data_4AY5
#
_model_server_result.job_id            Z7TqXzusfTS1coEqPIgX8A 
_model_server_result.datetime_utc      '2024-11-27 13:10:58' 
_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          4ay5 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"L","auth_seq_id":1201}' 
#
_entry.id    4AY5 
#
_exptl.entry_id    4AY5 
_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         120 
_cell.entry_id            4AY5 
_cell.length_a            274.17 
_cell.length_b            274.17 
_cell.length_c            142.15 
_cell.Z_PDB               24 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 4AY5 
_symmetry.cell_setting             ? 
_symmetry.Int_Tables_number        150 
_symmetry.space_group_name_Hall    . 
_symmetry.space_group_name_H-M     'P 3 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 dimeric 2 author_and_software_defined_assembly 1 
PISA dimeric 2 author_and_software_defined_assembly 2 
PISA dimeric 2 author_and_software_defined_assembly 3 
PISA dimeric 2 author_and_software_defined_assembly 4 
#
loop_
_pdbx_struct_assembly_gen.asym_id_list
_pdbx_struct_assembly_gen.assembly_id
_pdbx_struct_assembly_gen.oper_expression
A,E,I,M 1 1 
B,F,J,N 2 1 
C,G,K,O 3 1 
D,H,L,P 4 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 I N N 
? 3 J N N 
? 3 K N N 
? 3 L 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
covale ? covale1 E OG SER 7 I SER 7 1_555 M C1 NAG . I NAG 1202 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.481 ? 
covale ? covale2 F OG SER 7 J SER 7 1_555 N C1 NAG . J NAG 1202 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.505 ? 
covale ? covale3 G OG SER 7 K SER 7 1_555 O C1 NAG . K NAG 1202 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.462 ? 
covale ? covale4 H OG SER 7 L SER 7 1_555 P C1 NAG . L NAG 1202 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.431 ? 
#
_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                     4AY5 
_atom_sites.fract_transf_matrix[1][1]    0.003647 
_atom_sites.fract_transf_matrix[1][2]    0.002106 
_atom_sites.fract_transf_matrix[1][3]    0 
_atom_sites.fract_transf_matrix[2][1]    0 
_atom_sites.fract_transf_matrix[2][2]    0.004212 
_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]    0.007035 
_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
I 3 UDP A 1 1201 1201 UDP UDP . 
J 3 UDP B 1 1201 1201 UDP UDP . 
K 3 UDP C 1 1201 1201 UDP UDP . 
L 3 UDP D 1 1201 1201 UDP UDP . 
M 4 NAG I 1 1202 1202 NAG NAG . 
N 4 NAG J 1 1202 1202 NAG NAG . 
O 4 NAG K 1 1202 1202 NAG NAG . 
P 4 NAG L 1 1202 1202 NAG NAG . 
#
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 3 178.211 -40.365 29.696 1 79.41 ? N1 UDP 1201 D 1 
HETATM 2 C C2 UDP . . . L 3 177.231 -41.009 30.521 1 83.9 ? C2 UDP 1201 D 1 
HETATM 3 N N3 UDP . . . L 3 177.644 -41.588 31.669 1 83.48 ? N3 UDP 1201 D 1 
HETATM 4 C C4 UDP . . . L 3 178.934 -41.581 32.052 1 79.19 ? C4 UDP 1201 D 1 
HETATM 5 C C5 UDP . . . L 3 179.901 -40.958 31.24 1 77.71 ? C5 UDP 1201 D 1 
HETATM 6 C C6 UDP . . . L 3 179.519 -40.346 30.043 1 76.8 ? C6 UDP 1201 D 1 
HETATM 7 O O2 UDP . . . L 3 175.988 -41.053 30.211 1 80.45 ? O2 UDP 1201 D 1 
HETATM 8 O O4 UDP . . . L 3 179.236 -42.128 33.146 1 75.68 ? O4 UDP 1201 D 1 
HETATM 9 C C1' UDP . . . L 3 177.755 -39.761 28.437 1 81.43 ? C1' UDP 1201 D 1 
HETATM 10 C C2' UDP . . . L 3 178.029 -38.27 28.213 1 75.62 ? C2' UDP 1201 D 1 
HETATM 11 O O2' UDP . . . L 3 177.168 -37.4 28.955 1 65.99 ? O2' UDP 1201 D 1 
HETATM 12 C C3' UDP . . . L 3 177.768 -38.205 26.73 1 70.19 ? C3' UDP 1201 D 1 
HETATM 13 C C4' UDP . . . L 3 178.524 -39.453 26.281 1 79.18 ? C4' UDP 1201 D 1 
HETATM 14 O O4' UDP . . . L 3 178.371 -40.429 27.323 1 81.43 ? O4' UDP 1201 D 1 
HETATM 15 O O3' UDP . . . L 3 176.377 -38.466 26.484 1 71.67 ? O3' UDP 1201 D 1 
HETATM 16 C C5' UDP . . . L 3 180.008 -39.211 26.036 1 75.35 ? C5' UDP 1201 D 1 
HETATM 17 O O5' UDP . . . L 3 180.259 -39.488 24.658 1 72.62 ? O5' UDP 1201 D 1 
HETATM 18 P PA UDP . . . L 3 181.47 -38.759 23.891 1 83.21 ? PA UDP 1201 D 1 
HETATM 19 O O1A UDP . . . L 3 182.807 -38.988 24.637 1 85.41 ? O1A UDP 1201 D 1 
HETATM 20 O O2A UDP . . . L 3 181.22 -39.02 22.427 1 77.08 ? O2A UDP 1201 D 1 
HETATM 21 O O3A UDP . . . L 3 181.085 -37.216 24.067 1 77.69 ? O3A UDP 1201 D 1 
HETATM 22 P PB UDP . . . L 3 182.132 -36.018 23.931 1 74.93 ? PB UDP 1201 D 1 
HETATM 23 O O1B UDP . . . L 3 182.485 -35.644 25.364 1 60.56 ? O1B UDP 1201 D 1 
HETATM 24 O O2B UDP . . . L 3 181.18 -35.135 23.149 1 70.96 ? O2B UDP 1201 D 1 
HETATM 25 O O3B UDP . . . L 3 183.297 -36.54 23.113 1 72.39 ? O3B UDP 1201 D 1 
#
_model_server_stats.io_time_ms              16 
_model_server_stats.parse_time_ms           9 
_model_server_stats.create_model_time_ms    148 
_model_server_stats.query_time_ms           520 
_model_server_stats.encode_time_ms          3 
_model_server_stats.element_count           25 
#