data_8GKN # _model_server_result.job_id HVvuxCGtYXuAsuuy7EPqCg _model_server_result.datetime_utc '2024-11-19 13:31:43' _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 8gkn # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"E","auth_seq_id":501}' # _entry.id 8GKN # _exptl.entry_id 8GKN _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 404.161 _entity.id 2 _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 _cell.angle_gamma 90 _cell.entry_id 8GKN _cell.length_a 89.728 _cell.length_b 167.566 _cell.length_c 63.108 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 8GKN _symmetry.cell_setting ? _symmetry.Int_Tables_number 18 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 21 21 2' # 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,D,G 1 1 B,E,F,H 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 ? 2 C N N ? 2 E N N # _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 392 n n N1 C6 UDP sing 393 n n N1 C1' UDP sing 394 n n C2 N3 UDP sing 395 n n C2 O2 UDP doub 396 n n N3 C4 UDP sing 397 n n N3 HN3 UDP sing 398 n n C4 C5 UDP sing 399 n n C4 O4 UDP doub 400 n n C5 C6 UDP doub 401 n n C5 H5 UDP sing 402 n n C6 H6 UDP sing 403 n n C1' C2' UDP sing 404 n n C1' O4' UDP sing 405 n n C1' H1' UDP sing 406 n n C2' O2' UDP sing 407 n n C2' C3' UDP sing 408 n n C2' H2' UDP sing 409 n n O2' HO2' UDP sing 410 n n C3' C4' UDP sing 411 n n C3' O3' UDP sing 412 n n C3' H3' UDP sing 413 n n C4' O4' UDP sing 414 n n C4' C5' UDP sing 415 n n C4' H4' UDP sing 416 n n O3' HO3' UDP sing 417 n n C5' O5' UDP sing 418 n n C5' "H5'1" UDP sing 419 n n C5' "H5'2" UDP sing 420 n n O5' PA UDP sing 421 n n PA O1A UDP doub 422 n n PA O2A UDP sing 423 n n PA O3A UDP sing 424 n n O2A HOA2 UDP sing 425 n n O3A PB UDP sing 426 n n PB O1B UDP doub 427 n n PB O2B UDP sing 428 n n PB O3B UDP sing 429 n n O2B HOB2 UDP sing 430 n n O3B HOB3 UDP sing 431 n n # _atom_sites.entry_id 8GKN _atom_sites.fract_transf_matrix[1][1] 0.011145 _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] 0.005968 _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] 0.015846 _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 C 2 UDP A 1 501 502 UDP UDP . D 3 NAR A 1 502 503 NAR NAR . E 2 UDP B 1 501 501 UDP UDP . F 3 NAR B 1 502 502 NAR NAR . G 4 HOH A 1 601 1 HOH HOH . G 4 HOH A 2 602 57 HOH HOH . G 4 HOH A 3 603 24 HOH HOH . G 4 HOH A 4 604 266 HOH HOH . G 4 HOH A 5 605 31 HOH HOH . G 4 HOH A 6 606 5 HOH HOH . G 4 HOH A 7 607 64 HOH HOH . G 4 HOH A 8 608 112 HOH HOH . G 4 HOH A 9 609 37 HOH HOH . G 4 HOH A 10 610 45 HOH HOH . G 4 HOH A 11 611 2 HOH HOH . G 4 HOH A 12 612 60 HOH HOH . G 4 HOH A 13 613 7 HOH HOH . G 4 HOH A 14 614 135 HOH HOH . G 4 HOH A 15 615 281 HOH HOH . G 4 HOH A 16 616 19 HOH HOH . G 4 HOH A 17 617 108 HOH HOH . G 4 HOH A 18 618 191 HOH HOH . G 4 HOH A 19 619 74 HOH HOH . G 4 HOH A 20 620 274 HOH HOH . G 4 HOH A 21 621 226 HOH HOH . G 4 HOH A 22 622 11 HOH HOH . G 4 HOH A 23 623 189 HOH HOH . G 4 HOH A 24 624 51 HOH HOH . G 4 HOH A 25 625 197 HOH HOH . G 4 HOH A 26 626 6 HOH HOH . G 4 HOH A 27 627 169 HOH HOH . G 4 HOH A 28 628 103 HOH HOH . G 4 HOH A 29 629 8 HOH HOH . G 4 HOH A 30 630 127 HOH HOH . G 4 HOH A 31 631 96 HOH HOH . G 4 HOH A 32 632 137 HOH HOH . G 4 HOH A 33 633 192 HOH HOH . G 4 HOH A 34 634 239 HOH HOH . G 4 HOH A 35 635 263 HOH HOH . G 4 HOH A 36 636 133 HOH HOH . G 4 HOH A 37 637 36 HOH HOH . G 4 HOH A 38 638 20 HOH HOH . G 4 HOH A 39 639 101 HOH HOH . G 4 HOH A 40 640 220 HOH HOH . G 4 HOH A 41 641 292 HOH HOH . G 4 HOH A 42 642 188 HOH HOH . G 4 HOH A 43 643 203 HOH HOH . G 4 HOH A 44 644 22 HOH HOH . G 4 HOH A 45 645 59 HOH HOH . G 4 HOH A 46 646 61 HOH HOH . G 4 HOH A 47 647 109 HOH HOH . G 4 HOH A 48 648 54 HOH HOH . G 4 HOH A 49 649 159 HOH HOH . G 4 HOH A 50 650 13 HOH HOH . G 4 HOH A 51 651 75 HOH HOH . G 4 HOH A 52 652 35 HOH HOH . G 4 HOH A 53 653 32 HOH HOH . G 4 HOH A 54 654 204 HOH HOH . G 4 HOH A 55 655 206 HOH HOH . G 4 HOH A 56 656 50 HOH HOH . G 4 HOH A 57 657 83 HOH HOH . G 4 HOH A 58 658 39 HOH HOH . G 4 HOH A 59 659 44 HOH HOH . G 4 HOH A 60 660 79 HOH HOH . G 4 HOH A 61 661 273 HOH HOH . G 4 HOH A 62 662 76 HOH HOH . G 4 HOH A 63 663 42 HOH HOH . G 4 HOH A 64 664 194 HOH HOH . G 4 HOH A 65 665 78 HOH HOH . G 4 HOH A 66 666 186 HOH HOH . G 4 HOH A 67 667 196 HOH HOH . G 4 HOH A 68 668 111 HOH HOH . G 4 HOH A 69 669 215 HOH HOH . G 4 HOH A 70 670 68 HOH HOH . G 4 HOH A 71 671 277 HOH HOH . G 4 HOH A 72 672 193 HOH HOH . G 4 HOH A 73 673 106 HOH HOH . G 4 HOH A 74 674 211 HOH HOH . G 4 HOH A 75 675 218 HOH HOH . G 4 HOH A 76 676 210 HOH HOH . G 4 HOH A 77 677 275 HOH HOH . G 4 HOH A 78 678 67 HOH HOH . G 4 HOH A 79 679 244 HOH HOH . G 4 HOH A 80 680 251 HOH HOH . G 4 HOH A 81 681 187 HOH HOH . G 4 HOH A 82 682 209 HOH HOH . G 4 HOH A 83 683 248 HOH HOH . G 4 HOH A 84 684 205 HOH HOH . G 4 HOH A 85 685 185 HOH HOH . G 4 HOH A 86 686 243 HOH HOH . G 4 HOH A 87 687 214 HOH HOH . H 4 HOH B 1 601 56 HOH HOH . H 4 HOH B 2 602 49 HOH HOH . H 4 HOH B 3 603 285 HOH HOH . H 4 HOH B 4 604 176 HOH HOH . H 4 HOH B 5 605 28 HOH HOH . H 4 HOH B 6 606 117 HOH HOH . H 4 HOH B 7 607 4 HOH HOH . H 4 HOH B 8 608 3 HOH HOH . H 4 HOH B 9 609 114 HOH HOH . H 4 HOH B 10 610 18 HOH HOH . H 4 HOH B 11 611 97 HOH HOH . H 4 HOH B 12 612 17 HOH HOH . H 4 HOH B 13 613 38 HOH HOH . H 4 HOH B 14 614 170 HOH HOH . H 4 HOH B 15 615 175 HOH HOH . H 4 HOH B 16 616 21 HOH HOH . H 4 HOH B 17 617 207 HOH HOH . H 4 HOH B 18 618 14 HOH HOH . H 4 HOH B 19 619 52 HOH HOH . H 4 HOH B 20 620 15 HOH HOH . H 4 HOH B 21 621 95 HOH HOH . H 4 HOH B 22 622 174 HOH HOH . H 4 HOH B 23 623 12 HOH HOH . H 4 HOH B 24 624 267 HOH HOH . H 4 HOH B 25 625 91 HOH HOH . H 4 HOH B 26 626 16 HOH HOH . H 4 HOH B 27 627 173 HOH HOH . H 4 HOH B 28 628 200 HOH HOH . H 4 HOH B 29 629 283 HOH HOH . H 4 HOH B 30 630 171 HOH HOH . H 4 HOH B 31 631 89 HOH HOH . H 4 HOH B 32 632 172 HOH HOH . H 4 HOH B 33 633 298 HOH HOH . H 4 HOH B 34 634 264 HOH HOH . H 4 HOH B 35 635 125 HOH HOH . H 4 HOH B 36 636 48 HOH HOH . H 4 HOH B 37 637 261 HOH HOH . H 4 HOH B 38 638 296 HOH HOH . H 4 HOH B 39 639 282 HOH HOH . H 4 HOH B 40 640 294 HOH HOH . H 4 HOH B 41 641 178 HOH HOH . H 4 HOH B 42 642 299 HOH HOH . H 4 HOH B 43 643 293 HOH HOH . H 4 HOH B 44 644 295 HOH HOH . H 4 HOH B 45 645 297 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 . . . E 2 0.044 -27.032 -17.335 1 43.18 0 N1 UDP 501 B 1 HETATM 2 C C2 UDP . . . E 2 -0.117 -25.714 -17.718 1 45.98 0 C2 UDP 501 B 1 HETATM 3 N N3 UDP . . . E 2 -1.194 -25.079 -17.156 1 48.35 0 N3 UDP 501 B 1 HETATM 4 C C4 UDP . . . E 2 -2.108 -25.615 -16.273 1 41.7 0 C4 UDP 501 B 1 HETATM 5 C C5 UDP . . . E 2 -1.875 -26.986 -15.926 1 42.18 0 C5 UDP 501 B 1 HETATM 6 C C6 UDP . . . E 2 -0.828 -27.634 -16.46 1 43.15 0 C6 UDP 501 B 1 HETATM 7 O O2 UDP . . . E 2 0.642 -25.151 -18.496 1 41.56 0 O2 UDP 501 B 1 HETATM 8 O O4 UDP . . . E 2 -3.028 -24.911 -15.856 1 37.23 0 O4 UDP 501 B 1 HETATM 9 C C1' UDP . . . E 2 1.186 -27.765 -17.911 1 50.16 0 C1' UDP 501 B 1 HETATM 10 C C2' UDP . . . E 2 2.443 -27.687 -17.049 1 47.13 0 C2' UDP 501 B 1 HETATM 11 O O2' UDP . . . E 2 3.15 -26.506 -17.358 1 44.97 0 O2' UDP 501 B 1 HETATM 12 C C3' UDP . . . E 2 3.178 -28.957 -17.494 1 45.88 0 C3' UDP 501 B 1 HETATM 13 C C4' UDP . . . E 2 2.033 -29.944 -17.772 1 47.45 0 C4' UDP 501 B 1 HETATM 14 O O4' UDP . . . E 2 0.85 -29.131 -17.992 1 58.24 0 O4' UDP 501 B 1 HETATM 15 O O3' UDP . . . E 2 3.956 -28.737 -18.663 1 47.02 0 O3' UDP 501 B 1 HETATM 16 C C5' UDP . . . E 2 1.763 -30.953 -16.684 1 45.31 0 C5' UDP 501 B 1 HETATM 17 O O5' UDP . . . E 2 2.772 -31.989 -16.749 1 47.71 0 O5' UDP 501 B 1 HETATM 18 P PA UDP . . . E 2 3.112 -32.835 -15.433 1 43.11 0 PA UDP 501 B 1 HETATM 19 O O1A UDP . . . E 2 4.059 -33.931 -15.786 1 41.21 0 O1A UDP 501 B 1 HETATM 20 O O2A UDP . . . E 2 3.497 -31.902 -14.335 1 47.95 0 O2A UDP 501 B 1 HETATM 21 O O3A UDP . . . E 2 1.684 -33.47 -15.082 1 47.02 0 O3A UDP 501 B 1 HETATM 22 P PB UDP . . . E 2 0.678 -34.454 -15.866 1 52.03 0 PB UDP 501 B 1 HETATM 23 O O1B UDP . . . E 2 0.131 -33.661 -17.021 1 56.59 0 O1B UDP 501 B 1 HETATM 24 O O2B UDP . . . E 2 -0.385 -34.839 -14.872 1 63.23 0 O2B UDP 501 B 1 HETATM 25 O O3B UDP . . . E 2 1.513 -35.626 -16.308 1 67 0 O3B UDP 501 B 1 # _model_server_stats.io_time_ms 28 _model_server_stats.parse_time_ms 23 _model_server_stats.create_model_time_ms 11 _model_server_stats.query_time_ms 235 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 25 #