data_8RPH # _model_server_result.job_id 8pa3Ja0bGZOVc1gMWYLSKQ _model_server_result.datetime_utc '2024-11-14 20:07:05' _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 8rph # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"I","auth_seq_id":703}' # _entry.id 8RPH # _exptl.entry_id 8RPH _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 527.403 _entity.id 4 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description '(2~{S})-2-[3-[(4-azanyl-2-methyl-pyrimidin-5-yl)methyl]-4-methyl-5-[2-[oxidanyl(phosphonooxy)phosphoryl]oxyethyl]-1,3-thiazol-2-yl]-2-oxidanyl-butanoic acid' _entity.pdbx_number_of_molecules 6 _entity.pdbx_parent_entity_id . _entity.pdbx_mutation ? _entity.pdbx_fragment ? _entity.pdbx_ec ? # _cell.angle_alpha 90 _cell.angle_beta 97.06 _cell.angle_gamma 90 _cell.entry_id 8RPH _cell.length_a 173.326 _cell.length_b 118.189 _cell.length_c 201.166 _cell.Z_PDB 24 _cell.pdbx_unique_axis ? # _symmetry.entry_id 8RPH _symmetry.cell_setting ? _symmetry.Int_Tables_number 5 _symmetry.space_group_name_Hall 'C 2y' _symmetry.space_group_name_H-M 'C 1 2 1' # loop_ _pdbx_struct_assembly.method_details _pdbx_struct_assembly.oligomeric_details _pdbx_struct_assembly.oligomeric_count _pdbx_struct_assembly.details _pdbx_struct_assembly.id PISA dimeric 2 author_and_software_defined_assembly 1 PISA dimeric 2 author_and_software_defined_assembly 2 PISA dimeric 2 author_and_software_defined_assembly 3 # loop_ _pdbx_struct_assembly_gen.asym_id_list _pdbx_struct_assembly_gen.assembly_id _pdbx_struct_assembly_gen.oper_expression A,B,G,H,I,J,K,L,Z 1 1 C,D,M,N,O,P,Q,R,S,AA 2 1 E,F,T,U,V,W,X,Y 3 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 # loop_ _struct_asym.details _struct_asym.entity_id _struct_asym.id _struct_asym.pdbx_modified _struct_asym.pdbx_blank_PDB_chainid_flag ? 4 I N N ? 4 L N N ? 4 O N N ? 4 S N N ? 4 V N N ? 4 Y N 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 460 A ASP 459 1_555 H MG MG . A MG 702 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.888 ? metalc ? metalc2 A OD1 ASN 487 A ASN 486 1_555 H MG MG . A MG 702 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.227 ? metalc ? metalc3 A O GLY 489 A GLY 488 1_555 H MG MG . A MG 702 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.314 ? metalc ? metalc4 H MG MG . A MG 702 1_555 I O2A A1H2A . A A1H2A 703 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.935 ? metalc ? metalc5 H MG MG . A MG 702 1_555 I O3B A1H2A . A A1H2A 703 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.947 ? metalc ? metalc6 B OD1 ASP 460 B ASP 459 1_555 K MG MG . B MG 702 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.028 ? metalc ? metalc7 B OD1 ASN 487 B ASN 486 1_555 K MG MG . B MG 702 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.082 ? metalc ? metalc8 B O GLY 489 B GLY 488 1_555 K MG MG . B MG 702 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.346 ? metalc ? metalc9 K MG MG . B MG 702 1_555 L O2A A1H2A . B A1H2A 703 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.018 ? metalc ? metalc10 C OD1 ASP 460 C ASP 459 1_555 N MG MG . C MG 702 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.931 ? metalc ? metalc11 C OD1 ASN 487 C ASN 486 1_555 N MG MG . C MG 702 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.266 ? metalc ? metalc12 C O GLY 489 C GLY 488 1_555 N MG MG . C MG 702 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.342 ? metalc ? metalc13 N MG MG . C MG 702 1_555 O O1B A1H2A . C A1H2A 703 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.989 ? metalc ? metalc14 N MG MG . C MG 702 1_555 O O2A A1H2A . C A1H2A 703 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.419 ? metalc ? metalc15 N MG MG . C MG 702 1_555 AA O HOH . C HOH 801 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.433 ? metalc ? metalc16 D OD1 ASP 460 D ASP 459 1_555 Q MG MG . D MG 702 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.05 ? metalc ? metalc17 D OD1 ASN 487 D ASN 486 1_555 Q MG MG . D MG 702 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.998 ? metalc ? metalc18 D O GLY 489 D GLY 488 1_555 Q MG MG . D MG 702 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.391 ? metalc ? metalc19 Q MG MG . D MG 702 1_555 S O3A A1H2A . D A1H2A 704 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.556 ? metalc ? metalc20 E OD1 ASP 460 E ASP 459 1_555 U MG MG . E MG 702 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.248 ? metalc ? metalc21 E OD1 ASN 487 E ASN 486 1_555 U MG MG . E MG 702 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.152 ? metalc ? metalc22 E O GLY 489 E GLY 488 1_555 U MG MG . E MG 702 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.127 ? metalc ? metalc23 U MG MG . E MG 702 1_555 V O2A A1H2A . E A1H2A 703 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.966 ? metalc ? metalc24 U MG MG . E MG 702 1_555 V O2B A1H2A . E A1H2A 703 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.988 ? metalc ? metalc25 U MG MG . E MG 702 1_555 V O3A A1H2A . E A1H2A 703 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.147 ? metalc ? metalc26 F OD1 ASP 460 F ASP 459 1_555 X MG MG . F MG 702 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.939 ? metalc ? metalc27 F OD1 ASN 487 F ASN 486 1_555 X MG MG . F MG 702 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.258 ? metalc ? metalc28 F O GLY 489 F GLY 488 1_555 X MG MG . F MG 702 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.303 ? metalc ? metalc29 X MG MG . F MG 702 1_555 Y O1B A1H2A . F A1H2A 703 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.012 ? metalc ? metalc30 X MG MG . F MG 702 1_555 Y O2A A1H2A . F A1H2A 703 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.32 ? # _chem_comp.formula 'C16 H25 N4 O10 P2 S 1' _chem_comp.formula_weight 527.403 _chem_comp.id A1H2A _chem_comp.mon_nstd_flag . _chem_comp.name '(2~{S})-2-[3-[(4-azanyl-2-methyl-pyrimidin-5-yl)methyl]-4-methyl-5-[2-[oxidanyl(phosphonooxy)phosphoryl]oxyethyl]-1,3-thiazol-2-yl]-2-oxidanyl-butanoic acid' _chem_comp.type non-polymer _chem_comp.pdbx_synonyms 'Ketobutyryl-thiamine diphosphate' # 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 N1' C2' A1H2A doub 1 n y N1' C6' A1H2A sing 2 n y C2' CM2 A1H2A sing 3 n n C2' N3' A1H2A sing 4 n y N3' C4' A1H2A doub 5 n y C4' N4' A1H2A sing 6 n n C4' C5' A1H2A sing 7 n y C5' C6' A1H2A doub 8 n y C5' C7' A1H2A sing 9 n n C7' N3 A1H2A sing 10 n n N3 C2 A1H2A doub 11 n y N3 C4 A1H2A sing 12 n y C2 S1 A1H2A sing 13 n y C2 C1 A1H2A sing 14 n n S1 C5 A1H2A sing 15 n y C5 C4 A1H2A doub 16 n y C5 C6 A1H2A sing 17 n n C4 CM4 A1H2A sing 18 n n C6 C7 A1H2A sing 19 n n C7 O7 A1H2A sing 20 n n O7 PA A1H2A sing 21 n n PA O1A A1H2A doub 22 n n PA O2A A1H2A sing 23 n n PA O3A A1H2A sing 24 n n O3A PB A1H2A sing 25 n n PB O1B A1H2A doub 26 n n PB O2B A1H2A sing 27 n n PB O3B A1H2A sing 28 n n C1 O2 A1H2A sing 29 n n C1 C3 A1H2A sing 30 n n C1 C8 A1H2A sing 31 n n C3 O9 A1H2A doub 32 n n C3 O10 A1H2A sing 33 n n C8 C9 A1H2A sing 34 n n O2 HO2 A1H2A sing 35 n n C9 H92 A1H2A sing 36 n n C9 H91 A1H2A sing 37 n n C9 H9 A1H2A sing 38 n n C8 H8 A1H2A sing 39 n n C8 H81 A1H2A sing 40 n n C7 H72 A1H2A sing 41 n n C7 H71 A1H2A sing 42 n n C6 H61 A1H2A sing 43 n n C6 H62 A1H2A sing 44 n n C6' H6' A1H2A sing 45 n n C7' "H7'1" A1H2A sing 46 n n C7' "H7'2" A1H2A sing 47 n n CM2 HM21 A1H2A sing 48 n n CM2 HM23 A1H2A sing 49 n n CM2 HM22 A1H2A sing 50 n n CM4 HM42 A1H2A sing 51 n n CM4 HM41 A1H2A sing 52 n n CM4 HM43 A1H2A sing 53 n n N4' HN42 A1H2A sing 54 n n N4' HN41 A1H2A sing 55 n n O10 H1 A1H2A sing 56 n n O2A H2 A1H2A sing 57 n n O2B H3 A1H2A sing 58 n n O3B H4 A1H2A sing 59 n n # _atom_sites.entry_id 8RPH _atom_sites.fract_transf_matrix[1][1] 0.005769 _atom_sites.fract_transf_matrix[1][2] 0 _atom_sites.fract_transf_matrix[1][3] 0.000715 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.008461 _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] 0.005009 _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 2 FAD A 1 701 701 FAD FAD . H 3 MG A 1 702 702 MG MG . I 4 A1H2A A 1 703 701 A1H2A HBT . J 2 FAD B 1 701 701 FAD FAD . K 3 MG B 1 702 702 MG MG . L 4 A1H2A B 1 703 701 A1H2A HBT . M 2 FAD C 1 701 701 FAD FAD . N 3 MG C 1 702 702 MG MG . O 4 A1H2A C 1 703 701 A1H2A HBT . P 2 FAD D 1 701 701 FAD FAD . Q 3 MG D 1 702 702 MG MG . R 5 PGE D 1 703 801 PGE PEG . S 4 A1H2A D 1 704 701 A1H2A HBT . T 2 FAD E 1 701 701 FAD FAD . U 3 MG E 1 702 702 MG MG . V 4 A1H2A E 1 703 701 A1H2A HBT . W 2 FAD F 1 701 701 FAD FAD . X 3 MG F 1 702 702 MG MG . Y 4 A1H2A F 1 703 701 A1H2A HBT . Z 6 HOH B 1 801 1 HOH HOH . AA 6 HOH C 1 801 2 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 O O2 A1H2A . . . I 4 63.229 -41.502 62.577 1 66.75 ? O2 A1H2A 703 A 1 HETATM 2 C C9 A1H2A . . . I 4 65.919 -40.812 63.516 1 66.94 ? C9 A1H2A 703 A 1 HETATM 3 C C8 A1H2A . . . I 4 65.324 -42.208 63.531 1 67.53 ? C8 A1H2A 703 A 1 HETATM 4 C C7 A1H2A . . . I 4 64.797 -48.074 62.814 1 65.74 ? C7 A1H2A 703 A 1 HETATM 5 C C6 A1H2A . . . I 4 63.637 -47.649 63.676 1 66.99 ? C6 A1H2A 703 A 1 HETATM 6 N N3 A1H2A . . . I 4 62.168 -44.224 63.068 1 66.15 ? N3 A1H2A 703 A 1 HETATM 7 S S1 A1H2A . . . I 4 64.4 -44.954 63.918 1 69.36 ? S1 A1H2A 703 A 1 HETATM 8 C C5 A1H2A . . . I 4 63.291 -46.192 63.524 1 67.78 ? C5 A1H2A 703 A 1 HETATM 9 C C4 A1H2A . . . I 4 62.138 -45.635 63.081 1 66.34 ? C4 A1H2A 703 A 1 HETATM 10 C C3 A1H2A . . . I 4 63.309 -41.652 65.001 1 67.64 ? C3 A1H2A 703 A 1 HETATM 11 C C1 A1H2A . . . I 4 63.78 -42.255 63.642 1 67.91 ? C1 A1H2A 703 A 1 HETATM 12 C C2 A1H2A . . . I 4 63.36 -43.685 63.507 1 67.46 ? C2 A1H2A 703 A 1 HETATM 13 C C2' A1H2A . . . I 4 60.445 -43.701 58.449 1 62.09 ? C2' A1H2A 703 A 1 HETATM 14 C C4' A1H2A . . . I 4 61.75 -42.992 60.212 1 64.15 ? C4' A1H2A 703 A 1 HETATM 15 C C5' A1H2A . . . I 4 60.83 -43.526 61.139 1 63.9 ? C5' A1H2A 703 A 1 HETATM 16 C C6' A1H2A . . . I 4 59.72 -44.142 60.588 1 62.31 ? C6' A1H2A 703 A 1 HETATM 17 C C7' A1H2A . . . I 4 61.013 -43.448 62.613 1 64.74 ? C7' A1H2A 703 A 1 HETATM 18 C CM2 A1H2A . . . I 4 60.236 -43.795 56.973 1 61.66 ? CM2 A1H2A 703 A 1 HETATM 19 C CM4 A1H2A . . . I 4 60.922 -46.377 62.637 1 64.63 ? CM4 A1H2A 703 A 1 HETATM 20 N N1' A1H2A . . . I 4 59.509 -44.241 59.262 1 61.78 ? N1' A1H2A 703 A 1 HETATM 21 N N3' A1H2A . . . I 4 61.539 -43.093 58.879 1 63.03 ? N3' A1H2A 703 A 1 HETATM 22 N N4' A1H2A . . . I 4 62.871 -42.367 60.592 1 64.57 ? N4' A1H2A 703 A 1 HETATM 23 O O10 A1H2A . . . I 4 62.073 -41.627 65.224 1 65.26 ? O10 A1H2A 703 A 1 HETATM 24 O O1A A1H2A . . . I 4 66.114 -49.702 60.638 1 66.16 ? O1A A1H2A 703 A 1 HETATM 25 O O1B A1H2A . . . I 4 69.06 -49.808 64.644 1 66.48 ? O1B A1H2A 703 A 1 HETATM 26 O O2A A1H2A . . . I 4 65.739 -51.75 62.113 1 66.25 ? O2A A1H2A 703 A 1 HETATM 27 O O2B A1H2A . . . I 4 66.628 -49.706 65.283 1 67.4 ? O2B A1H2A 703 A 1 HETATM 28 O O3A A1H2A . . . I 4 67.276 -49.934 62.874 1 64.62 ? O3A A1H2A 703 A 1 HETATM 29 O O3B A1H2A . . . I 4 67.609 -51.861 64.414 1 68.12 ? O3B A1H2A 703 A 1 HETATM 30 O O7 A1H2A . . . I 4 64.842 -49.517 62.789 1 65.84 ? O7 A1H2A 703 A 1 HETATM 31 O O9 A1H2A . . . I 4 64.19 -41.235 65.789 1 68.99 ? O9 A1H2A 703 A 1 HETATM 32 P PA A1H2A . . . I 4 65.987 -50.291 61.996 1 65.36 ? PA A1H2A 703 A 1 HETATM 33 P PB A1H2A . . . I 4 67.668 -50.347 64.388 1 66.25 ? PB A1H2A 703 A 1 # _model_server_stats.io_time_ms 77 _model_server_stats.parse_time_ms 31 _model_server_stats.create_model_time_ms 325 _model_server_stats.query_time_ms 276 _model_server_stats.encode_time_ms 4 _model_server_stats.element_count 33 #