 13 HOH B 13 613 52 HOH HOH . W 13 HOH B 14 614 45 HOH HOH . W 13 HOH B 15 615 4 HOH HOH . X 13 HOH C 1 601 24 HOH HOH . X 13 HOH C 2 602 10 HOH HOH . X 13 HOH C 3 603 31 HOH HOH . X 13 HOH C 4 604 34 HOH HOH . X 13 HOH C 5 605 32 HOH HOH . X 13 HOH C 6 606 16 HOH HOH . X 13 HOH C 7 607 67 HOH HOH . X 13 HOH C 8 608 35 HOH HOH . X 13 HOH C 9 609 41 HOH HOH . X 13 HOH C 10 610 11 HOH HOH . X 13 HOH C 11 611 76 HOH HOH . X 13 HOH C 12 612 53 HOH HOH . X 13 HOH C 13 613 26 HOH HOH . X 13 HOH C 14 614 30 HOH HOH . X 13 HOH C 15 615 22 HOH HOH . X 13 HOH C 16 616 1 HOH HOH . X 13 HOH C 17 617 66 HOH HOH . X 13 HOH C 18 618 15 HOH HOH . X 13 HOH C 19 619 25 HOH HOH . X 13 HOH C 20 620 70 HOH HOH . X 13 HOH C 21 621 50 HOH HOH . X 13 HOH C 22 622 47 HOH HOH . X 13 HOH C 23 623 43 HOH HOH . X 13 HOH C 24 624 60 HOH HOH . X 13 HOH C 25 625 62 HOH HOH . X 13 HOH C 26 626 51 HOH HOH . X 13 HOH C 27 627 58 HOH HOH . X 13 HOH C 28 628 68 HOH HOH . Y 13 HOH D 1 601 6 HOH HOH . Y 13 HOH D 2 602 29 HOH HOH . Y 13 HOH D 3 603 46 HOH HOH . Y 13 HOH D 4 604 63 HOH HOH . Z 13 HOH E 1 201 71 HOH HOH . Z 13 HOH E 2 202 65 HOH HOH . Z 13 HOH E 3 203 27 HOH HOH . Z 13 HOH E 4 204 55 HOH HOH . AA 13 HOH F 1 501 8 HOH HOH . AA 13 HOH F 2 502 39 HOH HOH . AA 13 HOH F 3 503 12 HOH HOH . AA 13 HOH F 4 504 42 HOH HOH . AA 13 HOH F 5 505 20 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 . . . U 12 48.536 93.634 8.025 0 92.49 ? PG ACP 401 F 1 HETATM 2 O O1G ACP . . . U 12 49.124 92.851 9.134 0 92.6 ? O1G ACP 401 F 1 HETATM 3 O O2G ACP . . . U 12 47.085 93.031 7.677 0 92.54 ? O2G ACP 401 F 1 HETATM 4 O O3G ACP . . . U 12 49.475 93.549 6.72 0 89.06 ? O3G ACP 401 F 1 HETATM 5 P PB ACP . . . U 12 48.621 95.574 10.304 0 95.61 ? PB ACP 401 F 1 HETATM 6 O O1B ACP . . . U 12 49.886 94.938 10.731 0 93.42 ? O1B ACP 401 F 1 HETATM 7 O O2B ACP . . . U 12 47.39 94.915 11.106 0 96.7 ? O2B ACP 401 F 1 HETATM 8 C C3B ACP . . . U 12 48.332 95.363 8.526 0 95.07 ? C3B ACP 401 F 1 HETATM 9 P PA ACP . . . U 12 49.959 98.029 10.245 0 95.3 ? PA ACP 401 F 1 HETATM 10 O O1A ACP . . . U 12 50.548 97.478 8.968 0 93.5 ? O1A ACP 401 F 1 HETATM 11 O O2A ACP . . . U 12 50.831 98.168 11.47 0 93.19 ? O2A ACP 401 F 1 HETATM 12 O O3A ACP . . . U 12 48.657 97.153 10.605 0 96.81 ? O3A ACP 401 F 1 HETATM 13 O O5' ACP . . . U 12 49.283 99.447 9.9 0 99.23 ? O5' ACP 401 F 1 HETATM 14 C C5' ACP . . . U 12 47.913 99.472 9.503 0 101.59 ? C5' ACP 401 F 1 HETATM 15 C C4' ACP . . . U 12 47.641 100.692 8.634 0 103.58 ? C4' ACP 401 F 1 HETATM 16 O O4' ACP . . . U 12 48.075 101.879 9.3 0 104.11 ? O4' ACP 401 F 1 HETATM 17 C C3' ACP . . . U 12 48.392 100.618 7.316 0 102.01 ? C3' ACP 401 F 1 HETATM 18 O O3' ACP . . . U 12 47.502 100.271 6.252 0 103.32 ? O3' ACP 401 F 1 HETATM 19 C C2' ACP . . . U 12 48.964 102.003 7.096 0 101.9 ? C2' ACP 401 F 1 HETATM 20 O O2' ACP . . . U 12 48.285 102.64 6.01 0 102.26 ? O2' ACP 401 F 1 HETATM 21 C C1' ACP . . . U 12 48.712 102.771 8.384 0 103.21 ? C1' ACP 401 F 1 HETATM 22 N N9 ACP . . . U 12 50.011 103.207 8.95 0 101.69 ? N9 ACP 401 F 1 HETATM 23 C C8 ACP . . . U 12 50.743 102.517 9.844 0 100.76 ? C8 ACP 401 F 1 HETATM 24 N N7 ACP . . . U 12 51.881 103.182 10.164 0 100.79 ? N7 ACP 401 F 1 HETATM 25 C C5 ACP . . . U 12 51.888 104.329 9.461 0 101.24 ? C5 ACP 401 F 1 HETATM 26 C C6 ACP . . . U 12 52.796 105.492 9.326 0 102.47 ? C6 ACP 401 F 1 HETATM 27 N N6 ACP . . . U 12 53.954 105.561 10.027 0 102.23 ? N6 ACP 401 F 1 HETATM 28 N N1 ACP . . . U 12 52.429 106.482 8.482 0 102.29 ? N1 ACP 401 F 1 HETATM 29 C C2 ACP . . . U 12 51.282 106.425 7.781 0 102.22 ? C2 ACP 401 F 1 HETATM 30 N N3 ACP . . . U 12 50.412 105.401 7.853 0 102.3 ? N3 ACP 401 F 1 HETATM 31 C C4 ACP . . . U 12 50.653 104.342 8.662 0 101.63 ? C4 ACP 401 F 1 # _model_server_stats.io_time_ms 0 _model_server_stats.parse_time_ms 12 _model_server_stats.create_model_time_ms 31 _model_server_stats.query_time_ms 316 _model_server_stats.encode_time_ms 3 _model_server_stats.element_count 31 #