data_1SLH # _model_server_result.job_id YOcFvh64qUPw3Ritmeb1-w _model_server_result.datetime_utc '2024-11-23 20:34:42' _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 1slh # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"E","auth_seq_id":2170}' # _entry.id 1SLH # _exptl.entry_id 1SLH _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 388.162 _entity.id 3 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description "DEOXYURIDINE-5'-DIPHOSPHATE" _entity.pdbx_number_of_molecules 3 _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 120 _cell.entry_id 1SLH _cell.length_a 108.273 _cell.length_b 108.273 _cell.length_c 100.792 _cell.Z_PDB 18 _cell.pdbx_unique_axis ? # _symmetry.entry_id 1SLH _symmetry.cell_setting ? _symmetry.Int_Tables_number 152 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 31 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 trimeric 3 author_and_software_defined_assembly 1 PISA hexameric 6 software_defined_assembly 2 # loop_ _pdbx_struct_assembly_gen.asym_id_list _pdbx_struct_assembly_gen.assembly_id _pdbx_struct_assembly_gen.oper_expression A,B,C,D,E,F,G,H,I,J,K,L,M,N 1 1 A,B,C,D,E,F,G,H,I,J,K,L,M,N 2 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' 5_555 x-y,-y,-z+2/3 1 0 0 0 -1 0 0 0 -1 0 0 67.194667 # 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 I N N ? 3 K 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 E O2B DUD . A DUD 2170 1_555 J MG MG . C MG 2171 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.43 ? metalc ? metalc2 E O1A DUD . A DUD 2170 1_555 J MG MG . C MG 2171 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.392 ? metalc ? metalc3 D MG MG . A MG 3171 1_555 M O HOH . B HOH 542 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.731 ? metalc ? metalc4 D MG MG . A MG 3171 1_555 M O HOH . B HOH 543 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.841 ? metalc ? metalc5 D MG MG . A MG 3171 1_555 I O1A DUD . B DUD 3170 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.329 ? metalc ? metalc6 D MG MG . A MG 3171 1_555 I O2B DUD . B DUD 3170 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.244 ? metalc ? metalc7 H MG MG . B MG 1171 1_555 K O3A DUD . C DUD 1170 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 3.067 ? metalc ? metalc8 H MG MG . B MG 1171 1_555 K O1B DUD . C DUD 1170 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.54 ? metalc ? metalc9 H MG MG . B MG 1171 1_555 K O1A DUD . C DUD 1170 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 3.034 ? # _chem_comp.formula 'C9 H14 N2 O11 P2' _chem_comp.formula_weight 388.162 _chem_comp.id DUD _chem_comp.mon_nstd_flag . _chem_comp.name "DEOXYURIDINE-5'-DIPHOSPHATE" _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 N1 C2 DUD sing 70 n n N1 C6 DUD sing 71 n n N1 C1' DUD sing 72 n n C2 N3 DUD sing 73 n n C2 O2 DUD doub 74 n n N3 C4 DUD sing 75 n n N3 HN3 DUD sing 76 n n C4 C5 DUD sing 77 n n C4 O4 DUD doub 78 n n C5 C6 DUD doub 79 n n C5 H5 DUD sing 80 n n C6 H6 DUD sing 81 n n C1' C2' DUD sing 82 n n C1' O4' DUD sing 83 n n C1' H1' DUD sing 84 n n C2' C3' DUD sing 85 n n C2' "H2'1" DUD sing 86 n n C2' "H2'2" DUD sing 87 n n C3' C4' DUD sing 88 n n C3' O3' DUD sing 89 n n C3' H3' DUD sing 90 n n C4' O4' DUD sing 91 n n C4' C5' DUD sing 92 n n C4' H4' DUD sing 93 n n O3' HO3' DUD sing 94 n n C5' O5' DUD sing 95 n n C5' "H5'1" DUD sing 96 n n C5' "H5'2" DUD sing 97 n n O5' PA DUD sing 98 n n PA O1A DUD doub 99 n n PA O2A DUD sing 100 n n PA O3A DUD sing 101 n n O2A HOA2 DUD sing 102 n n O3A PB DUD sing 103 n n PB O1B DUD doub 104 n n PB O2B DUD sing 105 n n PB O3B DUD sing 106 n n O2B HOB2 DUD sing 107 n n O3B HOB3 DUD sing 108 n n # _atom_sites.entry_id 1SLH _atom_sites.fract_transf_matrix[1][1] 0.009236 _atom_sites.fract_transf_matrix[1][2] 0.005332 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.010665 _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] 0.009921 _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 2 MG A 1 3171 503 MG MG2 . E 3 DUD A 1 2170 170 DUD DUD . F 4 TRS A 1 504 504 TRS TRS . G 4 TRS A 1 505 505 TRS TRS . H 2 MG B 1 1171 501 MG MG2 . I 3 DUD B 1 3170 170 DUD DUD . J 2 MG C 1 2171 502 MG MG2 . K 3 DUD C 1 1170 170 DUD DUD . L 5 HOH A 1 506 506 HOH HOH . L 5 HOH A 2 507 507 HOH HOH . L 5 HOH A 3 509 509 HOH HOH . L 5 HOH A 4 514 514 HOH HOH . L 5 HOH A 5 515 515 HOH HOH . L 5 HOH A 6 516 516 HOH HOH . L 5 HOH A 7 517 517 HOH HOH . L 5 HOH A 8 524 524 HOH HOH . L 5 HOH A 9 526 526 HOH HOH . L 5 HOH A 10 528 528 HOH HOH . L 5 HOH A 11 531 531 HOH HOH . L 5 HOH A 12 533 533 HOH HOH . L 5 HOH A 13 534 534 HOH HOH . L 5 HOH A 14 541 541 HOH HOH . L 5 HOH A 15 544 544 HOH HOH . L 5 HOH A 16 545 545 HOH HOH . L 5 HOH A 17 548 548 HOH HOH . L 5 HOH A 18 549 549 HOH HOH . M 5 HOH B 1 512 512 HOH HOH . M 5 HOH B 2 520 520 HOH HOH . M 5 HOH B 3 522 522 HOH HOH . M 5 HOH B 4 523 523 HOH HOH . M 5 HOH B 5 530 530 HOH HOH . M 5 HOH B 6 535 535 HOH HOH . M 5 HOH B 7 536 536 HOH HOH . M 5 HOH B 8 540 540 HOH HOH . M 5 HOH B 9 542 542 HOH HOH . M 5 HOH B 10 543 543 HOH HOH . M 5 HOH B 11 547 547 HOH HOH . N 5 HOH C 1 508 508 HOH HOH . N 5 HOH C 2 510 510 HOH HOH . N 5 HOH C 3 513 513 HOH HOH . N 5 HOH C 4 519 519 HOH HOH . N 5 HOH C 5 521 521 HOH HOH . N 5 HOH C 6 525 525 HOH HOH . N 5 HOH C 7 527 527 HOH HOH . N 5 HOH C 8 529 529 HOH HOH . N 5 HOH C 9 537 537 HOH HOH . N 5 HOH C 10 539 539 HOH HOH . N 5 HOH C 11 550 550 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 DUD . . . E 3 75.583 12.615 21.587 1 44.58 ? N1 DUD 2170 A 1 HETATM 2 C C2 DUD . . . E 3 75.545 13.736 22.439 1 43.6 ? C2 DUD 2170 A 1 HETATM 3 N N3 DUD . . . E 3 74.572 14.677 22.097 1 44.92 ? N3 DUD 2170 A 1 HETATM 4 C C4 DUD . . . E 3 73.667 14.611 20.999 1 46.31 ? C4 DUD 2170 A 1 HETATM 5 C C5 DUD . . . E 3 73.778 13.436 20.174 1 45.39 ? C5 DUD 2170 A 1 HETATM 6 C C6 DUD . . . E 3 74.701 12.53 20.489 1 44.81 ? C6 DUD 2170 A 1 HETATM 7 O O2 DUD . . . E 3 76.278 13.897 23.419 1 41.86 ? O2 DUD 2170 A 1 HETATM 8 O O4 DUD . . . E 3 72.854 15.488 20.788 1 48.72 ? O4 DUD 2170 A 1 HETATM 9 C C1' DUD . . . E 3 76.571 11.531 21.837 1 45.98 ? C1' DUD 2170 A 1 HETATM 10 C C2' DUD . . . E 3 75.924 10.439 22.655 1 47.94 ? C2' DUD 2170 A 1 HETATM 11 C C3' DUD . . . E 3 75.556 9.321 21.691 1 49.18 ? C3' DUD 2170 A 1 HETATM 12 C C4' DUD . . . E 3 76.587 9.542 20.657 1 49.88 ? C4' DUD 2170 A 1 HETATM 13 O O4' DUD . . . E 3 76.991 10.921 20.626 1 47.21 ? O4' DUD 2170 A 1 HETATM 14 O O3' DUD . . . E 3 75.678 8.004 22.283 1 50.43 ? O3' DUD 2170 A 1 HETATM 15 C C5' DUD . . . E 3 75.908 9.18 19.371 1 53.8 ? C5' DUD 2170 A 1 HETATM 16 O O5' DUD . . . E 3 76.7 9.385 18.266 1 57.44 ? O5' DUD 2170 A 1 HETATM 17 P PA DUD . . . E 3 75.915 9.544 16.833 1 60.61 ? PA DUD 2170 A 1 HETATM 18 O O1A DUD . . . E 3 75.739 8.195 16.167 1 61.64 ? O1A DUD 2170 A 1 HETATM 19 O O2A DUD . . . E 3 74.706 10.504 16.913 1 57.81 ? O2A DUD 2170 A 1 HETATM 20 O O3A DUD . . . E 3 77.192 10.285 16.09 1 61.95 ? O3A DUD 2170 A 1 HETATM 21 P PB DUD . . . E 3 78.2 9.955 14.889 1 63.35 ? PB DUD 2170 A 1 HETATM 22 O O1B DUD . . . E 3 78.084 10.999 13.854 1 62.07 ? O1B DUD 2170 A 1 HETATM 23 O O2B DUD . . . E 3 77.809 8.647 14.361 1 63.78 ? O2B DUD 2170 A 1 HETATM 24 O O3B DUD . . . E 3 79.536 9.977 15.568 1 62.45 ? O3B DUD 2170 A 1 # _model_server_stats.io_time_ms 10 _model_server_stats.parse_time_ms 7 _model_server_stats.create_model_time_ms 3 _model_server_stats.query_time_ms 220 _model_server_stats.encode_time_ms 3 _model_server_stats.element_count 24 #