data_5F84 # _model_server_result.job_id NkXROzqiFFLyH6kGfCu1KQ _model_server_result.datetime_utc '2024-11-23 01:04:53' _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 5f84 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"C","auth_seq_id":501}' # _entry.id 5F84 # _exptl.entry_id 5F84 _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 1 _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 5F84 _cell.length_a 271.016 _cell.length_b 271.016 _cell.length_c 47.427 _cell.Z_PDB 18 _cell.pdbx_unique_axis ? # _symmetry.entry_id 5F84 _symmetry.cell_setting ? _symmetry.Int_Tables_number 155 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'H 3 2' # _pdbx_struct_assembly.method_details PISA _pdbx_struct_assembly.oligomeric_details dimeric _pdbx_struct_assembly.oligomeric_count 2 _pdbx_struct_assembly.details software_defined_assembly _pdbx_struct_assembly.id 1 # _pdbx_struct_assembly_gen.asym_id_list A,B,C,D,E,F,G,H,I,J,K _pdbx_struct_assembly_gen.assembly_id 1 _pdbx_struct_assembly_gen.oper_expression 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 # _struct_asym.details ? _struct_asym.entity_id 3 _struct_asym.id C _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 disulf ? disulf1 A SG CYS 52 A CYS 64 1_555 A SG CYS 63 A CYS 75 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.068 ? disulf ? disulf2 A SG CYS 61 A CYS 73 1_555 A SG CYS 366 A CYS 378 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.037 ? disulf ? disulf3 A SG CYS 108 A CYS 120 1_555 A SG CYS 114 A CYS 126 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.041 ? disulf ? disulf4 A SG CYS 270 A CYS 282 1_555 A SG CYS 293 A CYS 305 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.055 ? disulf ? disulf5 B SG CYS 9 B CYS 51 1_555 B SG CYS 20 B CYS 62 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.031 ? disulf ? disulf6 B SG CYS 14 B CYS 56 1_555 B SG CYS 29 B CYS 71 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.02 ? disulf ? disulf7 B SG CYS 31 B CYS 73 1_555 B SG CYS 40 B CYS 82 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.066 ? covale ? covale1 B OG SER 11 B SER 53 1_555 I C1 BGC . B BGC 101 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.363 ? # _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 386 n n N1 C6 UDP sing 387 n n N1 C1' UDP sing 388 n n C2 N3 UDP sing 389 n n C2 O2 UDP doub 390 n n N3 C4 UDP sing 391 n n N3 HN3 UDP sing 392 n n C4 C5 UDP sing 393 n n C4 O4 UDP doub 394 n n C5 C6 UDP doub 395 n n C5 H5 UDP sing 396 n n C6 H6 UDP sing 397 n n C1' C2' UDP sing 398 n n C1' O4' UDP sing 399 n n C1' H1' UDP sing 400 n n C2' O2' UDP sing 401 n n C2' C3' UDP sing 402 n n C2' H2' UDP sing 403 n n O2' HO2' UDP sing 404 n n C3' C4' UDP sing 405 n n C3' O3' UDP sing 406 n n C3' H3' UDP sing 407 n n C4' O4' UDP sing 408 n n C4' C5' UDP sing 409 n n C4' H4' UDP sing 410 n n O3' HO3' UDP sing 411 n n C5' O5' UDP sing 412 n n C5' "H5'1" UDP sing 413 n n C5' "H5'2" UDP sing 414 n n O5' PA UDP sing 415 n n PA O1A UDP doub 416 n n PA O2A UDP sing 417 n n PA O3A UDP sing 418 n n O2A HOA2 UDP sing 419 n n O3A PB UDP sing 420 n n PB O1B UDP doub 421 n n PB O2B UDP sing 422 n n PB O3B UDP sing 423 n n O2B HOB2 UDP sing 424 n n O3B HOB3 UDP sing 425 n n # _atom_sites.entry_id 5F84 _atom_sites.fract_transf_matrix[1][1] 0.00369 _atom_sites.fract_transf_matrix[1][2] 0.00213 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.004261 _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] 0.021085 _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 3 UDP A 1 501 1 UDP UDP . D 4 SO4 A 1 502 1 SO4 SO4 . E 4 SO4 A 1 503 2 SO4 SO4 . F 4 SO4 A 1 504 3 SO4 SO4 . G 4 SO4 A 1 505 4 SO4 SO4 . H 4 SO4 A 1 506 5 SO4 SO4 . I 5 BGC B 1 101 455 BGC BGC . J 6 HOH A 1 601 73 HOH HOH . J 6 HOH A 2 602 88 HOH HOH . J 6 HOH A 3 603 19 HOH HOH . J 6 HOH A 4 604 58 HOH HOH . J 6 HOH A 5 605 46 HOH HOH . J 6 HOH A 6 606 89 HOH HOH . J 6 HOH A 7 607 18 HOH HOH . J 6 HOH A 8 608 36 HOH HOH . J 6 HOH A 9 609 85 HOH HOH . J 6 HOH A 10 610 48 HOH HOH . J 6 HOH A 11 611 50 HOH HOH . J 6 HOH A 12 612 92 HOH HOH . J 6 HOH A 13 613 22 HOH HOH . J 6 HOH A 14 614 43 HOH HOH . J 6 HOH A 15 615 44 HOH HOH . J 6 HOH A 16 616 10 HOH HOH . J 6 HOH A 17 617 87 HOH HOH . J 6 HOH A 18 618 63 HOH HOH . J 6 HOH A 19 619 21 HOH HOH . J 6 HOH A 20 620 17 HOH HOH . J 6 HOH A 21 621 83 HOH HOH . J 6 HOH A 22 622 57 HOH HOH . J 6 HOH A 23 623 12 HOH HOH . J 6 HOH A 24 624 15 HOH HOH . J 6 HOH A 25 625 99 HOH HOH . J 6 HOH A 26 626 40 HOH HOH . J 6 HOH A 27 627 51 HOH HOH . J 6 HOH A 28 628 35 HOH HOH . J 6 HOH A 29 629 79 HOH HOH . J 6 HOH A 30 630 61 HOH HOH . J 6 HOH A 31 631 29 HOH HOH . J 6 HOH A 32 632 39 HOH HOH . J 6 HOH A 33 633 47 HOH HOH . J 6 HOH A 34 634 97 HOH HOH . J 6 HOH A 35 635 11 HOH HOH . J 6 HOH A 36 636 8 HOH HOH . J 6 HOH A 37 637 84 HOH HOH . J 6 HOH A 38 638 80 HOH HOH . J 6 HOH A 39 639 4 HOH HOH . J 6 HOH A 40 640 38 HOH HOH . J 6 HOH A 41 641 32 HOH HOH . J 6 HOH A 42 642 13 HOH HOH . J 6 HOH A 43 643 74 HOH HOH . J 6 HOH A 44 644 16 HOH HOH . J 6 HOH A 45 645 7 HOH HOH . J 6 HOH A 46 646 25 HOH HOH . J 6 HOH A 47 647 49 HOH HOH . J 6 HOH A 48 648 34 HOH HOH . J 6 HOH A 49 649 42 HOH HOH . J 6 HOH A 50 650 31 HOH HOH . J 6 HOH A 51 651 91 HOH HOH . J 6 HOH A 52 652 41 HOH HOH . J 6 HOH A 53 653 67 HOH HOH . J 6 HOH A 54 654 33 HOH HOH . J 6 HOH A 55 655 70 HOH HOH . J 6 HOH A 56 656 90 HOH HOH . J 6 HOH A 57 657 5 HOH HOH . J 6 HOH A 58 658 9 HOH HOH . J 6 HOH A 59 659 53 HOH HOH . J 6 HOH A 60 660 81 HOH HOH . J 6 HOH A 61 661 37 HOH HOH . J 6 HOH A 62 662 68 HOH HOH . J 6 HOH A 63 663 30 HOH HOH . J 6 HOH A 64 664 20 HOH HOH . J 6 HOH A 65 665 78 HOH HOH . J 6 HOH A 66 666 69 HOH HOH . J 6 HOH A 67 667 6 HOH HOH . J 6 HOH A 68 668 23 HOH HOH . J 6 HOH A 69 669 95 HOH HOH . J 6 HOH A 70 670 86 HOH HOH . J 6 HOH A 71 671 28 HOH HOH . J 6 HOH A 72 672 54 HOH HOH . J 6 HOH A 73 673 52 HOH HOH . J 6 HOH A 74 674 55 HOH HOH . J 6 HOH A 75 675 75 HOH HOH . J 6 HOH A 76 676 14 HOH HOH . J 6 HOH A 77 677 3 HOH HOH . J 6 HOH A 78 678 66 HOH HOH . J 6 HOH A 79 679 94 HOH HOH . J 6 HOH A 80 680 26 HOH HOH . J 6 HOH A 81 681 60 HOH HOH . J 6 HOH A 82 682 56 HOH HOH . J 6 HOH A 83 683 64 HOH HOH . J 6 HOH A 84 684 76 HOH HOH . J 6 HOH A 85 685 82 HOH HOH . J 6 HOH A 86 686 77 HOH HOH . J 6 HOH A 87 687 65 HOH HOH . K 6 HOH B 1 201 45 HOH HOH . K 6 HOH B 2 202 96 HOH HOH . K 6 HOH B 3 203 59 HOH HOH . K 6 HOH B 4 204 24 HOH HOH . K 6 HOH B 5 205 72 HOH HOH . K 6 HOH B 6 206 62 HOH HOH . K 6 HOH B 7 207 27 HOH HOH . K 6 HOH B 8 208 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 N N1 UDP . . . C 3 54 15.832 14.035 1 28.43 ? N1 UDP 501 A 1 HETATM 2 C C2 UDP . . . C 3 53.921 15.503 15.405 1 28.3 ? C2 UDP 501 A 1 HETATM 3 N N3 UDP . . . C 3 54.828 14.674 15.923 1 28.88 ? N3 UDP 501 A 1 HETATM 4 C C4 UDP . . . C 3 55.8 14.138 15.174 1 28.45 ? C4 UDP 501 A 1 HETATM 5 C C5 UDP . . . C 3 55.895 14.437 13.824 1 28.58 ? C5 UDP 501 A 1 HETATM 6 C C6 UDP . . . C 3 54.97 15.301 13.262 1 28.49 ? C6 UDP 501 A 1 HETATM 7 O O2 UDP . . . C 3 53.025 15.986 16.143 1 29.19 ? O2 UDP 501 A 1 HETATM 8 O O4 UDP . . . C 3 56.625 13.358 15.692 1 28.97 ? O4 UDP 501 A 1 HETATM 9 C C1' UDP . . . C 3 53.004 16.726 13.447 1 26.82 ? C1' UDP 501 A 1 HETATM 10 C C2' UDP . . . C 3 53.567 18.076 13.041 1 25.82 ? C2' UDP 501 A 1 HETATM 11 O O2' UDP . . . C 3 53.514 19.027 14.104 1 24.22 ? O2' UDP 501 A 1 HETATM 12 C C3' UDP . . . C 3 52.666 18.431 11.876 1 25.91 ? C3' UDP 501 A 1 HETATM 13 C C4' UDP . . . C 3 52.315 17.09 11.237 1 26.32 ? C4' UDP 501 A 1 HETATM 14 O O4' UDP . . . C 3 52.493 16.111 12.261 1 26.49 ? O4' UDP 501 A 1 HETATM 15 O O3' UDP . . . C 3 51.466 19.041 12.336 1 24.42 ? O3' UDP 501 A 1 HETATM 16 C C5' UDP . . . C 3 53.201 16.737 10.045 1 26.24 ? C5' UDP 501 A 1 HETATM 17 O O5' UDP . . . C 3 54.565 17.045 10.333 1 26.1 ? O5' UDP 501 A 1 HETATM 18 P PA UDP . . . C 3 55.746 16.879 9.239 1 26.49 ? PA UDP 501 A 1 HETATM 19 O O1A UDP . . . C 3 55.764 15.463 8.726 1 25.53 ? O1A UDP 501 A 1 HETATM 20 O O2A UDP . . . C 3 57.022 17.418 9.815 1 26.17 ? O2A UDP 501 A 1 HETATM 21 O O3A UDP . . . C 3 55.23 17.808 8.003 1 25.99 ? O3A UDP 501 A 1 HETATM 22 P PB UDP . . . C 3 55.033 19.404 7.99 1 24.31 ? PB UDP 501 A 1 HETATM 23 O O1B UDP . . . C 3 55.588 19.785 6.643 1 25.9 ? O1B UDP 501 A 1 HETATM 24 O O2B UDP . . . C 3 55.814 19.927 9.161 1 25.07 ? O2B UDP 501 A 1 HETATM 25 O O3B UDP . . . C 3 53.556 19.592 8.054 1 25.56 ? O3B UDP 501 A 1 # _model_server_stats.io_time_ms 9 _model_server_stats.parse_time_ms 10 _model_server_stats.create_model_time_ms 27 _model_server_stats.query_time_ms 326 _model_server_stats.encode_time_ms 3 _model_server_stats.element_count 25 #