data_6EJJ # _model_server_result.job_id twoIc2xj4wp8cPGnWxesaQ _model_server_result.datetime_utc '2024-11-04 18:18:38' _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 6ejj # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"J","auth_seq_id":401}' # _entry.id 6EJJ # _exptl.entry_id 6EJJ _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 404.161 _entity.id 3 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description "URIDINE-5'-DIPHOSPHATE" _entity.pdbx_number_of_molecules 2 _entity.pdbx_parent_entity_id . _entity.pdbx_mutation ? _entity.pdbx_fragment ? _entity.pdbx_ec ? # _cell.angle_alpha 90 _cell.angle_beta 90.28 _cell.angle_gamma 90 _cell.entry_id 6EJJ _cell.length_a 60.51 _cell.length_b 125.78 _cell.length_c 71.01 _cell.Z_PDB 4 _cell.pdbx_unique_axis ? # _symmetry.entry_id 6EJJ _symmetry.cell_setting ? _symmetry.Int_Tables_number 4 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 1 21 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 ? monomeric 1 author_defined_assembly 1 ? monomeric 1 author_defined_assembly 2 # loop_ _pdbx_struct_assembly_gen.asym_id_list _pdbx_struct_assembly_gen.assembly_id _pdbx_struct_assembly_gen.oper_expression A,C,E,F,G,H,I,N 1 1 B,D,J,K,L,M,O 2 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 ? 3 E N N ? 3 J N N # _pdbx_entity_branch.entity_id 2 _pdbx_entity_branch.type oligosaccharide # loop_ _pdbx_entity_branch_link.link_id _pdbx_entity_branch_link.details _pdbx_entity_branch_link.entity_id _pdbx_entity_branch_link.entity_branch_list_num_1 _pdbx_entity_branch_link.entity_branch_list_num_2 _pdbx_entity_branch_link.comp_id_1 _pdbx_entity_branch_link.comp_id_2 _pdbx_entity_branch_link.atom_id_1 _pdbx_entity_branch_link.leaving_atom_id_1 _pdbx_entity_branch_link.atom_stereo_config_1 _pdbx_entity_branch_link.atom_id_2 _pdbx_entity_branch_link.leaving_atom_id_2 _pdbx_entity_branch_link.atom_stereo_config_2 _pdbx_entity_branch_link.value_order 1 ? 2 2 1 A2G NDG C1 O1 . O3 HO3 . sing 2 ? 2 3 2 A2G A2G C1 O1 . O4 HO4 . sing # loop_ _pdbx_branch_scheme.entity_id _pdbx_branch_scheme.hetero _pdbx_branch_scheme.asym_id _pdbx_branch_scheme.mon_id _pdbx_branch_scheme.num _pdbx_branch_scheme.pdb_asym_id _pdbx_branch_scheme.pdb_seq_num _pdbx_branch_scheme.pdb_mon_id _pdbx_branch_scheme.auth_asym_id _pdbx_branch_scheme.auth_seq_num _pdbx_branch_scheme.auth_mon_id 2 n C NDG 1 C 1 NDG C 1 LLO 2 n C A2G 2 C 2 A2G C 1 LLO 2 n C A2G 3 C 3 A2G C 1 LLO 2 n D NDG 1 D 1 NDG C 2 LLO 2 n D A2G 2 D 2 A2G C 2 LLO 2 n D A2G 3 D 3 A2G C 2 LLO # 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 I O34 BUE . A BUE 408 1_555 C C1 NDG . C NDG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.419 ? covale ? covale2 M O36 BUE . B BUE 407 1_555 D C1 NDG . D NDG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.419 ? covale ? covale3 C O3 NDG . C NDG 1 1_555 C C1 A2G . C A2G 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.378 ? covale ? covale4 C O4 A2G . C A2G 2 1_555 C C1 A2G . C A2G 3 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.413 ? covale ? covale5 D O3 NDG . D NDG 1 1_555 D C1 A2G . D A2G 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.387 ? covale ? covale6 D O4 A2G . D A2G 2 1_555 D C1 A2G . D A2G 3 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.412 ? metalc ? metalc1 A OE2 GLU 267 A GLU 267 1_555 G NA NA . A NA 403 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.693 ? metalc ? metalc2 F NA NA . A NA 402 1_555 I O36 BUE . A BUE 408 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.605 ? metalc ? metalc3 F NA NA . A NA 402 1_555 I O37 BUE . A BUE 408 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.633 ? metalc ? metalc4 F NA NA . A NA 402 1_555 N O HOH . A HOH 513 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.407 ? metalc ? metalc5 B O ILE 189 B ILE 189 1_555 K NA NA . B NA 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 3.07 ? metalc ? metalc6 J O2A UDP . B UDP 401 1_555 K NA NA . B NA 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.399 ? metalc ? metalc7 L NA NA . B NA 403 1_555 M O34 BUE . B BUE 407 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.803 ? metalc ? metalc8 L NA NA . B NA 403 1_555 M O37 BUE . B BUE 407 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.438 ? # _chem_comp.formula 'C9 H14 N2 O12 P2' _chem_comp.formula_weight 404.161 _chem_comp.id UDP _chem_comp.mon_nstd_flag . _chem_comp.name "URIDINE-5'-DIPHOSPHATE" _chem_comp.type 'rna linking' _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 N1 C2 UDP sing 482 n n N1 C6 UDP sing 483 n n N1 C1' UDP sing 484 n n C2 N3 UDP sing 485 n n C2 O2 UDP doub 486 n n N3 C4 UDP sing 487 n n N3 HN3 UDP sing 488 n n C4 C5 UDP sing 489 n n C4 O4 UDP doub 490 n n C5 C6 UDP doub 491 n n C5 H5 UDP sing 492 n n C6 H6 UDP sing 493 n n C1' C2' UDP sing 494 n n C1' O4' UDP sing 495 n n C1' H1' UDP sing 496 n n C2' O2' UDP sing 497 n n C2' C3' UDP sing 498 n n C2' H2' UDP sing 499 n n O2' HO2' UDP sing 500 n n C3' C4' UDP sing 501 n n C3' O3' UDP sing 502 n n C3' H3' UDP sing 503 n n C4' O4' UDP sing 504 n n C4' C5' UDP sing 505 n n C4' H4' UDP sing 506 n n O3' HO3' UDP sing 507 n n C5' O5' UDP sing 508 n n C5' "H5'1" UDP sing 509 n n C5' "H5'2" UDP sing 510 n n O5' PA UDP sing 511 n n PA O1A UDP doub 512 n n PA O2A UDP sing 513 n n PA O3A UDP sing 514 n n O2A HOA2 UDP sing 515 n n O3A PB UDP sing 516 n n PB O1B UDP doub 517 n n PB O2B UDP sing 518 n n PB O3B UDP sing 519 n n O2B HOB2 UDP sing 520 n n O3B HOB3 UDP sing 521 n n # _atom_sites.entry_id 6EJJ _atom_sites.fract_transf_matrix[1][1] 0.016526 _atom_sites.fract_transf_matrix[1][2] 0 _atom_sites.fract_transf_matrix[1][3] 0.000082 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.00795 _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] 0.014083 _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 E 3 UDP A 1 401 1 UDP LIG . F 4 NA A 1 402 3 NA NA . G 4 NA A 1 403 6 NA NA . H 5 CL A 1 404 1 CL CL . I 6 BUE A 1 408 1 BUE LLO . J 3 UDP B 1 401 2 UDP LIG . K 4 NA B 1 402 4 NA NA . L 4 NA B 1 403 5 NA NA . M 6 BUE B 1 407 2 BUE LLO . N 7 HOH A 1 501 18 HOH HOH . N 7 HOH A 2 502 54 HOH HOH . N 7 HOH A 3 503 72 HOH HOH . N 7 HOH A 4 504 67 HOH HOH . N 7 HOH A 5 505 4 HOH HOH . N 7 HOH A 6 506 21 HOH HOH . N 7 HOH A 7 507 16 HOH HOH . N 7 HOH A 8 508 66 HOH HOH . N 7 HOH A 9 509 70 HOH HOH . N 7 HOH A 10 510 69 HOH HOH . N 7 HOH A 11 511 40 HOH HOH . N 7 HOH A 12 512 57 HOH HOH . N 7 HOH A 13 513 73 HOH HOH . N 7 HOH A 14 514 48 HOH HOH . N 7 HOH A 15 515 56 HOH HOH . N 7 HOH A 16 516 63 HOH HOH . N 7 HOH A 17 517 51 HOH HOH . N 7 HOH A 18 518 19 HOH HOH . N 7 HOH A 19 519 68 HOH HOH . N 7 HOH A 20 520 3 HOH HOH . N 7 HOH A 21 521 5 HOH HOH . N 7 HOH A 22 522 7 HOH HOH . N 7 HOH A 23 523 6 HOH HOH . N 7 HOH A 24 524 71 HOH HOH . N 7 HOH A 25 525 65 HOH HOH . O 7 HOH B 1 501 38 HOH HOH . O 7 HOH B 2 502 53 HOH HOH . O 7 HOH B 3 503 37 HOH HOH . O 7 HOH B 4 504 62 HOH HOH . O 7 HOH B 5 505 29 HOH HOH . O 7 HOH B 6 506 35 HOH HOH . O 7 HOH B 7 507 2 HOH HOH . O 7 HOH B 8 508 30 HOH HOH . O 7 HOH B 9 509 23 HOH HOH . O 7 HOH B 10 510 20 HOH HOH . O 7 HOH B 11 511 17 HOH HOH . O 7 HOH B 12 512 12 HOH HOH . O 7 HOH B 13 513 75 HOH HOH . O 7 HOH B 14 514 52 HOH HOH . O 7 HOH B 15 515 1 HOH HOH . O 7 HOH B 16 516 13 HOH HOH . O 7 HOH B 17 517 43 HOH HOH . O 7 HOH B 18 518 22 HOH HOH . O 7 HOH B 19 519 42 HOH HOH . O 7 HOH B 20 520 74 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 N N1 UDP . . . J 3 84.651 42.327 22.174 1 48.76 ? N1 UDP 401 B 1 HETATM 2 C C2 UDP . . . J 3 84.399 41.721 23.394 1 48.62 ? C2 UDP 401 B 1 HETATM 3 N N3 UDP . . . J 3 85.238 40.731 23.84 1 48.84 ? N3 UDP 401 B 1 HETATM 4 C C4 UDP . . . J 3 86.309 40.348 23.086 1 49.18 ? C4 UDP 401 B 1 HETATM 5 C C5 UDP . . . J 3 86.557 40.952 21.873 1 49.33 ? C5 UDP 401 B 1 HETATM 6 C C6 UDP . . . J 3 85.717 41.944 21.424 1 49.12 ? C6 UDP 401 B 1 HETATM 7 O O2 UDP . . . J 3 83.429 42.063 24.075 1 48.35 ? O2 UDP 401 B 1 HETATM 8 O O4 UDP . . . J 3 87.059 39.468 23.481 1 49.39 ? O4 UDP 401 B 1 HETATM 9 C C1' UDP . . . J 3 83.798 43.345 21.689 1 48.6 ? C1' UDP 401 B 1 HETATM 10 C C2' UDP . . . J 3 84.46 44.662 21.796 1 48.68 ? C2' UDP 401 B 1 HETATM 11 O O2' UDP . . . J 3 84.254 45.207 23.117 1 48.45 ? O2' UDP 401 B 1 HETATM 12 C C3' UDP . . . J 3 83.763 45.464 20.8 1 48.66 ? C3' UDP 401 B 1 HETATM 13 C C4' UDP . . . J 3 83.413 44.534 19.711 1 48.79 ? C4' UDP 401 B 1 HETATM 14 O O4' UDP . . . J 3 83.545 43.174 20.268 1 48.77 ? O4' UDP 401 B 1 HETATM 15 O O3' UDP . . . J 3 82.548 45.984 21.389 1 48.3 ? O3' UDP 401 B 1 HETATM 16 C C5' UDP . . . J 3 84.326 44.71 18.562 1 49.2 ? C5' UDP 401 B 1 HETATM 17 O O5' UDP . . . J 3 83.695 45.481 17.579 1 49.23 ? O5' UDP 401 B 1 HETATM 18 P PA UDP . . . J 3 84.527 46.393 16.609 1 49.61 ? PA UDP 401 B 1 HETATM 19 O O1A UDP . . . J 3 84.062 47.809 16.746 1 49.47 ? O1A UDP 401 B 1 HETATM 20 O O2A UDP . . . J 3 86.004 46.335 16.954 1 49.95 ? O2A UDP 401 B 1 HETATM 21 O O3A UDP . . . J 3 84.293 45.975 15.081 1 49.87 ? O3A UDP 401 B 1 HETATM 22 P PB UDP . . . J 3 84.403 44.48 14.535 1 50.07 ? PB UDP 401 B 1 HETATM 23 O O1B UDP . . . J 3 84.516 44.524 13.02 1 50.45 ? O1B UDP 401 B 1 HETATM 24 O O2B UDP . . . J 3 85.625 43.82 15.13 1 50.28 ? O2B UDP 401 B 1 HETATM 25 O O3B UDP . . . J 3 83.192 43.676 14.919 1 49.74 ? O3B UDP 401 B 1 # _model_server_stats.io_time_ms 63 _model_server_stats.parse_time_ms 12 _model_server_stats.create_model_time_ms 10 _model_server_stats.query_time_ms 284 _model_server_stats.encode_time_ms 7 _model_server_stats.element_count 25 #