data_5HVM
#
_model_server_result.job_id            1Wh6nZNFsdwfVgh2UmaolA 
_model_server_result.datetime_utc      '2024-11-08 20:04:45' 
_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          5hvm 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"C","auth_seq_id":601}' 
#
_entry.id    5HVM 
#
_exptl.entry_id    5HVM 
_exptl.method      'X-RAY DIFFRACTION' 
#
_entity.details                     ? 
_entity.formula_weight              404.161 
_entity.id                          2 
_entity.src_method                  syn 
_entity.type                        non-polymer 
_entity.pdbx_description            "URIDINE-5'-DIPHOSPHATE" 
_entity.pdbx_number_of_molecules    2 
_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            5HVM 
_cell.length_a            83.915 
_cell.length_b            101.153 
_cell.length_c            146.992 
_cell.Z_PDB               8 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 5HVM 
_symmetry.cell_setting             ? 
_symmetry.Int_Tables_number        18 
_symmetry.space_group_name_Hall    . 
_symmetry.space_group_name_H-M     'P 21 2 21' 
#
loop_
_pdbx_struct_assembly.method_details
_pdbx_struct_assembly.oligomeric_details
_pdbx_struct_assembly.oligomeric_count
_pdbx_struct_assembly.details
_pdbx_struct_assembly.id
? dimeric 2 author_defined_assembly 1 
PISA tetrameric 4 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,C,D,E,F,G,H 1 1 
A,B,C,D,E,F,G,H 2 1,2 
#
loop_
_pdbx_struct_oper_list.id
_pdbx_struct_oper_list.type
_pdbx_struct_oper_list.name
_pdbx_struct_oper_list.symmetry_operation
_pdbx_struct_oper_list.matrix[1][1]
_pdbx_struct_oper_list.matrix[1][2]
_pdbx_struct_oper_list.matrix[1][3]
_pdbx_struct_oper_list.matrix[2][1]
_pdbx_struct_oper_list.matrix[2][2]
_pdbx_struct_oper_list.matrix[2][3]
_pdbx_struct_oper_list.matrix[3][1]
_pdbx_struct_oper_list.matrix[3][2]
_pdbx_struct_oper_list.matrix[3][3]
_pdbx_struct_oper_list.vector[1]
_pdbx_struct_oper_list.vector[2]
_pdbx_struct_oper_list.vector[3]
1 'identity operation' 1_555 x,y,z 1 0 0 0 1 0 0 0 1 0 0 0 
2 'crystal symmetry operation' 2_555 -x,y,-z -1 0 0 0 1 0 0 0 -1 0 0 0 
#
loop_
_struct_asym.details
_struct_asym.entity_id
_struct_asym.id
_struct_asym.pdbx_modified
_struct_asym.pdbx_blank_PDB_chainid_flag
? 2 C N N 
? 2 E N N 
#
_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 358 n n 
N1 C6 UDP sing 359 n n 
N1 C1' UDP sing 360 n n 
C2 N3 UDP sing 361 n n 
C2 O2 UDP doub 362 n n 
N3 C4 UDP sing 363 n n 
N3 HN3 UDP sing 364 n n 
C4 C5 UDP sing 365 n n 
C4 O4 UDP doub 366 n n 
C5 C6 UDP doub 367 n n 
C5 H5 UDP sing 368 n n 
C6 H6 UDP sing 369 n n 
C1' C2' UDP sing 370 n n 
C1' O4' UDP sing 371 n n 
C1' H1' UDP sing 372 n n 
C2' O2' UDP sing 373 n n 
C2' C3' UDP sing 374 n n 
C2' H2' UDP sing 375 n n 
O2' HO2' UDP sing 376 n n 
C3' C4' UDP sing 377 n n 
C3' O3' UDP sing 378 n n 
C3' H3' UDP sing 379 n n 
C4' O4' UDP sing 380 n n 
C4' C5' UDP sing 381 n n 
C4' H4' UDP sing 382 n n 
O3' HO3' UDP sing 383 n n 
C5' O5' UDP sing 384 n n 
C5' "H5'1" UDP sing 385 n n 
C5' "H5'2" UDP sing 386 n n 
O5' PA UDP sing 387 n n 
PA O1A UDP doub 388 n n 
PA O2A UDP sing 389 n n 
PA O3A UDP sing 390 n n 
O2A HOA2 UDP sing 391 n n 
O3A PB UDP sing 392 n n 
PB O1B UDP doub 393 n n 
PB O2B UDP sing 394 n n 
PB O3B UDP sing 395 n n 
O2B HOB2 UDP sing 396 n n 
O3B HOB3 UDP sing 397 n n 
#
_atom_sites.entry_id                     5HVM 
_atom_sites.fract_transf_matrix[1][1]    0.011917 
_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]    0.009886 
_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]    0.006803 
_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 2 UDP A 1 601 601 UDP UDP . 
D 3 VDM A 1 602 602 VDM VDM . 
E 2 UDP B 1 601 601 UDP UDP . 
F 3 VDM B 1 602 602 VDM VDM . 
G 4 HOH A 1 701 5 HOH HOH . 
G 4 HOH A 2 702 3 HOH HOH . 
G 4 HOH A 3 703 2 HOH HOH . 
G 4 HOH A 4 704 6 HOH HOH . 
G 4 HOH A 5 705 1 HOH HOH . 
G 4 HOH A 6 706 7 HOH HOH . 
H 4 HOH B 1 701 8 HOH HOH . 
H 4 HOH B 2 702 4 HOH HOH . 
H 4 HOH B 3 703 9 HOH HOH . 
H 4 HOH B 4 704 10 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 2 26.377 -19.81 -0.009 1 43.94 ? N1 UDP 601 A 1 
HETATM 2 C C2 UDP . . . C 2 26.363 -19.016 -1.243 1 51.66 ? C2 UDP 601 A 1 
HETATM 3 N N3 UDP . . . C 2 26.523 -17.565 -1.191 1 48.04 ? N3 UDP 601 A 1 
HETATM 4 C C4 UDP . . . C 2 26.692 -16.922 0.061 1 51.14 ? C4 UDP 601 A 1 
HETATM 5 C C5 UDP . . . C 2 26.704 -17.716 1.298 1 57.79 ? C5 UDP 601 A 1 
HETATM 6 C C6 UDP . . . C 2 26.552 -19.175 1.247 1 46.35 ? C6 UDP 601 A 1 
HETATM 7 O O2 UDP . . . C 2 26.216 -19.562 -2.321 1 53.36 ? O2 UDP 601 A 1 
HETATM 8 O O4 UDP . . . C 2 26.822 -15.717 0.122 1 54.12 ? O4 UDP 601 A 1 
HETATM 9 C C1' UDP . . . C 2 26.233 -21.184 -0.13 1 47.8 ? C1' UDP 601 A 1 
HETATM 10 C C2' UDP . . . C 2 26.189 -21.867 1.011 1 58.22 ? C2' UDP 601 A 1 
HETATM 11 O O2' UDP . . . C 2 27.496 -22.02 1.679 1 50.82 ? O2' UDP 601 A 1 
HETATM 12 C C3' UDP . . . C 2 25.615 -23.22 0.505 1 55.97 ? C3' UDP 601 A 1 
HETATM 13 C C4' UDP . . . C 2 24.535 -22.746 -0.55 1 51.64 ? C4' UDP 601 A 1 
HETATM 14 O O4' UDP . . . C 2 24.786 -21.492 -0.803 1 52.18 ? O4' UDP 601 A 1 
HETATM 15 O O3' UDP . . . C 2 26.505 -24.015 -0.093 1 48.68 ? O3' UDP 601 A 1 
HETATM 16 C C5' UDP . . . C 2 23.16 -22.927 0.045 1 37.76 ? C5' UDP 601 A 1 
HETATM 17 O O5' UDP . . . C 2 22.795 -24.224 -0.321 1 46.76 ? O5' UDP 601 A 1 
HETATM 18 P PA UDP . . . C 2 21.515 -24.938 0.267 1 52.67 ? PA UDP 601 A 1 
HETATM 19 O O1A UDP . . . C 2 21.744 -26.414 0.076 1 54.61 ? O1A UDP 601 A 1 
HETATM 20 O O2A UDP . . . C 2 21.31 -24.65 1.733 1 55 ? O2A UDP 601 A 1 
HETATM 21 O O3A UDP . . . C 2 20.152 -24.554 -0.445 1 55.91 ? O3A UDP 601 A 1 
HETATM 22 P PB UDP . . . C 2 19.853 -23.699 -1.72 1 70.7 ? PB UDP 601 A 1 
HETATM 23 O O1B UDP . . . C 2 20.457 -24.354 -2.917 1 57.18 ? O1B UDP 601 A 1 
HETATM 24 O O2B UDP . . . C 2 20.385 -22.314 -1.552 1 50.5 ? O2B UDP 601 A 1 
HETATM 25 O O3B UDP . . . C 2 18.369 -23.621 -1.866 1 55.18 ? O3B UDP 601 A 1 
HETATM 26 H HN3 UDP . . . C 2 26.509 -17.074 -1.96 1 57.65 ? HN3 UDP 601 A 1 
HETATM 27 H H5 UDP . . . C 2 26.825 -17.271 2.158 1 69.34 ? H5 UDP 601 A 1 
HETATM 28 H H6 UDP . . . C 2 26.563 -19.702 2.069 1 55.62 ? H6 UDP 601 A 1 
HETATM 29 H H1' UDP . . . C 2 26.944 -21.541 -0.7 1 57.36 ? H1' UDP 601 A 1 
HETATM 30 H H2' UDP . . . C 2 25.553 -21.446 1.623 1 69.86 ? H2' UDP 601 A 1 
HETATM 31 H HO2' UDP . . . C 2 27.675 -22.884 1.785 1 60.98 ? HO2' UDP 601 A 1 
HETATM 32 H H3' UDP . . . C 2 25.18 -23.696 1.24 1 67.16 ? H3' UDP 601 A 1 
HETATM 33 H H4' UDP . . . C 2 24.616 -23.274 -1.37 1 61.97 ? H4' UDP 601 A 1 
HETATM 34 H HO3' UDP . . . C 2 26.846 -23.597 -0.803 1 58.42 ? HO3' UDP 601 A 1 
HETATM 35 H "H5'1" UDP . . . C 2 22.533 -22.275 -0.331 1 45.31 ? "H5'1" UDP 601 A 1 
HETATM 36 H "H5'2" UDP . . . C 2 23.197 -22.845 1.02 1 45.31 ? "H5'2" UDP 601 A 1 
#
_model_server_stats.io_time_ms              8 
_model_server_stats.parse_time_ms           23 
_model_server_stats.create_model_time_ms    7 
_model_server_stats.query_time_ms           226 
_model_server_stats.encode_time_ms          2 
_model_server_stats.element_count           36 
#