data_8WMO # _model_server_result.job_id ru367gzhD392sJ5Wi053DQ _model_server_result.datetime_utc '2024-11-28 08:11:33' _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 8wmo # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"AA","auth_seq_id":401}' # _entry.id 8WMO # _exptl.entry_id 8WMO _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 505.208 _entity.id 13 _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 8WMO _cell.length_a 103.82 _cell.length_b 156.446 _cell.length_c 179.393 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 8WMO _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,DA,EA,FA _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 13 _struct_asym.id AA _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 G O1G GTP . A GTP 501 1_555 H MG MG . A MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.176 ? metalc ? metalc2 G O1B GTP . A GTP 501 1_555 H MG MG . A MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.392 ? metalc ? metalc3 K O1A GDP . B GDP 501 1_555 L MG MG . B MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.275 ? metalc ? metalc4 C OD1 ASP 39 C ASP 39 1_555 R CA CA . C CA 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.9 ? metalc ? metalc5 C OD2 ASP 39 C ASP 39 1_555 R CA CA . C CA 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.113 ? metalc ? metalc6 C O THR 41 C THR 41 1_555 R CA CA . C CA 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.367 ? metalc ? metalc7 C OG1 THR 41 C THR 41 1_555 R CA CA . C CA 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.111 ? metalc ? metalc8 C O GLY 44 C GLY 44 1_555 R CA CA . C CA 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.22 ? metalc ? metalc9 C OE1 GLU 55 C GLU 55 1_555 R CA CA . C CA 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.671 ? metalc ? metalc10 C OE2 GLU 55 C GLU 55 1_555 R CA CA . C CA 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.24 ? metalc ? metalc11 P O1G GTP . C GTP 501 1_555 Q MG MG . C MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.298 ? metalc ? metalc12 P O1B GTP . C GTP 501 1_555 Q MG MG . C MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.943 ? metalc ? metalc13 W O1A GTP . D GTP 501 1_555 X MG MG . D MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.08 ? # _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 8WMO _atom_sites.fract_transf_matrix[1][1] 0.009632 _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] 0.006392 _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] 0.005574 _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 EDO A 1 503 505 EDO EDO . J 8 PEG A 1 504 506 PEG PEG . 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 11 WIW B 1 504 504 WIW B1N . O 7 EDO B 1 505 505 EDO EDO . P 5 GTP C 1 501 501 GTP GTP . Q 6 MG C 1 502 502 MG MG . R 12 CA C 1 503 503 CA CA . S 7 EDO C 1 504 504 EDO EDO . T 7 EDO C 1 505 505 EDO EDO . U 7 EDO C 1 506 506 EDO EDO . V 7 EDO C 1 507 507 EDO EDO . W 5 GTP D 1 501 501 GTP GTP . X 6 MG D 1 502 502 MG MG . Y 7 EDO D 1 503 503 EDO EDO . Z 7 EDO D 1 504 504 EDO EDO . AA 13 ACP F 1 401 401 ACP ACP . BA 14 HOH A 1 601 31 HOH HOH . BA 14 HOH A 2 602 30 HOH HOH . BA 14 HOH A 3 603 17 HOH HOH . BA 14 HOH A 4 604 11 HOH HOH . BA 14 HOH A 5 605 26 HOH HOH . BA 14 HOH A 6 606 27 HOH HOH . BA 14 HOH A 7 607 29 HOH HOH . CA 14 HOH B 1 601 18 HOH HOH . CA 14 HOH B 2 602 5 HOH HOH . CA 14 HOH B 3 603 1 HOH HOH . CA 14 HOH B 4 604 28 HOH HOH . CA 14 HOH B 5 605 25 HOH HOH . CA 14 HOH B 6 606 2 HOH HOH . DA 14 HOH C 1 601 12 HOH HOH . DA 14 HOH C 2 602 3 HOH HOH . DA 14 HOH C 3 603 4 HOH HOH . DA 14 HOH C 4 604 6 HOH HOH . DA 14 HOH C 5 605 24 HOH HOH . DA 14 HOH C 6 606 7 HOH HOH . EA 14 HOH D 1 601 9 HOH HOH . EA 14 HOH D 2 602 13 HOH HOH . EA 14 HOH D 3 603 22 HOH HOH . EA 14 HOH D 4 604 23 HOH HOH . EA 14 HOH D 5 605 10 HOH HOH . EA 14 HOH D 6 606 21 HOH HOH . EA 14 HOH D 7 607 16 HOH HOH . EA 14 HOH D 8 608 14 HOH HOH . EA 14 HOH D 9 609 8 HOH HOH . FA 14 HOH F 1 501 19 HOH HOH . FA 14 HOH F 2 502 15 HOH HOH . FA 14 HOH F 3 503 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 . . . AA 13 -7.919 48.684 -94.047 0.96 122.82 ? PG ACP 401 F 1 HETATM 2 O O1G ACP . . . AA 13 -8.248 47.276 -93.656 0.96 123.95 ? O1G ACP 401 F 1 HETATM 3 O O2G ACP . . . AA 13 -8.553 49.716 -93.083 0.96 106.83 ? O2G ACP 401 F 1 HETATM 4 O O3G ACP . . . AA 13 -6.395 48.919 -94.113 0.96 94.44 ? O3G ACP 401 F 1 HETATM 5 P PB ACP . . . AA 13 -10.312 48.757 -95.813 0.96 112.73 ? PB ACP 401 F 1 HETATM 6 O O1B ACP . . . AA 13 -10.987 49.598 -94.754 0.96 106.77 ? O1B ACP 401 F 1 HETATM 7 O O2B ACP . . . AA 13 -10.555 47.24 -95.49 0.96 108.08 ? O2B ACP 401 F 1 HETATM 8 C C3B ACP . . . AA 13 -8.514 49.076 -95.697 0.96 105.56 ? C3B ACP 401 F 1 HETATM 9 P PA ACP . . . AA 13 -10.081 49.877 -98.354 0.96 112.8 ? PA ACP 401 F 1 HETATM 10 O O1A ACP . . . AA 13 -9.503 51.127 -97.83 0.96 107.85 ? O1A ACP 401 F 1 HETATM 11 O O2A ACP . . . AA 13 -10.959 50.131 -99.578 0.96 95.72 ? O2A ACP 401 F 1 HETATM 12 O O3A ACP . . . AA 13 -10.997 49.086 -97.26 0.96 106.1 ? O3A ACP 401 F 1 HETATM 13 O O5' ACP . . . AA 13 -8.918 48.88 -98.752 0.96 110.99 ? O5' ACP 401 F 1 HETATM 14 C C5' ACP . . . AA 13 -9.187 47.617 -99.4 0.96 103.53 ? C5' ACP 401 F 1 HETATM 15 C C4' ACP . . . AA 13 -8.462 47.582 -100.719 0.96 94.89 ? C4' ACP 401 F 1 HETATM 16 O O4' ACP . . . AA 13 -9.226 48.332 -101.674 0.96 97.34 ? O4' ACP 401 F 1 HETATM 17 C C3' ACP . . . AA 13 -7.097 48.255 -100.723 0.96 97 ? C3' ACP 401 F 1 HETATM 18 O O3' ACP . . . AA 13 -6.089 47.333 -100.33 0.96 100.37 ? O3' ACP 401 F 1 HETATM 19 C C2' ACP . . . AA 13 -6.929 48.699 -102.183 0.96 92.73 ? C2' ACP 401 F 1 HETATM 20 O O2' ACP . . . AA 13 -6.224 47.714 -102.927 0.96 93.73 ? O2' ACP 401 F 1 HETATM 21 C C1' ACP . . . AA 13 -8.371 48.792 -102.696 0.96 92.59 ? C1' ACP 401 F 1 HETATM 22 N N9 ACP . . . AA 13 -8.823 50.119 -103.104 0.96 91.57 ? N9 ACP 401 F 1 HETATM 23 C C8 ACP . . . AA 13 -9.64 50.976 -102.409 0.96 92.9 ? C8 ACP 401 F 1 HETATM 24 N N7 ACP . . . AA 13 -9.911 52.092 -103.044 0.96 92.51 ? N7 ACP 401 F 1 HETATM 25 C C5 ACP . . . AA 13 -9.243 51.95 -104.252 0.96 91.75 ? C5 ACP 401 F 1 HETATM 26 C C6 ACP . . . AA 13 -9.126 52.785 -105.38 0.96 92.99 ? C6 ACP 401 F 1 HETATM 27 N N6 ACP . . . AA 13 -9.708 53.984 -105.485 0.96 95.65 ? N6 ACP 401 F 1 HETATM 28 N N1 ACP . . . AA 13 -8.384 52.339 -106.416 0.96 94.13 ? N1 ACP 401 F 1 HETATM 29 C C2 ACP . . . AA 13 -7.802 51.141 -106.326 0.96 89.97 ? C2 ACP 401 F 1 HETATM 30 N N3 ACP . . . AA 13 -7.833 50.275 -105.314 0.96 88.09 ? N3 ACP 401 F 1 HETATM 31 C C4 ACP . . . AA 13 -8.576 50.736 -104.305 0.96 90.2 ? C4 ACP 401 F 1 # _model_server_stats.io_time_ms 19 _model_server_stats.parse_time_ms 13 _model_server_stats.create_model_time_ms 24 _model_server_stats.query_time_ms 310 _model_server_stats.encode_time_ms 3 _model_server_stats.element_count 31 #