data_5YLJ # _model_server_result.job_id JodACNjuJomaYRYymBGdXA _model_server_result.datetime_utc '2024-11-16 23:44:35' _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 5ylj # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"U","auth_seq_id":401}' # _entry.id 5YLJ # _exptl.entry_id 5YLJ _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 5YLJ _cell.length_a 105.231 _cell.length_b 157.367 _cell.length_c 182.684 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 5YLJ _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,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 ? ? ? ? ? ? ? ? ? ? ? ? 2.543 ? metalc ? metalc2 A OD2 ASP 39 A ASP 39 1_555 I CA CA . A CA 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.828 ? metalc ? metalc3 A O THR 41 A THR 41 1_555 I CA CA . A CA 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.616 ? metalc ? metalc4 A OG1 THR 41 A THR 41 1_555 I CA CA . A CA 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.992 ? metalc ? metalc5 A O GLY 44 A GLY 44 1_555 I CA CA . A CA 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.38 ? metalc ? metalc6 A OE1 GLU 55 A GLU 55 1_555 I CA CA . A CA 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 3.013 ? metalc ? metalc7 A OE2 GLU 55 A GLU 55 1_555 I CA CA . A CA 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.837 ? metalc ? metalc8 G O2G GTP . A GTP 501 1_555 H MG MG . A MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.089 ? metalc ? metalc9 G O1B GTP . A GTP 501 1_555 H MG MG . A MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.2 ? metalc ? metalc10 H MG MG . A MG 502 1_555 V O HOH . A HOH 601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.16 ? metalc ? metalc11 H MG MG . A MG 502 1_555 V O HOH . A HOH 602 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.223 ? metalc ? metalc12 H MG MG . A MG 502 1_555 V O HOH . A HOH 603 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.083 ? metalc ? metalc13 H MG MG . A MG 502 1_555 W O HOH . B HOH 604 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.259 ? metalc ? metalc14 B OE1 GLN 11 B GLN 11 1_555 L MG MG . B MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.238 ? metalc ? metalc15 K O1A GDP . B GDP 501 1_555 L MG MG . B MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.278 ? metalc ? metalc16 L MG MG . B MG 502 1_555 W O HOH . B HOH 608 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.594 ? metalc ? metalc17 L MG MG . B MG 502 1_555 W O HOH . B HOH 609 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.982 ? metalc ? metalc18 L MG MG . B MG 502 1_555 W O HOH . B HOH 611 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.443 ? metalc ? metalc19 L MG MG . B MG 502 1_555 X O HOH . C HOH 607 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.077 ? metalc ? metalc20 C OD1 ASP 39 C ASP 39 1_555 Q CA CA . C CA 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.744 ? metalc ? metalc21 C OD2 ASP 39 C ASP 39 1_555 Q CA CA . C CA 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.719 ? metalc ? metalc22 C O THR 41 C THR 41 1_555 Q CA CA . C CA 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.624 ? metalc ? metalc23 C OG1 THR 41 C THR 41 1_555 Q CA CA . C CA 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.596 ? metalc ? metalc24 C O GLY 44 C GLY 44 1_555 Q CA CA . C CA 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.427 ? metalc ? metalc25 C OE1 GLU 55 C GLU 55 1_555 Q CA CA . C CA 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.891 ? metalc ? metalc26 C OE2 GLU 55 C GLU 55 1_555 Q CA CA . C CA 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.681 ? metalc ? metalc27 O O1G GTP . C GTP 501 1_555 P MG MG . C MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.137 ? metalc ? metalc28 O O1B GTP . C GTP 501 1_555 P MG MG . C MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.013 ? metalc ? metalc29 P MG MG . C MG 502 1_555 X O HOH . C HOH 602 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.046 ? metalc ? metalc30 P MG MG . C MG 502 1_555 X O HOH . C HOH 603 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.202 ? metalc ? metalc31 P MG MG . C MG 502 1_555 X O HOH . C HOH 605 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.101 ? metalc ? metalc32 P MG MG . C MG 502 1_555 X O HOH . C HOH 606 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.076 ? metalc ? metalc33 R O1G GTP . D GTP 501 1_555 S MG MG . D MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.338 ? metalc ? metalc34 S MG MG . D MG 502 1_555 Y O HOH . D HOH 602 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.926 ? metalc ? metalc35 S MG MG . D MG 502 1_555 Y O HOH . D HOH 603 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.479 ? metalc ? metalc36 S MG MG . D MG 502 1_555 Y O HOH . D HOH 605 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.429 ? # _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 51 n n PG O2G ACP sing 52 n n PG O3G ACP sing 53 n n PG C3B ACP sing 54 n n O2G HOG2 ACP sing 55 n n O3G HOG3 ACP sing 56 n n PB O1B ACP doub 57 n n PB O2B ACP sing 58 n n PB C3B ACP sing 59 n n PB O3A ACP sing 60 n n O2B HOB2 ACP sing 61 n n C3B H3B1 ACP sing 62 n n C3B H3B2 ACP sing 63 n n PA O1A ACP doub 64 n n PA O2A ACP sing 65 n n PA O3A ACP sing 66 n n PA O5' ACP sing 67 n n O2A HOA2 ACP sing 68 n n O5' C5' ACP sing 69 n n C5' C4' ACP sing 70 n n C5' "H5'1" ACP sing 71 n n C5' "H5'2" ACP sing 72 n n C4' O4' ACP sing 73 n n C4' C3' ACP sing 74 n n C4' H4' ACP sing 75 n n O4' C1' ACP sing 76 n n C3' O3' ACP sing 77 n n C3' C2' ACP sing 78 n n C3' H3' ACP sing 79 n n O3' HO3' ACP sing 80 n n C2' O2' ACP sing 81 n n C2' C1' ACP sing 82 n n C2' H2' ACP sing 83 n n O2' HO2' ACP sing 84 n n C1' N9 ACP sing 85 n n C1' H1' ACP sing 86 n n N9 C8 ACP sing 87 n y N9 C4 ACP sing 88 n y C8 N7 ACP doub 89 n y C8 H8 ACP sing 90 n n N7 C5 ACP sing 91 n y C5 C6 ACP sing 92 n y C5 C4 ACP doub 93 n y C6 N6 ACP sing 94 n n C6 N1 ACP doub 95 n y N6 HN61 ACP sing 96 n n N6 HN62 ACP sing 97 n n N1 C2 ACP sing 98 n y C2 N3 ACP doub 99 n y C2 H2 ACP sing 100 n n N3 C4 ACP sing 101 n y # _atom_sites.entry_id 5YLJ _atom_sites.fract_transf_matrix[1][1] 0.009503 _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] 0.006355 _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] 0.005474 _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 8X0 B 1 504 1 8X0 MIL . 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 8X0 D 1 503 2 8X0 MIL . U 12 ACP F 1 401 401 ACP ACP . V 13 HOH A 1 601 3 HOH HOH . V 13 HOH A 2 602 1 HOH HOH . V 13 HOH A 3 603 4 HOH HOH . V 13 HOH A 4 604 5 HOH HOH . W 13 HOH B 1 601 9 HOH HOH . W 13 HOH B 2 602 11 HOH HOH . W 13 HOH B 3 603 10 HOH HOH . W 13 HOH B 4 604 2 HOH HOH . W 13 HOH B 5 605 7 HOH HOH . W 13 HOH B 6 606 8 HOH HOH . W 13 HOH B 7 607 6 HOH HOH . W 13 HOH B 8 608 14 HOH HOH . W 13 HOH B 9 609 16 HOH HOH . W 13 HOH B 10 610 12 HOH HOH . W 13 HOH B 11 611 13 HOH HOH . X 13 HOH C 1 601 22 HOH HOH . X 13 HOH C 2 602 18 HOH HOH . X 13 HOH C 3 603 21 HOH HOH . X 13 HOH C 4 604 17 HOH HOH . X 13 HOH C 5 605 19 HOH HOH . X 13 HOH C 6 606 20 HOH HOH . X 13 HOH C 7 607 15 HOH HOH . Y 13 HOH D 1 601 27 HOH HOH . Y 13 HOH D 2 602 23 HOH HOH . Y 13 HOH D 3 603 25 HOH HOH . Y 13 HOH D 4 604 26 HOH HOH . Y 13 HOH D 5 605 24 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 8.137 206.468 94.272 1 137.95 ? PG ACP 401 F 1 HETATM 2 O O1G ACP . . . U 12 9.069 207.142 93.146 1 133.59 ? O1G ACP 401 F 1 HETATM 3 O O2G ACP . . . U 12 8.213 204.996 94.137 1 139.53 ? O2G ACP 401 F 1 HETATM 4 O O3G ACP . . . U 12 6.61 206.94 94.072 1 133.73 ? O3G ACP 401 F 1 HETATM 5 P PB ACP . . . U 12 10.502 206.713 96.059 1 130.37 ? PB ACP 401 F 1 HETATM 6 O O1B ACP . . . U 12 11.206 207.711 95.223 1 130.69 ? O1B ACP 401 F 1 HETATM 7 O O2B ACP . . . U 12 10.876 205.247 95.509 1 129.21 ? O2B ACP 401 F 1 HETATM 8 C C3B ACP . . . U 12 8.706 206.944 95.926 1 132.45 ? C3B ACP 401 F 1 HETATM 9 P PA ACP . . . U 12 10.516 207.959 98.653 1 123.54 ? PA ACP 401 F 1 HETATM 10 O O1A ACP . . . U 12 9.94 209.145 97.92 1 125.59 ? O1A ACP 401 F 1 HETATM 11 O O2A ACP . . . U 12 11.633 208.203 99.638 1 121.88 ? O2A ACP 401 F 1 HETATM 12 O O3A ACP . . . U 12 11.011 206.843 97.588 1 127.91 ? O3A ACP 401 F 1 HETATM 13 O O5' ACP . . . U 12 9.325 207.215 99.444 1 121.75 ? O5' ACP 401 F 1 HETATM 14 C C5' ACP . . . U 12 9.483 205.875 99.924 1 117.39 ? C5' ACP 401 F 1 HETATM 15 C C4' ACP . . . U 12 8.523 205.508 101.059 1 112.71 ? C4' ACP 401 F 1 HETATM 16 O O4' ACP . . . U 12 9.101 205.855 102.322 1 109.74 ? O4' ACP 401 F 1 HETATM 17 C C3' ACP . . . U 12 7.16 206.185 100.968 1 110.42 ? C3' ACP 401 F 1 HETATM 18 O O3' ACP . . . U 12 6.174 205.253 100.511 1 109.78 ? O3' ACP 401 F 1 HETATM 19 C C2' ACP . . . U 12 6.874 206.716 102.364 1 108.76 ? C2' ACP 401 F 1 HETATM 20 O O2' ACP . . . U 12 5.827 205.986 103.011 1 110.36 ? O2' ACP 401 F 1 HETATM 21 C C1' ACP . . . U 12 8.169 206.555 103.15 1 107.45 ? C1' ACP 401 F 1 HETATM 22 N N9 ACP . . . U 12 8.713 207.89 103.521 1 105.46 ? N9 ACP 401 F 1 HETATM 23 C C8 ACP . . . U 12 9.577 208.624 102.79 1 105.26 ? C8 ACP 401 F 1 HETATM 24 N N7 ACP . . . U 12 9.878 209.795 103.404 1 106.4 ? N7 ACP 401 F 1 HETATM 25 C C5 ACP . . . U 12 9.196 209.829 104.563 1 105.66 ? C5 ACP 401 F 1 HETATM 26 C C6 ACP . . . U 12 9.053 210.779 105.701 1 105.32 ? C6 ACP 401 F 1 HETATM 27 N N6 ACP . . . U 12 9.722 211.957 105.717 1 104.05 ? N6 ACP 401 F 1 HETATM 28 N N1 ACP . . . U 12 8.233 210.427 106.725 1 106.75 ? N1 ACP 401 F 1 HETATM 29 C C2 ACP . . . U 12 7.556 209.256 106.73 1 107.65 ? C2 ACP 401 F 1 HETATM 30 N N3 ACP . . . U 12 7.64 208.35 105.73 1 106.51 ? N3 ACP 401 F 1 HETATM 31 C C4 ACP . . . U 12 8.428 208.57 104.639 1 105.47 ? C4 ACP 401 F 1 # _model_server_stats.io_time_ms 14 _model_server_stats.parse_time_ms 13 _model_server_stats.create_model_time_ms 31 _model_server_stats.query_time_ms 310 _model_server_stats.encode_time_ms 6 _model_server_stats.element_count 31 #