data_4UKD
#
_model_server_result.job_id            5SG_Njt7iLqTwPZ4WVRpww 
_model_server_result.datetime_utc      '2024-10-16 10:37:57' 
_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          4ukd 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"D","auth_seq_id":196}' 
#
_entry.id    4UKD 
#
_exptl.entry_id    4UKD 
_exptl.method      'X-RAY DIFFRACTION' 
#
_entity.details                     ? 
_entity.formula_weight              404.161 
_entity.id                          4 
_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         90 
_cell.entry_id            4UKD 
_cell.length_a            78.1 
_cell.length_b            78.1 
_cell.length_c            101.9 
_cell.Z_PDB               8 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 4UKD 
_symmetry.cell_setting             ? 
_symmetry.Int_Tables_number        92 
_symmetry.space_group_name_Hall    . 
_symmetry.space_group_name_H-M     'P 41 21 2' 
#
_pdbx_struct_assembly.method_details        ? 
_pdbx_struct_assembly.oligomeric_details    monomeric 
_pdbx_struct_assembly.oligomeric_count      1 
_pdbx_struct_assembly.details               author_defined_assembly 
_pdbx_struct_assembly.id                    1 
#
_pdbx_struct_assembly_gen.asym_id_list       A,B,C,D,E,F 
_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                      4 
_struct_asym.id                             D 
_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 C O3B ADP . A ADP 195 1_555 E F2 BF2 . A BF2 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.377 ? 
metalc ? metalc1 C O2B ADP . A ADP 195 1_555 B MG MG . A MG 500 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.285 ? 
metalc ? metalc2 C O3B ADP . A ADP 195 1_555 E BE BF2 . A BF2 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.55 ? 
metalc ? metalc3 D O3B UDP . A UDP 196 1_555 E BE BF2 . A BF2 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.579 ? 
metalc ? metalc4 F O HOH . A HOH 198 1_555 B MG MG . A MG 500 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.233 ? 
metalc ? metalc5 F O HOH . A HOH 215 1_555 B MG MG . A MG 500 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.383 ? 
metalc ? metalc6 F O HOH . A HOH 220 1_555 B MG MG . A MG 500 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.176 ? 
metalc ? metalc7 B MG MG . A MG 500 1_555 E F2 BF2 . A BF2 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.978 ? 
metalc ? metalc8 B MG MG . A MG 500 1_555 F O HOH . A HOH 900 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.44 ? 
#
_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 404 n n 
N1 C6 UDP sing 405 n n 
N1 C1' UDP sing 406 n n 
C2 N3 UDP sing 407 n n 
C2 O2 UDP doub 408 n n 
N3 C4 UDP sing 409 n n 
N3 HN3 UDP sing 410 n n 
C4 C5 UDP sing 411 n n 
C4 O4 UDP doub 412 n n 
C5 C6 UDP doub 413 n n 
C5 H5 UDP sing 414 n n 
C6 H6 UDP sing 415 n n 
C1' C2' UDP sing 416 n n 
C1' O4' UDP sing 417 n n 
C1' H1' UDP sing 418 n n 
C2' O2' UDP sing 419 n n 
C2' C3' UDP sing 420 n n 
C2' H2' UDP sing 421 n n 
O2' HO2' UDP sing 422 n n 
C3' C4' UDP sing 423 n n 
C3' O3' UDP sing 424 n n 
C3' H3' UDP sing 425 n n 
C4' O4' UDP sing 426 n n 
C4' C5' UDP sing 427 n n 
C4' H4' UDP sing 428 n n 
O3' HO3' UDP sing 429 n n 
C5' O5' UDP sing 430 n n 
C5' "H5'1" UDP sing 431 n n 
C5' "H5'2" UDP sing 432 n n 
O5' PA UDP sing 433 n n 
PA O1A UDP doub 434 n n 
PA O2A UDP sing 435 n n 
PA O3A UDP sing 436 n n 
O2A HOA2 UDP sing 437 n n 
O3A PB UDP sing 438 n n 
PB O1B UDP doub 439 n n 
PB O2B UDP sing 440 n n 
PB O3B UDP sing 441 n n 
O2B HOB2 UDP sing 442 n n 
O3B HOB3 UDP sing 443 n n 
#
_atom_sites.entry_id                     4UKD 
_atom_sites.fract_transf_matrix[1][1]    0.012804 
_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]    0.012804 
_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]    0.009814 
_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
B 2 MG A 1 500 500 MG MG . 
C 3 ADP A 1 195 195 ADP ADP . 
D 4 UDP A 1 196 196 UDP UDP . 
E 5 BF2 A 1 501 501 BF2 BF2 . 
F 6 HOH A 1 198 198 HOH HOH . 
F 6 HOH A 2 199 199 HOH HOH . 
F 6 HOH A 3 200 200 HOH HOH . 
F 6 HOH A 4 201 201 HOH HOH . 
F 6 HOH A 5 202 202 HOH HOH . 
F 6 HOH A 6 204 204 HOH HOH . 
F 6 HOH A 7 206 206 HOH HOH . 
F 6 HOH A 8 207 207 HOH HOH . 
F 6 HOH A 9 208 208 HOH HOH . 
F 6 HOH A 10 210 210 HOH HOH . 
F 6 HOH A 11 211 211 HOH HOH . 
F 6 HOH A 12 212 212 HOH HOH . 
F 6 HOH A 13 214 214 HOH HOH . 
F 6 HOH A 14 215 215 HOH HOH . 
F 6 HOH A 15 216 216 HOH HOH . 
F 6 HOH A 16 218 218 HOH HOH . 
F 6 HOH A 17 220 220 HOH HOH . 
F 6 HOH A 18 221 221 HOH HOH . 
F 6 HOH A 19 222 222 HOH HOH . 
F 6 HOH A 20 223 223 HOH HOH . 
F 6 HOH A 21 226 226 HOH HOH . 
F 6 HOH A 22 227 227 HOH HOH . 
F 6 HOH A 23 229 229 HOH HOH . 
F 6 HOH A 24 231 231 HOH HOH . 
F 6 HOH A 25 232 232 HOH HOH . 
F 6 HOH A 26 236 236 HOH HOH . 
F 6 HOH A 27 238 238 HOH HOH . 
F 6 HOH A 28 239 239 HOH HOH . 
F 6 HOH A 29 242 242 HOH HOH . 
F 6 HOH A 30 244 244 HOH HOH . 
F 6 HOH A 31 245 245 HOH HOH . 
F 6 HOH A 32 509 509 HOH HOH . 
F 6 HOH A 33 512 512 HOH HOH . 
F 6 HOH A 34 528 528 HOH HOH . 
F 6 HOH A 35 531 531 HOH HOH . 
F 6 HOH A 36 532 532 HOH HOH . 
F 6 HOH A 37 533 533 HOH HOH . 
F 6 HOH A 38 536 536 HOH HOH . 
F 6 HOH A 39 538 538 HOH HOH . 
F 6 HOH A 40 543 543 HOH HOH . 
F 6 HOH A 41 553 553 HOH HOH . 
F 6 HOH A 42 558 558 HOH HOH . 
F 6 HOH A 43 559 559 HOH HOH . 
F 6 HOH A 44 562 562 HOH HOH . 
F 6 HOH A 45 564 564 HOH HOH . 
F 6 HOH A 46 565 565 HOH HOH . 
F 6 HOH A 47 568 568 HOH HOH . 
F 6 HOH A 48 577 577 HOH HOH . 
F 6 HOH A 49 580 580 HOH HOH . 
F 6 HOH A 50 582 582 HOH HOH . 
F 6 HOH A 51 591 591 HOH HOH . 
F 6 HOH A 52 592 592 HOH HOH . 
F 6 HOH A 53 597 597 HOH HOH . 
F 6 HOH A 54 601 601 HOH HOH . 
F 6 HOH A 55 605 605 HOH HOH . 
F 6 HOH A 56 608 608 HOH HOH . 
F 6 HOH A 57 640 640 HOH HOH . 
F 6 HOH A 58 646 646 HOH HOH . 
F 6 HOH A 59 650 650 HOH HOH . 
F 6 HOH A 60 664 664 HOH HOH . 
F 6 HOH A 61 670 670 HOH HOH . 
F 6 HOH A 62 712 712 HOH HOH . 
F 6 HOH A 63 717 717 HOH HOH . 
F 6 HOH A 64 727 727 HOH HOH . 
F 6 HOH A 65 732 732 HOH HOH . 
F 6 HOH A 66 737 737 HOH HOH . 
F 6 HOH A 67 739 739 HOH HOH . 
F 6 HOH A 68 741 741 HOH HOH . 
F 6 HOH A 69 744 744 HOH HOH . 
F 6 HOH A 70 750 750 HOH HOH . 
F 6 HOH A 71 752 752 HOH HOH . 
F 6 HOH A 72 753 753 HOH HOH . 
F 6 HOH A 73 774 774 HOH HOH . 
F 6 HOH A 74 778 778 HOH HOH . 
F 6 HOH A 75 786 786 HOH HOH . 
F 6 HOH A 76 793 793 HOH HOH . 
F 6 HOH A 77 797 797 HOH HOH . 
F 6 HOH A 78 807 807 HOH HOH . 
F 6 HOH A 79 810 810 HOH HOH . 
F 6 HOH A 80 814 814 HOH HOH . 
F 6 HOH A 81 818 818 HOH HOH . 
F 6 HOH A 82 819 819 HOH HOH . 
F 6 HOH A 83 826 826 HOH HOH . 
F 6 HOH A 84 828 828 HOH HOH . 
F 6 HOH A 85 829 829 HOH HOH . 
F 6 HOH A 86 833 833 HOH HOH . 
F 6 HOH A 87 838 838 HOH HOH . 
F 6 HOH A 88 839 839 HOH HOH . 
F 6 HOH A 89 843 843 HOH HOH . 
F 6 HOH A 90 844 844 HOH HOH . 
F 6 HOH A 91 848 848 HOH HOH . 
F 6 HOH A 92 849 849 HOH HOH . 
F 6 HOH A 93 853 853 HOH HOH . 
F 6 HOH A 94 857 857 HOH HOH . 
F 6 HOH A 95 858 858 HOH HOH . 
F 6 HOH A 96 861 861 HOH HOH . 
F 6 HOH A 97 864 864 HOH HOH . 
F 6 HOH A 98 865 865 HOH HOH . 
F 6 HOH A 99 871 871 HOH HOH . 
F 6 HOH A 100 877 877 HOH HOH . 
F 6 HOH A 101 880 880 HOH HOH . 
F 6 HOH A 102 881 881 HOH HOH . 
F 6 HOH A 103 900 900 HOH HOH . 
F 6 HOH A 104 901 901 HOH HOH . 
F 6 HOH A 105 902 902 HOH HOH . 
F 6 HOH A 106 903 903 HOH HOH . 
F 6 HOH A 107 904 904 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 . . . D 4 40.742 75.026 -18.047 1 19.62 ? N1 UDP 196 A 1 
HETATM 2 C C2 UDP . . . D 4 41.595 75.624 -18.947 1 21 ? C2 UDP 196 A 1 
HETATM 3 N N3 UDP . . . D 4 42.86 75.311 -19.179 1 20.65 ? N3 UDP 196 A 1 
HETATM 4 C C4 UDP . . . D 4 43.512 74.485 -18.346 1 20.88 ? C4 UDP 196 A 1 
HETATM 5 C C5 UDP . . . D 4 42.794 73.986 -17.313 1 20.6 ? C5 UDP 196 A 1 
HETATM 6 C C6 UDP . . . D 4 41.492 74.224 -17.087 1 19.32 ? C6 UDP 196 A 1 
HETATM 7 O O2 UDP . . . D 4 41.051 76.48 -19.835 1 20.7 ? O2 UDP 196 A 1 
HETATM 8 O O4 UDP . . . D 4 44.775 74.173 -18.678 1 21.88 ? O4 UDP 196 A 1 
HETATM 9 C C1' UDP . . . D 4 39.385 75.581 -17.847 1 20.02 ? C1' UDP 196 A 1 
HETATM 10 C C2' UDP . . . D 4 38.362 74.927 -18.748 1 19.67 ? C2' UDP 196 A 1 
HETATM 11 O O2' UDP . . . D 4 37.28 75.789 -19.014 1 20.17 ? O2' UDP 196 A 1 
HETATM 12 C C3' UDP . . . D 4 37.969 73.786 -17.845 1 19.77 ? C3' UDP 196 A 1 
HETATM 13 C C4' UDP . . . D 4 37.788 74.544 -16.548 1 19.95 ? C4' UDP 196 A 1 
HETATM 14 O O4' UDP . . . D 4 38.969 75.284 -16.523 1 20.11 ? O4' UDP 196 A 1 
HETATM 15 O O3' UDP . . . D 4 36.787 73.2 -18.262 1 19.3 ? O3' UDP 196 A 1 
HETATM 16 C C5' UDP . . . D 4 37.815 73.666 -15.28 1 21.85 ? C5' UDP 196 A 1 
HETATM 17 O O5' UDP . . . D 4 38.994 72.821 -15.289 1 20.39 ? O5' UDP 196 A 1 
HETATM 18 P PA UDP . . . D 4 39.215 71.656 -14.243 1 21.11 ? PA UDP 196 A 1 
HETATM 19 O O1A UDP . . . D 4 38.997 72.258 -12.923 1 21.8 ? O1A UDP 196 A 1 
HETATM 20 O O2A UDP . . . D 4 40.463 70.956 -14.426 1 18.89 ? O2A UDP 196 A 1 
HETATM 21 O O3A UDP . . . D 4 38.012 70.692 -14.598 1 20.27 ? O3A UDP 196 A 1 
HETATM 22 P PB UDP . . . D 4 37.751 69.28 -15.297 1 20.8 ? PB UDP 196 A 1 
HETATM 23 O O1B UDP . . . D 4 38.878 68.866 -16.074 1 22.06 ? O1B UDP 196 A 1 
HETATM 24 O O2B UDP . . . D 4 36.502 69.437 -15.984 1 21.62 ? O2B UDP 196 A 1 
HETATM 25 O O3B UDP . . . D 4 37.604 68.183 -14.237 1 19.47 ? O3B UDP 196 A 1 
#
_model_server_stats.io_time_ms              6 
_model_server_stats.parse_time_ms           7 
_model_server_stats.create_model_time_ms    2 
_model_server_stats.query_time_ms           291 
_model_server_stats.encode_time_ms          1 
_model_server_stats.element_count           25 
#