data_5S50 # _model_server_result.job_id dfVmY8_u_KsHoVSkL-IC7g _model_server_result.datetime_utc '2024-11-07 16:51:22' _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 5s50 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"V","auth_seq_id":401}' # _entry.id 5S50 # _exptl.entry_id 5S50 _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 505.208 _entity.id 11 _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 5S50 _cell.length_a 104.03 _cell.length_b 158.02 _cell.length_c 180.88 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 5S50 _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,Z,AA,BA _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 11 _struct_asym.id V _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 ? ? ? ? ? ? ? ? ? ? ? ? 2.422 ? metalc ? metalc2 A OD2 ASP 39 A ASP 39 1_555 I CA CA . A CA 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.486 ? metalc ? metalc3 A O THR 41 A THR 41 1_555 I CA CA . A CA 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.483 ? metalc ? metalc4 A OG1 THR 41 A THR 41 1_555 I CA CA . A CA 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.364 ? metalc ? metalc5 A O GLY 44 A GLY 44 1_555 I CA CA . A CA 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.624 ? metalc ? metalc6 A OE1 GLU 55 A GLU 55 1_555 I CA CA . A CA 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.663 ? metalc ? metalc7 A OE2 GLU 55 A GLU 55 1_555 I CA CA . A CA 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.327 ? metalc ? metalc8 A OE1 GLU 71 A GLU 71 1_555 H MG MG . A MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.525 ? metalc ? metalc9 G O1G GTP . A GTP 501 1_555 H MG MG . A MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.45 ? metalc ? metalc10 G O1B GTP . A GTP 501 1_555 H MG MG . A MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.922 ? metalc ? metalc11 H MG MG . A MG 502 1_555 X O HOH . A HOH 601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.807 ? metalc ? metalc12 H MG MG . A MG 502 1_555 X O HOH . A HOH 603 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.837 ? metalc ? metalc13 I CA CA . A CA 503 1_555 X O HOH . A HOH 602 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.451 ? metalc ? metalc14 J CA CA . A CA 504 1_555 BA O HOH . E HOH 201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.541 ? metalc ? metalc15 B OE1 GLN 11 B GLN 11 1_555 L MG MG . B MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.729 ? metalc ? metalc16 B OE1 GLU 111 B GLU 113 1_555 M CA CA . B CA 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.925 ? metalc ? metalc17 L MG MG . B MG 502 1_555 Y O HOH . B HOH 601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.304 ? metalc ? metalc18 L MG MG . B MG 502 1_555 Y O HOH . B HOH 602 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.964 ? metalc ? metalc19 L MG MG . B MG 502 1_555 Y O HOH . B HOH 604 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.141 ? metalc ? metalc20 M CA CA . B CA 503 4_455 C OE1 GLU 284 C GLU 284 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 3.189 ? metalc ? metalc21 C OD1 ASP 39 C ASP 39 1_555 Q CA CA . C CA 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.425 ? metalc ? metalc22 C OD2 ASP 39 C ASP 39 1_555 Q CA CA . C CA 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.301 ? metalc ? metalc23 C O THR 41 C THR 41 1_555 Q CA CA . C CA 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.627 ? metalc ? metalc24 C OG1 THR 41 C THR 41 1_555 Q CA CA . C CA 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.287 ? metalc ? metalc25 C O GLY 44 C GLY 44 1_555 Q CA CA . C CA 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.479 ? metalc ? metalc26 C OE1 GLU 55 C GLU 55 1_555 Q CA CA . C CA 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.935 ? metalc ? metalc27 C OE2 GLU 55 C GLU 55 1_555 Q CA CA . C CA 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.221 ? metalc ? metalc28 P O1G GTP . C GTP 501 1_555 R MG MG . D MG 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.116 ? metalc ? metalc29 P O1B GTP . C GTP 501 1_555 R MG MG . D MG 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.399 ? metalc ? metalc30 Q CA CA . C CA 502 1_555 Z O HOH . C HOH 601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.436 ? metalc ? metalc31 Z O HOH . C HOH 602 1_555 R MG MG . D MG 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.71 ? metalc ? metalc32 Z O HOH . C HOH 605 1_555 R MG MG . D MG 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.012 ? metalc ? metalc33 D OE1 GLN 11 D GLN 11 1_555 T MG MG . D MG 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.506 ? metalc ? metalc34 T MG MG . D MG 503 1_555 AA O HOH . D HOH 601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.301 ? metalc ? metalc35 F OE2 GLU 331 F GLU 331 1_555 W MG MG . F MG 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.897 ? metalc ? metalc36 V O1B ACP . F ACP 401 1_555 W MG MG . F MG 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.608 ? # _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 5S50 _atom_sites.fract_transf_matrix[1][1] 0.009613 _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] 0.006328 _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] 0.005529 _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 7 CA A 1 504 504 CA CA . K 8 GDP B 1 501 501 GDP GDP . L 6 MG B 1 502 502 MG MG . M 7 CA B 1 503 503 CA CA . N 9 MES B 1 504 504 MES MES . O 10 WZD B 1 505 601 WZD DRG . P 5 GTP C 1 501 501 GTP GTP . Q 7 CA C 1 502 503 CA CA . R 6 MG D 1 501 502 MG MG . S 8 GDP D 1 502 501 GDP GDP . T 6 MG D 1 503 502 MG MG . U 10 WZD D 1 504 601 WZD DRG . V 11 ACP F 1 401 401 ACP ACP . W 6 MG F 1 402 402 MG MG . X 12 HOH A 1 601 180 HOH HOH . X 12 HOH A 2 602 22 HOH HOH . X 12 HOH A 3 603 78 HOH HOH . X 12 HOH A 4 604 135 HOH HOH . Y 12 HOH B 1 601 440 HOH HOH . Y 12 HOH B 2 602 405 HOH HOH . Y 12 HOH B 3 603 345 HOH HOH . Y 12 HOH B 4 604 1335 HOH HOH . Z 12 HOH C 1 601 641 HOH HOH . Z 12 HOH C 2 602 732 HOH HOH . Z 12 HOH C 3 603 800 HOH HOH . Z 12 HOH C 4 604 664 HOH HOH . Z 12 HOH C 5 605 888 HOH HOH . Z 12 HOH C 6 606 995 HOH HOH . Z 12 HOH C 7 607 931 HOH HOH . Z 12 HOH C 8 608 1000 HOH HOH . Z 12 HOH C 9 609 938 HOH HOH . Z 12 HOH C 10 610 436 HOH HOH . Z 12 HOH C 11 611 874 HOH HOH . Z 12 HOH C 12 612 963 HOH HOH . AA 12 HOH D 1 601 1200 HOH HOH . AA 12 HOH D 2 602 1222 HOH HOH . BA 12 HOH E 1 201 1334 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 . . . V 11 8.136 50.004 94.1 1 190.16 ? PG ACP 401 F 1 HETATM 2 O O1G ACP . . . V 11 7.276 49.001 93.432 1 185.91 ? O1G ACP 401 F 1 HETATM 3 O O2G ACP . . . V 11 7.225 51.056 94.914 1 176.46 ? O2G ACP 401 F 1 HETATM 4 O O3G ACP . . . V 11 9.001 50.772 92.978 1 178.74 ? O3G ACP 401 F 1 HETATM 5 P PB ACP . . . V 11 10.917 49.894 95.144 1 190.55 ? PB ACP 401 F 1 HETATM 6 O O1B ACP . . . V 11 10.885 51.139 94.345 1 185.62 ? O1B ACP 401 F 1 HETATM 7 O O2B ACP . . . V 11 11.921 48.84 94.453 1 182.17 ? O2B ACP 401 F 1 HETATM 8 C C3B ACP . . . V 11 9.257 49.173 95.255 1 188.52 ? C3B ACP 401 F 1 HETATM 9 P PA ACP . . . V 11 10.574 51.23 97.579 1 183.43 ? PA ACP 401 F 1 HETATM 10 O O1A ACP . . . V 11 9.344 51.659 96.814 1 180.4 ? O1A ACP 401 F 1 HETATM 11 O O2A ACP . . . V 11 11.498 52.293 98.129 1 178.02 ? O2A ACP 401 F 1 HETATM 12 O O3A ACP . . . V 11 11.396 50.189 96.657 1 188.44 ? O3A ACP 401 F 1 HETATM 13 O O5' ACP . . . V 11 10.054 50.296 98.78 1 186.6 ? O5' ACP 401 F 1 HETATM 14 C C5' ACP . . . V 11 8.647 50.202 98.985 1 186.36 ? C5' ACP 401 F 1 HETATM 15 C C4' ACP . . . V 11 8.319 49.417 100.246 1 186.52 ? C4' ACP 401 F 1 HETATM 16 O O4' ACP . . . V 11 9.211 49.777 101.301 1 176.48 ? O4' ACP 401 F 1 HETATM 17 C C3' ACP . . . V 11 6.907 49.749 100.693 1 186.26 ? C3' ACP 401 F 1 HETATM 18 O O3' ACP . . . V 11 6.078 48.586 100.633 1 199 ? O3' ACP 401 F 1 HETATM 19 C C2' ACP . . . V 11 7.027 50.237 102.121 1 177.8 ? C2' ACP 401 F 1 HETATM 20 O O2' ACP . . . V 11 6.219 49.424 102.977 1 182.16 ? O2' ACP 401 F 1 HETATM 21 C C1' ACP . . . V 11 8.496 50.109 102.492 1 175.97 ? C1' ACP 401 F 1 HETATM 22 N N9 ACP . . . V 11 9.007 51.405 103.006 1 172.56 ? N9 ACP 401 F 1 HETATM 23 C C8 ACP . . . V 11 9.899 52.193 102.375 1 169.72 ? C8 ACP 401 F 1 HETATM 24 N N7 ACP . . . V 11 10.172 53.308 103.099 1 161.17 ? N7 ACP 401 F 1 HETATM 25 C C5 ACP . . . V 11 9.442 53.242 104.225 1 162.4 ? C5 ACP 401 F 1 HETATM 26 C C6 ACP . . . V 11 9.258 54.093 105.422 1 163.54 ? C6 ACP 401 F 1 HETATM 27 N N6 ACP . . . V 11 9.927 55.264 105.555 1 162.24 ? N6 ACP 401 F 1 HETATM 28 N N1 ACP . . . V 11 8.402 53.661 106.375 1 165.36 ? N1 ACP 401 F 1 HETATM 29 C C2 ACP . . . V 11 7.733 52.499 106.252 1 166.01 ? C2 ACP 401 F 1 HETATM 30 N N3 ACP . . . V 11 7.852 51.677 105.194 1 167.26 ? N3 ACP 401 F 1 HETATM 31 C C4 ACP . . . V 11 8.678 51.985 104.164 1 167.69 ? C4 ACP 401 F 1 # _model_server_stats.io_time_ms 30 _model_server_stats.parse_time_ms 11 _model_server_stats.create_model_time_ms 40 _model_server_stats.query_time_ms 235 _model_server_stats.encode_time_ms 3 _model_server_stats.element_count 31 #