data_2AIZ
#
_model_server_result.job_id            TZgLQ1aNI3876LsZza7XQg 
_model_server_result.datetime_utc      '2024-11-05 01:21:30' 
_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          2aiz 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"D","auth_seq_id":102}' 
#
_entry.id    2AIZ 
#
_exptl.entry_id    2AIZ 
_exptl.method      'SOLUTION NMR' 
#
_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                     ? 
#
_pdbx_struct_assembly.method_details        ? 
_pdbx_struct_assembly.oligomeric_details    dimeric 
_pdbx_struct_assembly.oligomeric_count      2 
_pdbx_struct_assembly.details               author_defined_assembly 
_pdbx_struct_assembly.id                    1 
#
_pdbx_struct_assembly_gen.asym_id_list       A,B,C,D 
_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    ? 
_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 B C ALA 1 U ALA 3 1_555 B N DGL 2 U DGL 4 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.331 ? 
covale ? covale2 B N ALA 1 U ALA 3 1_555 C C10 AMU . U AMU 101 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.331 ? 
covale ? covale3 B C DGL 2 U DGL 4 1_555 B N 6CL 3 U 6CL 5 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.331 ? 
covale ? covale4 B C 6CL 3 U 6CL 5 1_555 B N DAL 4 U DAL 6 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.326 ? 
covale ? covale5 B C DAL 4 U DAL 6 1_555 B N DAL 5 U DAL 7 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.324 ? 
covale ? covale6 C O1 AMU . U AMU 101 1_555 D PB UDP . U UDP 102 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.601 ? 
#
_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 405 n n 
N1 C6 UDP sing 406 n n 
N1 C1' UDP sing 407 n n 
C2 N3 UDP sing 408 n n 
C2 O2 UDP doub 409 n n 
N3 C4 UDP sing 410 n n 
N3 HN3 UDP sing 411 n n 
C4 C5 UDP sing 412 n n 
C4 O4 UDP doub 413 n n 
C5 C6 UDP doub 414 n n 
C5 H5 UDP sing 415 n n 
C6 H6 UDP sing 416 n n 
C1' C2' UDP sing 417 n n 
C1' O4' UDP sing 418 n n 
C1' H1' UDP sing 419 n n 
C2' O2' UDP sing 420 n n 
C2' C3' UDP sing 421 n n 
C2' H2' UDP sing 422 n n 
O2' HO2' UDP sing 423 n n 
C3' C4' UDP sing 424 n n 
C3' O3' UDP sing 425 n n 
C3' H3' UDP sing 426 n n 
C4' O4' UDP sing 427 n n 
C4' C5' UDP sing 428 n n 
C4' H4' UDP sing 429 n n 
O3' HO3' UDP sing 430 n n 
C5' O5' UDP sing 431 n n 
C5' "H5'1" UDP sing 432 n n 
C5' "H5'2" UDP sing 433 n n 
O5' PA UDP sing 434 n n 
PA O1A UDP doub 435 n n 
PA O2A UDP sing 436 n n 
PA O3A UDP sing 437 n n 
O2A HOA2 UDP sing 438 n n 
O3A PB UDP sing 439 n n 
PB O1B UDP doub 440 n n 
PB O2B UDP sing 441 n n 
PB O3B UDP sing 442 n n 
O2B HOB2 UDP sing 443 n n 
O3B HOB3 UDP sing 444 n n 
#
_atom_sites.entry_id                     2AIZ 
_atom_sites.fract_transf_matrix[1][1]    1 
_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]    1 
_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]    1 
_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 AMU U 1 101 2 AMU AMU . 
D 4 UDP U 1 102 1 UDP UDP . 
#
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 4 147.04 13.542 -9.264 1 0 ? N1 UDP 102 U 1 
HETATM 2 C C2 UDP . . . D 4 147.533 13.773 -7.994 1 0 ? C2 UDP 102 U 1 
HETATM 3 N N3 UDP . . . D 4 146.936 14.81 -7.321 1 0 ? N3 UDP 102 U 1 
HETATM 4 C C4 UDP . . . D 4 145.92 15.622 -7.78 1 0 ? C4 UDP 102 U 1 
HETATM 5 C C5 UDP . . . D 4 145.468 15.317 -9.103 1 0 ? C5 UDP 102 U 1 
HETATM 6 C C6 UDP . . . D 4 146.028 14.313 -9.786 1 0 ? C6 UDP 102 U 1 
HETATM 7 O O2 UDP . . . D 4 148.428 13.108 -7.502 1 0 ? O2 UDP 102 U 1 
HETATM 8 O O4 UDP . . . D 4 145.486 16.519 -7.057 1 0 ? O4 UDP 102 U 1 
HETATM 9 C C1' UDP . . . D 4 147.638 12.445 -10.037 1 0 ? C1' UDP 102 U 1 
HETATM 10 C C2' UDP . . . D 4 146.951 11.097 -9.828 1 0 ? C2' UDP 102 U 1 
HETATM 11 O O2' UDP . . . D 4 147.9 10.069 -10.033 1 0 ? O2' UDP 102 U 1 
HETATM 12 C C3' UDP . . . D 4 145.911 11.118 -10.941 1 0 ? C3' UDP 102 U 1 
HETATM 13 C C4' UDP . . . D 4 146.643 11.827 -12.072 1 0 ? C4' UDP 102 U 1 
HETATM 14 O O4' UDP . . . D 4 147.538 12.764 -11.414 1 0 ? O4' UDP 102 U 1 
HETATM 15 O O3' UDP . . . D 4 145.508 9.807 -11.322 1 0 ? O3' UDP 102 U 1 
HETATM 16 C C5' UDP . . . D 4 145.759 12.595 -13.027 1 0 ? C5' UDP 102 U 1 
HETATM 17 O O5' UDP . . . D 4 146.281 12.512 -14.351 1 0 ? O5' UDP 102 U 1 
HETATM 18 P PA UDP . . . D 4 145.666 13.391 -15.528 1 0 ? PA UDP 102 U 1 
HETATM 19 O O1A UDP . . . D 4 146.629 13.352 -16.658 1 0 ? O1A UDP 102 U 1 
HETATM 20 O O2A UDP . . . D 4 145.27 14.701 -14.954 1 0 ? O2A UDP 102 U 1 
HETATM 21 O O3A UDP . . . D 4 144.329 12.628 -15.99 1 0 ? O3A UDP 102 U 1 
HETATM 22 P PB UDP . . . D 4 142.811 13.152 -16.061 1 0 ? PB UDP 102 U 1 
HETATM 23 O O1B UDP . . . D 4 142.598 13.744 -17.406 1 0 ? O1B UDP 102 U 1 
HETATM 24 O O3B UDP . . . D 4 142.557 13.976 -14.852 1 0 ? O3B UDP 102 U 1 
HETATM 25 H HN3 UDP . . . D 4 147.277 14.999 -6.39 1 0 ? HN3 UDP 102 U 1 
HETATM 26 H H5 UDP . . . D 4 144.667 15.903 -9.553 1 0 ? H5 UDP 102 U 1 
HETATM 27 H H6 UDP . . . D 4 145.667 14.098 -10.792 1 0 ? H6 UDP 102 U 1 
HETATM 28 H H1' UDP . . . D 4 148.702 12.405 -9.798 1 0 ? H1' UDP 102 U 1 
HETATM 29 H H2' UDP . . . D 4 146.467 11.039 -8.85 1 0 ? H2' UDP 102 U 1 
HETATM 30 H HO2' UDP . . . D 4 147.541 9.269 -9.649 1 0 ? HO2' UDP 102 U 1 
HETATM 31 H H3' UDP . . . D 4 145.001 11.643 -10.656 1 0 ? H3' UDP 102 U 1 
HETATM 32 H H4' UDP . . . D 4 147.16 11.058 -12.646 1 0 ? H4' UDP 102 U 1 
HETATM 33 H HO3' UDP . . . D 4 145.659 9.64 -12.276 1 0 ? HO3' UDP 102 U 1 
HETATM 34 H "H5'1" UDP . . . D 4 144.753 12.175 -13.002 1 0 ? "H5'1" UDP 102 U 1 
HETATM 35 H "H5'2" UDP . . . D 4 145.718 13.636 -12.712 1 0 ? "H5'2" UDP 102 U 1 
#
_model_server_stats.io_time_ms              16 
_model_server_stats.parse_time_ms           7 
_model_server_stats.create_model_time_ms    57 
_model_server_stats.query_time_ms           5470 
_model_server_stats.encode_time_ms          2 
_model_server_stats.element_count           35 
#