data_5YLS # _model_server_result.job_id 4xQUIQD31oJH53b2otbkQg _model_server_result.datetime_utc '2024-11-22 07:13:46' _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 5yls # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"U","auth_seq_id":401}' # _entry.id 5YLS # _exptl.entry_id 5YLS _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 5YLS _cell.length_a 105.767 _cell.length_b 159.054 _cell.length_c 183.151 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 5YLS _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,T,U,V,W,X,Y _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 ? ? ? ? ? ? ? ? ? ? ? ? 2.809 ? metalc ? metalc2 A OD2 ASP 39 A ASP 39 1_555 I CA CA . A CA 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 3.15 ? metalc ? metalc3 A O THR 41 A THR 41 1_555 I CA CA . A CA 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.707 ? metalc ? metalc4 A OG1 THR 41 A THR 41 1_555 I CA CA . A CA 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.752 ? metalc ? metalc5 A O GLY 44 A GLY 44 1_555 I CA CA . A CA 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.339 ? metalc ? metalc6 A OE2 GLU 55 A GLU 55 1_555 I CA CA . A CA 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.356 ? metalc ? metalc7 G O1G GTP . A GTP 501 1_555 H MG MG . A MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.949 ? metalc ? metalc8 G O1B GTP . A GTP 501 1_555 H MG MG . A MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.987 ? metalc ? metalc9 H MG MG . A MG 502 1_555 V O HOH . A HOH 602 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.089 ? metalc ? metalc10 H MG MG . A MG 502 1_555 V O HOH . A HOH 603 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.022 ? metalc ? metalc11 H MG MG . A MG 502 1_555 V O HOH . A HOH 604 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.373 ? metalc ? metalc12 H MG MG . A MG 502 1_555 V O HOH . A HOH 605 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.46 ? metalc ? metalc13 B OE1 GLN 11 B GLN 11 1_555 L MG MG . B MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.227 ? metalc ? metalc14 K O1A GDP . B GDP 501 1_555 L MG MG . B MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.379 ? metalc ? metalc15 L MG MG . B MG 502 1_555 W O HOH . B HOH 604 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.831 ? metalc ? metalc16 L MG MG . B MG 502 1_555 W O HOH . B HOH 605 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.202 ? metalc ? metalc17 L MG MG . B MG 502 1_555 W O HOH . B HOH 606 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.301 ? metalc ? metalc18 L MG MG . B MG 502 1_555 X O HOH . C HOH 605 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.972 ? metalc ? metalc19 C OD1 ASP 39 C ASP 39 1_555 Q CA CA . C CA 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.598 ? metalc ? metalc20 C OD2 ASP 39 C ASP 39 1_555 Q CA CA . C CA 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.731 ? metalc ? metalc21 C O THR 41 C THR 41 1_555 Q CA CA . C CA 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.609 ? metalc ? metalc22 C OG1 THR 41 C THR 41 1_555 Q CA CA . C CA 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.508 ? metalc ? metalc23 C O GLY 44 C GLY 44 1_555 Q CA CA . C CA 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.417 ? metalc ? metalc24 C OE1 GLU 55 C GLU 55 1_555 Q CA CA . C CA 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.902 ? metalc ? metalc25 C OE2 GLU 55 C GLU 55 1_555 Q CA CA . C CA 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.677 ? metalc ? metalc26 O O1G GTP . C GTP 501 1_555 P MG MG . C MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.143 ? metalc ? metalc27 O O1B GTP . C GTP 501 1_555 P MG MG . C MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.038 ? metalc ? metalc28 P MG MG . C MG 502 1_555 X O HOH . C HOH 601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.164 ? metalc ? metalc29 P MG MG . C MG 502 1_555 X O HOH . C HOH 602 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.023 ? metalc ? metalc30 P MG MG . C MG 502 1_555 X O HOH . C HOH 603 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.15 ? metalc ? metalc31 P MG MG . C MG 502 1_555 X O HOH . C HOH 604 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.57 ? # _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 5YLS _atom_sites.fract_transf_matrix[1][1] 0.009455 _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] 0.006287 _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] 0.00546 _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 1 504 601 GOL GOL . K 9 GDP B 1 501 501 GDP GDP . L 6 MG B 1 502 502 MG MG . M 10 MES B 1 503 505 MES MES . N 11 Y50 B 1 504 1 Y50 Y50 . O 5 GTP C 1 501 501 GTP GTP . P 6 MG C 1 502 502 MG MG . Q 7 CA C 1 503 504 CA CA . R 5 GTP D 1 501 501 GTP GTP . S 6 MG D 1 502 502 MG MG . T 11 Y50 D 1 503 2 Y50 Y50 . U 12 ACP F 1 401 401 ACP ACP . V 13 HOH A 1 601 11 HOH HOH . V 13 HOH A 2 602 2 HOH HOH . V 13 HOH A 3 603 1 HOH HOH . V 13 HOH A 4 604 3 HOH HOH . V 13 HOH A 5 605 4 HOH HOH . W 13 HOH B 1 601 17 HOH HOH . W 13 HOH B 2 602 18 HOH HOH . W 13 HOH B 3 603 10 HOH HOH . W 13 HOH B 4 604 12 HOH HOH . W 13 HOH B 5 605 15 HOH HOH . W 13 HOH B 6 606 16 HOH HOH . W 13 HOH B 7 607 13 HOH HOH . X 13 HOH C 1 601 5 HOH HOH . X 13 HOH C 2 602 6 HOH HOH . X 13 HOH C 3 603 7 HOH HOH . X 13 HOH C 4 604 8 HOH HOH . X 13 HOH C 5 605 14 HOH HOH . Y 13 HOH D 1 601 9 HOH HOH . Y 13 HOH D 2 602 19 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 7.854 209.855 94.271 1 160.29 ? PG ACP 401 F 1 HETATM 2 O O1G ACP . . . U 12 8.288 208.783 93.346 1 157.59 ? O1G ACP 401 F 1 HETATM 3 O O2G ACP . . . U 12 8.4 211.274 93.743 1 160.2 ? O2G ACP 401 F 1 HETATM 4 O O3G ACP . . . U 12 6.246 209.897 94.343 1 161.18 ? O3G ACP 401 F 1 HETATM 5 P PB ACP . . . U 12 10.325 209.691 95.908 1 155.97 ? PB ACP 401 F 1 HETATM 6 O O1B ACP . . . U 12 10.724 210.848 95.076 1 155.01 ? O1B ACP 401 F 1 HETATM 7 O O2B ACP . . . U 12 10.965 208.356 95.272 1 155.92 ? O2B ACP 401 F 1 HETATM 8 C C3B ACP . . . U 12 8.518 209.532 95.924 1 157.47 ? C3B ACP 401 F 1 HETATM 9 P PA ACP . . . U 12 10.31 211.005 98.435 1 145.6 ? PA ACP 401 F 1 HETATM 10 O O1A ACP . . . U 12 9.757 212.158 97.632 1 149.29 ? O1A ACP 401 F 1 HETATM 11 O O2A ACP . . . U 12 11.37 211.284 99.474 1 141.32 ? O2A ACP 401 F 1 HETATM 12 O O3A ACP . . . U 12 10.882 209.891 97.411 1 150.27 ? O3A ACP 401 F 1 HETATM 13 O O5' ACP . . . U 12 9.066 210.289 99.174 1 143.67 ? O5' ACP 401 F 1 HETATM 14 C C5' ACP . . . U 12 9.13 208.944 99.662 1 138.45 ? C5' ACP 401 F 1 HETATM 15 C C4' ACP . . . U 12 8.199 208.674 100.851 1 134.07 ? C4' ACP 401 F 1 HETATM 16 O O4' ACP . . . U 12 8.837 209.018 102.086 1 127.11 ? O4' ACP 401 F 1 HETATM 17 C C3' ACP . . . U 12 6.868 209.419 100.797 1 131.51 ? C3' ACP 401 F 1 HETATM 18 O O3' ACP . . . U 12 5.821 208.538 100.372 1 131.61 ? O3' ACP 401 F 1 HETATM 19 C C2' ACP . . . U 12 6.646 209.963 102.2 1 128.45 ? C2' ACP 401 F 1 HETATM 20 O O2' ACP . . . U 12 5.556 209.311 102.863 1 129.7 ? O2' ACP 401 F 1 HETATM 21 C C1' ACP . . . U 12 7.939 209.705 102.964 1 124.77 ? C1' ACP 401 F 1 HETATM 22 N N9 ACP . . . U 12 8.544 210.988 103.416 1 121.29 ? N9 ACP 401 F 1 HETATM 23 C C8 ACP . . . U 12 9.478 211.699 102.751 1 121.44 ? C8 ACP 401 F 1 HETATM 24 N N7 ACP . . . U 12 9.829 212.822 103.427 1 121.06 ? N7 ACP 401 F 1 HETATM 25 C C5 ACP . . . U 12 9.104 212.848 104.561 1 121.43 ? C5 ACP 401 F 1 HETATM 26 C C6 ACP . . . U 12 8.974 213.757 105.734 1 120.89 ? C6 ACP 401 F 1 HETATM 27 N N6 ACP . . . U 12 9.714 214.888 105.821 1 118.89 ? N6 ACP 401 F 1 HETATM 28 N N1 ACP . . . U 12 8.093 213.416 106.712 1 120.07 ? N1 ACP 401 F 1 HETATM 29 C C2 ACP . . . U 12 7.349 212.289 106.637 1 121.72 ? C2 ACP 401 F 1 HETATM 30 N N3 ACP . . . U 12 7.416 211.422 105.602 1 121.12 ? N3 ACP 401 F 1 HETATM 31 C C4 ACP . . . U 12 8.258 211.637 104.552 1 120.68 ? C4 ACP 401 F 1 # _model_server_stats.io_time_ms 70 _model_server_stats.parse_time_ms 10 _model_server_stats.create_model_time_ms 22 _model_server_stats.query_time_ms 310 _model_server_stats.encode_time_ms 12 _model_server_stats.element_count 31 #