data_2QRO
#
_model_server_result.job_id            ewvj_MH5grYDKGwpLl599A 
_model_server_result.datetime_utc      '2024-11-23 00:57:05' 
_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          2qro 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"L","auth_seq_id":402}' 
#
_entry.id    2QRO 
#
_exptl.entry_id    2QRO 
_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    4 
_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            2QRO 
_cell.length_a            93.688 
_cell.length_b            93.688 
_cell.length_c            332.408 
_cell.Z_PDB               32 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 2QRO 
_symmetry.cell_setting             ? 
_symmetry.Int_Tables_number        96 
_symmetry.space_group_name_Hall    ? 
_symmetry.space_group_name_H-M     'P 43 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
PISA dimeric 2 author_and_software_defined_assembly 1 
PISA dimeric 2 author_and_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,E,F,G,H,I,J 1 1 
C,D,K,L,M,N,O,P 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 F N N 
? 3 I N N 
? 3 L N N 
? 3 O 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 A OG SER 55 A SER 35 1_555 E MG MG . A MG 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.134 ? 
metalc ? metalc2 A OE2 GLU 147 A GLU 127 1_555 E MG MG . A MG 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.345 ? 
metalc ? metalc3 E MG MG . A MG 401 1_555 F O1B UDP . A UDP 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.417 ? 
metalc ? metalc4 B OG SER 55 B SER 35 1_555 H MG MG . B MG 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.384 ? 
metalc ? metalc5 H MG MG . B MG 401 1_555 I O1B UDP . B UDP 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.36 ? 
metalc ? metalc6 C OG SER 55 C SER 35 1_555 K MG MG . C MG 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.348 ? 
metalc ? metalc7 K MG MG . C MG 401 1_555 L O1B UDP . C UDP 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.398 ? 
metalc ? metalc8 D OG SER 55 D SER 35 1_555 N MG MG . D MG 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.256 ? 
metalc ? metalc9 D OE2 GLU 147 D GLU 127 1_555 N MG MG . D MG 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.373 ? 
metalc ? metalc10 N MG MG . D MG 401 1_555 O O1B UDP . D UDP 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.485 ? 
#
_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 394 n n 
N1 C6 UDP sing 395 n n 
N1 C1' UDP sing 396 n n 
C2 N3 UDP sing 397 n n 
C2 O2 UDP doub 398 n n 
N3 C4 UDP sing 399 n n 
N3 HN3 UDP sing 400 n n 
C4 C5 UDP sing 401 n n 
C4 O4 UDP doub 402 n n 
C5 C6 UDP doub 403 n n 
C5 H5 UDP sing 404 n n 
C6 H6 UDP sing 405 n n 
C1' C2' UDP sing 406 n n 
C1' O4' UDP sing 407 n n 
C1' H1' UDP sing 408 n n 
C2' O2' UDP sing 409 n n 
C2' C3' UDP sing 410 n n 
C2' H2' UDP sing 411 n n 
O2' HO2' UDP sing 412 n n 
C3' C4' UDP sing 413 n n 
C3' O3' UDP sing 414 n n 
C3' H3' UDP sing 415 n n 
C4' O4' UDP sing 416 n n 
C4' C5' UDP sing 417 n n 
C4' H4' UDP sing 418 n n 
O3' HO3' UDP sing 419 n n 
C5' O5' UDP sing 420 n n 
C5' "H5'1" UDP sing 421 n n 
C5' "H5'2" UDP sing 422 n n 
O5' PA UDP sing 423 n n 
PA O1A UDP doub 424 n n 
PA O2A UDP sing 425 n n 
PA O3A UDP sing 426 n n 
O2A HOA2 UDP sing 427 n n 
O3A PB UDP sing 428 n n 
PB O1B UDP doub 429 n n 
PB O2B UDP sing 430 n n 
PB O3B UDP sing 431 n n 
O2B HOB2 UDP sing 432 n n 
O3B HOB3 UDP sing 433 n n 
#
_atom_sites.entry_id                     2QRO 
_atom_sites.fract_transf_matrix[1][1]    0.010674 
_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]    0.010674 
_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]    0.003008 
_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 2 MG A 1 401 401 MG MG . 
F 3 UDP A 1 402 402 UDP UDP . 
G 4 D5M A 1 503 503 D5M D5M . 
H 2 MG B 1 401 401 MG MG . 
I 3 UDP B 1 402 402 UDP UDP . 
J 4 D5M B 1 503 503 D5M D5M . 
K 2 MG C 1 401 401 MG MG . 
L 3 UDP C 1 402 402 UDP UDP . 
M 4 D5M C 1 503 503 D5M D5M . 
N 2 MG D 1 401 401 MG MG . 
O 3 UDP D 1 402 402 UDP UDP . 
P 4 D5M D 1 503 503 D5M D5M . 
#
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 . . . L 3 34.38 58.212 27.83 1 75.4 ? N1 UDP 402 C 1 
HETATM 2 C C2 UDP . . . L 3 35.03 59.372 28.15 1 75.4 ? C2 UDP 402 C 1 
HETATM 3 N N3 UDP . . . L 3 36.14 59.354 28.939 1 75.4 ? N3 UDP 402 C 1 
HETATM 4 C C4 UDP . . . L 3 36.632 58.147 29.433 1 75.4 ? C4 UDP 402 C 1 
HETATM 5 C C5 UDP . . . L 3 35.956 56.92 29.098 1 75.4 ? C5 UDP 402 C 1 
HETATM 6 C C6 UDP . . . L 3 34.85 56.967 28.309 1 75.4 ? C6 UDP 402 C 1 
HETATM 7 O O2 UDP . . . L 3 34.604 60.448 27.722 1 75.4 ? O2 UDP 402 C 1 
HETATM 8 O O4 UDP . . . L 3 37.631 58.13 30.145 1 75.4 ? O4 UDP 402 C 1 
HETATM 9 C C1' UDP . . . L 3 33.185 58.254 26.988 1 75.4 ? C1' UDP 402 C 1 
HETATM 10 C C2' UDP . . . L 3 33.578 58.117 25.502 1 75.4 ? C2' UDP 402 C 1 
HETATM 11 O O2' UDP . . . L 3 33.583 59.399 24.858 1 75.4 ? O2' UDP 402 C 1 
HETATM 12 C C3' UDP . . . L 3 32.526 57.233 24.91 1 75.4 ? C3' UDP 402 C 1 
HETATM 13 C C4' UDP . . . L 3 31.596 56.888 26.085 1 75.4 ? C4' UDP 402 C 1 
HETATM 14 O O4' UDP . . . L 3 32.361 57.14 27.268 1 75.4 ? O4' UDP 402 C 1 
HETATM 15 O O3' UDP . . . L 3 31.8 57.933 23.874 1 75.4 ? O3' UDP 402 C 1 
HETATM 16 C C5' UDP . . . L 3 31.215 55.46 26.035 1 75.4 ? C5' UDP 402 C 1 
HETATM 17 O O5' UDP . . . L 3 30.471 55.149 27.148 1 75.4 ? O5' UDP 402 C 1 
HETATM 18 P PA UDP . . . L 3 30.238 53.571 27.126 1 75.4 ? PA UDP 402 C 1 
HETATM 19 O O1A UDP . . . L 3 29.493 53.196 25.89 1 75.4 ? O1A UDP 402 C 1 
HETATM 20 O O2A UDP . . . L 3 31.67 52.816 27.145 1 75.4 ? O2A UDP 402 C 1 
HETATM 21 O O3A UDP . . . L 3 29.365 53.134 28.452 1 75.4 ? O3A UDP 402 C 1 
HETATM 22 P PB UDP . . . L 3 29.161 51.497 28.385 1 75.4 ? PB UDP 402 C 1 
HETATM 23 O O1B UDP . . . L 3 28.436 51.126 27.069 1 75.4 ? O1B UDP 402 C 1 
HETATM 24 O O2B UDP . . . L 3 28.418 51.013 29.552 1 75.4 ? O2B UDP 402 C 1 
HETATM 25 O O3B UDP . . . L 3 30.593 50.811 28.384 1 75.4 ? O3B UDP 402 C 1 
#
_model_server_stats.io_time_ms              7 
_model_server_stats.parse_time_ms           7 
_model_server_stats.create_model_time_ms    21 
_model_server_stats.query_time_ms           287 
_model_server_stats.encode_time_ms          6 
_model_server_stats.element_count           25 
#