data_8HJN
#
_model_server_result.job_id            01F4LbPTl0qvs6UG4iLoTw 
_model_server_result.datetime_utc      '2024-11-28 03:59:44' 
_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          8hjn 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"D","auth_seq_id":501}' 
#
_entry.id    8HJN 
#
_exptl.entry_id    8HJN 
_exptl.method      'X-RAY DIFFRACTION' 
#
_entity.details                     ? 
_entity.formula_weight              566.302 
_entity.id                          2 
_entity.src_method                  syn 
_entity.type                        non-polymer 
_entity.pdbx_description            "URIDINE-5'-DIPHOSPHATE-GLUCOSE" 
_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            8HJN 
_cell.length_a            64.22 
_cell.length_b            80.095 
_cell.length_c            172.508 
_cell.Z_PDB               8 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 8HJN 
_symmetry.cell_setting             ? 
_symmetry.Int_Tables_number        19 
_symmetry.space_group_name_Hall    'P 2ac 2ab' 
_symmetry.space_group_name_H-M     'P 21 21 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
PISA monomeric 1 author_and_software_defined_assembly 1 
PISA monomeric 1 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,C 1 1 
B,D 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
? 2 C N N 
? 2 D 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
disulf ? disulf1 A SG CYS 199 A CYS 199 1_555 A SG CYS 204 A CYS 204 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.025 ? 
disulf ? disulf2 B SG CYS 199 B CYS 199 1_555 B SG CYS 204 B CYS 204 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.032 ? 
#
_chem_comp.formula           'C15 H24 N2 O17 P2' 
_chem_comp.formula_weight    566.302 
_chem_comp.id                UPG 
_chem_comp.mon_nstd_flag     . 
_chem_comp.name              "URIDINE-5'-DIPHOSPHATE-GLUCOSE" 
_chem_comp.type              non-polymer 
_chem_comp.pdbx_synonyms     "URIDINE-5'-MONOPHOSPHATE GLUCOPYRANOSYL-MONOPHOSPHATE ESTER" 
#
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 UPG sing 356 n n 
N1 C6 UPG sing 357 n n 
N1 C1C UPG sing 358 n n 
C2 N3 UPG sing 359 n n 
C2 O2 UPG doub 360 n n 
N3 C4 UPG sing 361 n n 
N3 HN3 UPG sing 362 n n 
C4 C5 UPG sing 363 n n 
C4 O4 UPG doub 364 n n 
C5 C6 UPG doub 365 n n 
C5 H5 UPG sing 366 n n 
C6 H6 UPG sing 367 n n 
C1C C2C UPG sing 368 n n 
C1C O4C UPG sing 369 n n 
C1C H1C UPG sing 370 n n 
C2C O2C UPG sing 371 n n 
C2C C3C UPG sing 372 n n 
C2C H2C UPG sing 373 n n 
O2C HO2C UPG sing 374 n n 
C3C C4C UPG sing 375 n n 
C3C O3C UPG sing 376 n n 
C3C H3C UPG sing 377 n n 
C4C O4C UPG sing 378 n n 
C4C C5C UPG sing 379 n n 
C4C H4C UPG sing 380 n n 
O3C HO3C UPG sing 381 n n 
C5C O5C UPG sing 382 n n 
C5C H5C1 UPG sing 383 n n 
C5C H5C2 UPG sing 384 n n 
O5C PA UPG sing 385 n n 
PA O1A UPG doub 386 n n 
PA O2A UPG sing 387 n n 
PA O3A UPG sing 388 n n 
O2A HOA2 UPG sing 389 n n 
O3A PB UPG sing 390 n n 
PB O1B UPG doub 391 n n 
PB O2B UPG sing 392 n n 
PB O3B UPG sing 393 n n 
O2B HOB2 UPG sing 394 n n 
O3B C1' UPG sing 395 n n 
C1' C2' UPG sing 396 n n 
C1' O5' UPG sing 397 n n 
C1' H1' UPG sing 398 n n 
C2' C3' UPG sing 399 n n 
C2' O2' UPG sing 400 n n 
C2' H2' UPG sing 401 n n 
C3' C4' UPG sing 402 n n 
C3' O3' UPG sing 403 n n 
C3' H3' UPG sing 404 n n 
C4' C5' UPG sing 405 n n 
C4' O4' UPG sing 406 n n 
C4' H4' UPG sing 407 n n 
C5' C6' UPG sing 408 n n 
C5' O5' UPG sing 409 n n 
C5' H5' UPG sing 410 n n 
C6' O6' UPG sing 411 n n 
C6' "H6'1" UPG sing 412 n n 
C6' "H6'2" UPG sing 413 n n 
O2' HO2' UPG sing 414 n n 
O3' HO3' UPG sing 415 n n 
O4' HO4' UPG sing 416 n n 
O6' HO6' UPG sing 417 n n 
#
_atom_sites.entry_id                     8HJN 
_atom_sites.fract_transf_matrix[1][1]    0.015571 
_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]    0.012485 
_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]    0.005797 
_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 UPG A 1 501 2 UPG UPG . 
D 2 UPG B 1 501 1 UPG UPG . 
#
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 UPG . . . D 2 19.513 -55.384 -21.727 1 26.91 ? N1 UPG 501 B 1 
HETATM 2 C C2 UPG . . . D 2 20.329 -56.29 -21.069 1 36.05 ? C2 UPG 501 B 1 
HETATM 3 N N3 UPG . . . D 2 19.679 -57.113 -20.184 1 28.21 ? N3 UPG 501 B 1 
HETATM 4 C C4 UPG . . . D 2 18.329 -57.132 -19.9 1 36.54 ? C4 UPG 501 B 1 
HETATM 5 C C5 UPG . . . D 2 17.553 -56.169 -20.625 1 36.47 ? C5 UPG 501 B 1 
HETATM 6 C C6 UPG . . . D 2 18.16 -55.345 -21.491 1 28.04 ? C6 UPG 501 B 1 
HETATM 7 O O2 UPG . . . D 2 21.54 -56.355 -21.233 1 61.55 ? O2 UPG 501 B 1 
HETATM 8 O O4 UPG . . . D 2 17.899 -57.938 -19.076 1 41.3 ? O4 UPG 501 B 1 
HETATM 9 C C1C UPG . . . D 2 20.135 -54.46 -22.699 1 40.13 ? C1C UPG 501 B 1 
HETATM 10 C C2C UPG . . . D 2 20.772 -53.231 -22.06 1 42.56 ? C2C UPG 501 B 1 
HETATM 11 O O2C UPG . . . D 2 19.761 -52.312 -21.703 1 27.68 ? O2C UPG 501 B 1 
HETATM 12 C C3C UPG . . . D 2 21.688 -52.761 -23.199 1 40.64 ? C3C UPG 501 B 1 
HETATM 13 C C4C UPG . . . D 2 22.005 -54.046 -23.988 1 42.53 ? C4C UPG 501 B 1 
HETATM 14 O O4C UPG . . . D 2 21.188 -55.088 -23.391 1 50.13 ? O4C UPG 501 B 1 
HETATM 15 O O3C UPG . . . D 2 20.991 -51.853 -24.04 1 47.87 ? O3C UPG 501 B 1 
HETATM 16 C C5C UPG . . . D 2 23.448 -54.485 -24.017 1 47.56 ? C5C UPG 501 B 1 
HETATM 17 O O5C UPG . . . D 2 23.917 -54.699 -22.665 1 46.85 ? O5C UPG 501 B 1 
HETATM 18 P PA UPG . . . D 2 25.434 -54.328 -22.304 1 75.08 ? PA UPG 501 B 1 
HETATM 19 O O1A UPG . . . D 2 25.491 -53.824 -20.901 1 70.57 ? O1A UPG 501 B 1 
HETATM 20 O O2A UPG . . . D 2 26.011 -53.461 -23.375 1 45.99 ? O2A UPG 501 B 1 
HETATM 21 O O3A UPG . . . D 2 26.127 -55.77 -22.393 1 72.64 ? O3A UPG 501 B 1 
HETATM 22 P PB UPG . . . D 2 26.655 -56.611 -23.652 1 102.24 ? PB UPG 501 B 1 
HETATM 23 O O1B UPG . . . D 2 25.493 -56.984 -24.515 1 62.77 ? O1B UPG 501 B 1 
HETATM 24 O O2B UPG . . . D 2 27.55 -57.694 -23.146 1 80.66 ? O2B UPG 501 B 1 
HETATM 25 O O3B UPG . . . D 2 27.562 -55.517 -24.401 1 83.73 ? O3B UPG 501 B 1 
HETATM 26 C C1' UPG . . . D 2 28.957 -55.459 -24.237 1 80.75 ? C1' UPG 501 B 1 
HETATM 27 C C2' UPG . . . D 2 29.417 -54.027 -24.459 1 69.1 ? C2' UPG 501 B 1 
HETATM 28 C C3' UPG . . . D 2 30.935 -53.946 -24.282 1 62.89 ? C3' UPG 501 B 1 
HETATM 29 C C4' UPG . . . D 2 31.67 -55.004 -25.104 1 61.63 ? C4' UPG 501 B 1 
HETATM 30 C C5' UPG . . . D 2 31.039 -56.391 -24.961 1 64.76 ? C5' UPG 501 B 1 
HETATM 31 C C6' UPG . . . D 2 31.251 -57.042 -23.613 1 64.13 ? C6' UPG 501 B 1 
HETATM 32 O O2' UPG . . . D 2 29.013 -53.594 -25.755 1 54.31 ? O2' UPG 501 B 1 
HETATM 33 O O3' UPG . . . D 2 31.27 -54.101 -22.904 1 58.03 ? O3' UPG 501 B 1 
HETATM 34 O O4' UPG . . . D 2 31.659 -54.654 -26.485 1 73.99 ? O4' UPG 501 B 1 
HETATM 35 O O5' UPG . . . D 2 29.612 -56.307 -25.165 1 75.35 ? O5' UPG 501 B 1 
HETATM 36 O O6' UPG . . . D 2 30.955 -58.438 -23.672 1 58.51 ? O6' UPG 501 B 1 
#
_model_server_stats.io_time_ms              71 
_model_server_stats.parse_time_ms           55 
_model_server_stats.create_model_time_ms    19 
_model_server_stats.query_time_ms           1183 
_model_server_stats.encode_time_ms          8 
_model_server_stats.element_count           36 
#