data_4E0Y # _model_server_result.job_id ZVFVy0uJc9dE4yaHjTjiSw _model_server_result.datetime_utc '2025-07-04 17:45:45' _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 4e0y # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"E","auth_seq_id":101}' # _entry.id 4E0Y # _exptl.entry_id 4E0Y _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 322.208 _entity.id 5 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description "THYMIDINE-5'-PHOSPHATE" _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 112.42 _cell.angle_gamma 90 _cell.entry_id 4E0Y _cell.length_a 116.984 _cell.length_b 119.442 _cell.length_c 56.922 _cell.Z_PDB 4 _cell.pdbx_unique_axis ? # _symmetry.entry_id 4E0Y _symmetry.cell_setting ? _symmetry.Int_Tables_number 5 _symmetry.space_group_name_Hall . _symmetry.space_group_name_H-M 'C 1 2 1' # _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 _pdbx_struct_assembly_gen.assembly_id 1 _pdbx_struct_assembly_gen.oper_expression 1,2 # loop_ _pdbx_struct_oper_list.id _pdbx_struct_oper_list.type _pdbx_struct_oper_list.name _pdbx_struct_oper_list.symmetry_operation _pdbx_struct_oper_list.matrix[1][1] _pdbx_struct_oper_list.matrix[1][2] _pdbx_struct_oper_list.matrix[1][3] _pdbx_struct_oper_list.matrix[2][1] _pdbx_struct_oper_list.matrix[2][2] _pdbx_struct_oper_list.matrix[2][3] _pdbx_struct_oper_list.matrix[3][1] _pdbx_struct_oper_list.matrix[3][2] _pdbx_struct_oper_list.matrix[3][3] _pdbx_struct_oper_list.vector[1] _pdbx_struct_oper_list.vector[2] _pdbx_struct_oper_list.vector[3] 1 'identity operation' 1_555 x,y,z 1 0 0 0 1 0 0 0 1 0 0 0 2 'crystal symmetry operation' 2_555 -x,y,-z -1 0 0 0 1 0 0 0 -1 0 0 0 # _struct_asym.details ? _struct_asym.entity_id 5 _struct_asym.id E _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 covale ? covale1 A C SER 424 A SER 404 1_555 A N PTR 425 A PTR 405 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.328 ? covale ? covale2 A C PTR 425 A PTR 405 1_555 A N MET 426 A MET 406 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.326 ? hydrog WATSON-CRICK hydrog1 B N3 DC 1 C DC 1 1_555 C N1 DG 19 D DG 32 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog2 B N4 DC 1 C DC 1 1_555 C O6 DG 19 D DG 32 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog3 B O2 DC 1 C DC 1 1_555 C N2 DG 19 D DG 32 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog4 B N1 DA 2 C DA 2 1_555 C N3 DT 18 D DT 31 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog5 B N6 DA 2 C DA 2 1_555 C O4 DT 18 D DT 31 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog6 B N3 DT 3 C DT 3 1_555 C N1 DA 17 D DA 30 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog7 B O4 DT 3 C DT 3 1_555 C N6 DA 17 D DA 30 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog8 B N1 DA 4 C DA 4 1_555 C N3 DT 16 D DT 29 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog9 B N6 DA 4 C DA 4 1_555 C O4 DT 16 D DT 29 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog10 B N1 DA 5 C DA 5 1_555 C N3 DT 15 D DT 28 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog11 B N6 DA 5 C DA 5 1_555 C O4 DT 15 D DT 28 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog12 B N3 DT 6 C DT 6 1_555 C N1 DA 14 D DA 27 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog13 B O4 DT 6 C DT 6 1_555 C N6 DA 14 D DA 27 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog14 B N1 DA 7 C DA 7 1_555 C N3 DT 13 D DT 26 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog15 B N6 DA 7 C DA 7 1_555 C O4 DT 13 D DT 26 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog16 B N1 DA 8 C DA 8 1_555 C N3 DT 12 D DT 25 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog17 B N6 DA 8 C DA 8 1_555 C O4 DT 12 D DT 25 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog18 B N3 DC 9 C DC 9 1_555 C N1 DG 11 D DG 24 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog19 B N4 DC 9 C DC 9 1_555 C O6 DG 11 D DG 24 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog20 B O2 DC 9 C DC 9 1_555 C N2 DG 11 D DG 24 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog21 B N1 DA 10 C DA 10 1_555 C N3 DT 10 D DT 23 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog22 B N6 DA 10 C DA 10 1_555 C O4 DT 10 D DT 23 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog23 B N1 DA 11 C DA 11 1_555 C N3 DT 9 D DT 22 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog24 B N6 DA 11 C DA 11 1_555 C O4 DT 9 D DT 22 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog25 B N3 DT 12 C DT 12 1_555 C N1 DA 8 D DA 21 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog26 B O4 DT 12 C DT 12 1_555 C N6 DA 8 D DA 21 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog27 B N1 DA 13 C DA 13 1_555 C N3 DT 7 D DT 20 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog28 B N6 DA 13 C DA 13 1_555 C O4 DT 7 D DT 20 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? # _chem_comp.formula 'C10 H15 N2 O8 P' _chem_comp.formula_weight 322.208 _chem_comp.id TMP _chem_comp.mon_nstd_flag . _chem_comp.name "THYMIDINE-5'-PHOSPHATE" _chem_comp.type non-polymer _chem_comp.pdbx_synonyms ? # 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 P O1P TMP doub 497 n n P O2P TMP sing 498 n n P O3P TMP sing 499 n n P O5' TMP sing 500 n n O2P HOP2 TMP sing 501 n n O3P HOP3 TMP sing 502 n n O5' C5' TMP sing 503 n n C5' C4' TMP sing 504 n n C5' "H5'1" TMP sing 505 n n C5' "H5'2" TMP sing 506 n n C4' O4' TMP sing 507 n n C4' C3' TMP sing 508 n n C4' H4' TMP sing 509 n n O4' C1' TMP sing 510 n n C3' O3' TMP sing 511 n n C3' C2' TMP sing 512 n n C3' H3' TMP sing 513 n n O3' HO3' TMP sing 514 n n C2' C1' TMP sing 515 n n C2' "H2'1" TMP sing 516 n n C2' "H2'2" TMP sing 517 n n C1' N1 TMP sing 518 n n C1' H1' TMP sing 519 n n N1 C2 TMP sing 520 n n N1 C6 TMP sing 521 n n C2 O2 TMP doub 522 n n C2 N3 TMP sing 523 n n N3 C4 TMP sing 524 n n N3 HN3 TMP sing 525 n n C4 O4 TMP doub 526 n n C4 C5 TMP sing 527 n n C5 C5M TMP sing 528 n n C5 C6 TMP doub 529 n n C5M H51 TMP sing 530 n n C5M H52 TMP sing 531 n n C5M H53 TMP sing 532 n n C6 H6 TMP sing 533 n n # _atom_sites.entry_id 4E0Y _atom_sites.fract_transf_matrix[1][1] 0.008548 _atom_sites.fract_transf_matrix[1][2] 0 _atom_sites.fract_transf_matrix[1][3] 0.003527 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.008372 _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] 0.019004 _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 D 4 GOL C 1 101 1 GOL GOL . E 5 TMP D 1 101 1 TMP DT . F 6 HOH A 1 501 1 HOH HOH . F 6 HOH A 2 502 3 HOH HOH . F 6 HOH A 3 503 4 HOH HOH . F 6 HOH A 4 504 6 HOH HOH . F 6 HOH A 5 505 11 HOH HOH . F 6 HOH A 6 506 12 HOH HOH . F 6 HOH A 7 507 13 HOH HOH . F 6 HOH A 8 508 14 HOH HOH . F 6 HOH A 9 509 15 HOH HOH . F 6 HOH A 10 510 16 HOH HOH . F 6 HOH A 11 511 17 HOH HOH . F 6 HOH A 12 512 18 HOH HOH . F 6 HOH A 13 513 19 HOH HOH . F 6 HOH A 14 514 21 HOH HOH . F 6 HOH A 15 515 23 HOH HOH . F 6 HOH A 16 516 24 HOH HOH . F 6 HOH A 17 517 26 HOH HOH . F 6 HOH A 18 518 27 HOH HOH . F 6 HOH A 19 519 28 HOH HOH . F 6 HOH A 20 520 29 HOH HOH . F 6 HOH A 21 521 30 HOH HOH . F 6 HOH A 22 522 31 HOH HOH . F 6 HOH A 23 523 32 HOH HOH . F 6 HOH A 24 524 33 HOH HOH . F 6 HOH A 25 525 34 HOH HOH . F 6 HOH A 26 526 38 HOH HOH . F 6 HOH A 27 527 39 HOH HOH . F 6 HOH A 28 528 40 HOH HOH . F 6 HOH A 29 529 41 HOH HOH . F 6 HOH A 30 530 42 HOH HOH . F 6 HOH A 31 531 43 HOH HOH . F 6 HOH A 32 532 44 HOH HOH . F 6 HOH A 33 533 46 HOH HOH . F 6 HOH A 34 534 48 HOH HOH . F 6 HOH A 35 535 49 HOH HOH . F 6 HOH A 36 536 50 HOH HOH . F 6 HOH A 37 537 53 HOH HOH . F 6 HOH A 38 538 54 HOH HOH . F 6 HOH A 39 539 55 HOH HOH . F 6 HOH A 40 540 56 HOH HOH . F 6 HOH A 41 541 57 HOH HOH . F 6 HOH A 42 542 58 HOH HOH . F 6 HOH A 43 543 59 HOH HOH . F 6 HOH A 44 544 60 HOH HOH . F 6 HOH A 45 545 61 HOH HOH . F 6 HOH A 46 546 62 HOH HOH . F 6 HOH A 47 547 63 HOH HOH . F 6 HOH A 48 548 67 HOH HOH . F 6 HOH A 49 549 69 HOH HOH . F 6 HOH A 50 550 70 HOH HOH . F 6 HOH A 51 551 71 HOH HOH . F 6 HOH A 52 552 73 HOH HOH . F 6 HOH A 53 553 82 HOH HOH . F 6 HOH A 54 554 83 HOH HOH . F 6 HOH A 55 555 87 HOH HOH . F 6 HOH A 56 556 89 HOH HOH . F 6 HOH A 57 557 91 HOH HOH . F 6 HOH A 58 558 92 HOH HOH . F 6 HOH A 59 559 95 HOH HOH . F 6 HOH A 60 560 97 HOH HOH . F 6 HOH A 61 561 98 HOH HOH . F 6 HOH A 62 562 100 HOH HOH . F 6 HOH A 63 563 101 HOH HOH . F 6 HOH A 64 564 102 HOH HOH . F 6 HOH A 65 565 104 HOH HOH . F 6 HOH A 66 566 105 HOH HOH . F 6 HOH A 67 567 106 HOH HOH . F 6 HOH A 68 568 108 HOH HOH . F 6 HOH A 69 569 109 HOH HOH . F 6 HOH A 70 570 110 HOH HOH . F 6 HOH A 71 571 111 HOH HOH . F 6 HOH A 72 572 112 HOH HOH . F 6 HOH A 73 573 114 HOH HOH . F 6 HOH A 74 574 115 HOH HOH . F 6 HOH A 75 575 117 HOH HOH . F 6 HOH A 76 576 118 HOH HOH . F 6 HOH A 77 577 121 HOH HOH . F 6 HOH A 78 578 124 HOH HOH . F 6 HOH A 79 579 126 HOH HOH . F 6 HOH A 80 580 130 HOH HOH . F 6 HOH A 81 581 132 HOH HOH . F 6 HOH A 82 582 133 HOH HOH . F 6 HOH A 83 583 136 HOH HOH . F 6 HOH A 84 584 138 HOH HOH . F 6 HOH A 85 585 140 HOH HOH . F 6 HOH A 86 586 141 HOH HOH . F 6 HOH A 87 587 142 HOH HOH . F 6 HOH A 88 588 143 HOH HOH . F 6 HOH A 89 589 145 HOH HOH . F 6 HOH A 90 590 147 HOH HOH . G 6 HOH C 1 201 9 HOH HOH . G 6 HOH C 2 202 10 HOH HOH . G 6 HOH C 3 203 25 HOH HOH . G 6 HOH C 4 204 65 HOH HOH . G 6 HOH C 5 205 66 HOH HOH . G 6 HOH C 6 206 68 HOH HOH . G 6 HOH C 7 207 75 HOH HOH . G 6 HOH C 8 208 76 HOH HOH . G 6 HOH C 9 209 77 HOH HOH . G 6 HOH C 10 210 79 HOH HOH . G 6 HOH C 11 211 94 HOH HOH . G 6 HOH C 12 212 96 HOH HOH . G 6 HOH C 13 213 103 HOH HOH . G 6 HOH C 14 214 116 HOH HOH . G 6 HOH C 15 215 119 HOH HOH . G 6 HOH C 16 216 120 HOH HOH . G 6 HOH C 17 217 134 HOH HOH . H 6 HOH D 1 201 7 HOH HOH . H 6 HOH D 2 202 8 HOH HOH . H 6 HOH D 3 203 22 HOH HOH . H 6 HOH D 4 204 35 HOH HOH . H 6 HOH D 5 205 36 HOH HOH . H 6 HOH D 6 206 37 HOH HOH . H 6 HOH D 7 207 51 HOH HOH . H 6 HOH D 8 208 52 HOH HOH . H 6 HOH D 9 209 64 HOH HOH . H 6 HOH D 10 210 72 HOH HOH . H 6 HOH D 11 211 74 HOH HOH . H 6 HOH D 12 212 78 HOH HOH . H 6 HOH D 13 213 84 HOH HOH . H 6 HOH D 14 214 85 HOH HOH . H 6 HOH D 15 215 86 HOH HOH . H 6 HOH D 16 216 88 HOH HOH . H 6 HOH D 17 217 90 HOH HOH . H 6 HOH D 18 218 93 HOH HOH . H 6 HOH D 19 219 99 HOH HOH . H 6 HOH D 20 220 107 HOH HOH . H 6 HOH D 21 221 113 HOH HOH . H 6 HOH D 22 222 122 HOH HOH . H 6 HOH D 23 223 125 HOH HOH . H 6 HOH D 24 224 128 HOH HOH . H 6 HOH D 25 225 129 HOH HOH . H 6 HOH D 26 226 131 HOH HOH . H 6 HOH D 27 227 137 HOH HOH . H 6 HOH D 28 228 148 HOH HOH . H 6 HOH D 29 229 149 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 O5' TMP . . . E 5 10.521 -22.217 0.815 1 114.8 ? O5' TMP 101 D 1 HETATM 2 C C5' TMP . . . E 5 10.423 -20.958 1.474 1 113.91 ? C5' TMP 101 D 1 HETATM 3 C C4' TMP . . . E 5 10.141 -19.87 0.456 1 120.16 ? C4' TMP 101 D 1 HETATM 4 O O4' TMP . . . E 5 9.748 -18.631 1.089 1 124.5 ? O4' TMP 101 D 1 HETATM 5 C C3' TMP . . . E 5 11.307 -19.469 -0.443 1 115.09 ? C3' TMP 101 D 1 HETATM 6 O O3' TMP . . . E 5 11.195 -20.144 -1.688 1 99.1 ? O3' TMP 101 D 1 HETATM 7 C C2' TMP . . . E 5 11.143 -17.954 -0.609 1 121.12 ? C2' TMP 101 D 1 HETATM 8 C C1' TMP . . . E 5 9.774 -17.712 0.021 1 127.37 ? C1' TMP 101 D 1 HETATM 9 N N1 TMP . . . E 5 9.498 -16.297 0.453 1 133.57 ? N1 TMP 101 D 1 HETATM 10 C C2 TMP . . . E 5 8.789 -16.022 1.604 1 133.58 ? C2 TMP 101 D 1 HETATM 11 O O2 TMP . . . E 5 8.346 -16.861 2.365 1 119.86 ? O2 TMP 101 D 1 HETATM 12 N N3 TMP . . . E 5 8.611 -14.687 1.851 1 141.17 ? N3 TMP 101 D 1 HETATM 13 C C4 TMP . . . E 5 9.046 -13.619 1.092 1 140.06 ? C4 TMP 101 D 1 HETATM 14 O O4 TMP . . . E 5 8.828 -12.456 1.411 1 134.91 ? O4 TMP 101 D 1 HETATM 15 C C5 TMP . . . E 5 9.773 -13.971 -0.096 1 136.58 ? C5 TMP 101 D 1 HETATM 16 C C5M TMP . . . E 5 10.299 -12.898 -1.001 1 128.31 ? C5M TMP 101 D 1 HETATM 17 C C6 TMP . . . E 5 9.955 -15.271 -0.353 1 135.46 ? C6 TMP 101 D 1 # _model_server_stats.io_time_ms 74 _model_server_stats.parse_time_ms 8 _model_server_stats.create_model_time_ms 9 _model_server_stats.query_time_ms 312 _model_server_stats.encode_time_ms 5 _model_server_stats.element_count 17 #