data_4KQM
#
_model_server_result.job_id            BgtVgN64dDzw7YhNYHjgbA 
_model_server_result.datetime_utc      '2024-10-19 05:24:34' 
_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          4kqm 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"P","auth_seq_id":801}' 
#
_entry.id    4KQM 
#
_exptl.entry_id    4KQM 
_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    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            4KQM 
_cell.length_a            192.71 
_cell.length_b            204.443 
_cell.length_c            206.332 
_cell.Z_PDB               32 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 4KQM 
_symmetry.cell_setting             ? 
_symmetry.Int_Tables_number        23 
_symmetry.space_group_name_Hall    ? 
_symmetry.space_group_name_H-M     'I 2 2 2' 
#
_pdbx_struct_assembly.method_details        PISA 
_pdbx_struct_assembly.oligomeric_details    tetrameric 
_pdbx_struct_assembly.oligomeric_count      4 
_pdbx_struct_assembly.details               author_and_software_defined_assembly 
_pdbx_struct_assembly.id                    1 
#
_pdbx_struct_assembly_gen.asym_id_list       A,B,C,D,E,F,G,H,I,J,K,L,M,N,O,P,Q,R 
_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    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 E N N 
? 2 H N N 
? 2 M N N 
? 2 P 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 449 n n 
N1 C6 UDP sing 450 n n 
N1 C1' UDP sing 451 n n 
C2 N3 UDP sing 452 n n 
C2 O2 UDP doub 453 n n 
N3 C4 UDP sing 454 n n 
N3 HN3 UDP sing 455 n n 
C4 C5 UDP sing 456 n n 
C4 O4 UDP doub 457 n n 
C5 C6 UDP doub 458 n n 
C5 H5 UDP sing 459 n n 
C6 H6 UDP sing 460 n n 
C1' C2' UDP sing 461 n n 
C1' O4' UDP sing 462 n n 
C1' H1' UDP sing 463 n n 
C2' O2' UDP sing 464 n n 
C2' C3' UDP sing 465 n n 
C2' H2' UDP sing 466 n n 
O2' HO2' UDP sing 467 n n 
C3' C4' UDP sing 468 n n 
C3' O3' UDP sing 469 n n 
C3' H3' UDP sing 470 n n 
C4' O4' UDP sing 471 n n 
C4' C5' UDP sing 472 n n 
C4' H4' UDP sing 473 n n 
O3' HO3' UDP sing 474 n n 
C5' O5' UDP sing 475 n n 
C5' "H5'1" UDP sing 476 n n 
C5' "H5'2" UDP sing 477 n n 
O5' PA UDP sing 478 n n 
PA O1A UDP doub 479 n n 
PA O2A UDP sing 480 n n 
PA O3A UDP sing 481 n n 
O2A HOA2 UDP sing 482 n n 
O3A PB UDP sing 483 n n 
PB O1B UDP doub 484 n n 
PB O2B UDP sing 485 n n 
PB O3B UDP sing 486 n n 
O2B HOB2 UDP sing 487 n n 
O3B HOB3 UDP sing 488 n n 
#
_atom_sites.entry_id                     4KQM 
_atom_sites.fract_transf_matrix[1][1]    0.005189 
_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]    0.004891 
_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]    0.004847 
_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 UDP A 1 801 801 UDP UDP . 
F 3 G6P A 1 802 901 G6P G6P . 
G 4 PEG A 1 803 1001 PEG PEG . 
H 2 UDP B 1 801 801 UDP UDP . 
I 3 G6P B 1 802 901 G6P G6P . 
J 4 PEG B 1 803 1001 PEG PEG . 
K 5 GLC C 1 801 701 GLC GLC . 
L 6 BGC C 1 802 1101 BGC BGC . 
M 2 UDP C 1 803 801 UDP UDP . 
N 3 G6P C 1 804 901 G6P G6P . 
O 4 PEG C 1 805 1001 PEG PEG . 
P 2 UDP D 1 801 801 UDP UDP . 
Q 3 G6P D 1 802 901 G6P G6P . 
R 4 PEG D 1 803 1001 PEG PEG . 
#
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 . . . P 2 15.268 43.327 118.811 1 57.22 ? N1 UDP 801 D 1 
HETATM 2 C C2 UDP . . . P 2 15.732 43.26 117.501 1 56.38 ? C2 UDP 801 D 1 
HETATM 3 N N3 UDP . . . P 2 16.03 44.385 116.825 1 61.16 ? N3 UDP 801 D 1 
HETATM 4 C C4 UDP . . . P 2 15.885 45.6 117.403 1 54.81 ? C4 UDP 801 D 1 
HETATM 5 C C5 UDP . . . P 2 15.419 45.694 118.719 1 51.2 ? C5 UDP 801 D 1 
HETATM 6 C C6 UDP . . . P 2 15.111 44.526 119.417 1 56.5 ? C6 UDP 801 D 1 
HETATM 7 O O2 UDP . . . P 2 15.86 42.133 116.999 1 56.87 ? O2 UDP 801 D 1 
HETATM 8 O O4 UDP . . . P 2 16.177 46.639 116.76 1 48.18 ? O4 UDP 801 D 1 
HETATM 9 C C1' UDP . . . P 2 14.974 42.051 119.459 1 58.17 ? C1' UDP 801 D 1 
HETATM 10 C C2' UDP . . . P 2 15.684 41.931 120.795 1 60.6 ? C2' UDP 801 D 1 
HETATM 11 O O2' UDP . . . P 2 16.877 41.174 120.623 1 57.6 ? O2' UDP 801 D 1 
HETATM 12 C C3' UDP . . . P 2 14.681 41.217 121.676 1 62.21 ? C3' UDP 801 D 1 
HETATM 13 C C4' UDP . . . P 2 13.336 41.384 120.979 1 59.19 ? C4' UDP 801 D 1 
HETATM 14 O O4' UDP . . . P 2 13.573 41.914 119.686 1 58.45 ? O4' UDP 801 D 1 
HETATM 15 O O3' UDP . . . P 2 15.015 39.827 121.768 1 62.86 ? O3' UDP 801 D 1 
HETATM 16 C C5' UDP . . . P 2 12.444 42.368 121.699 1 58.77 ? C5' UDP 801 D 1 
HETATM 17 O O5' UDP . . . P 2 11.969 41.75 122.88 1 59.02 ? O5' UDP 801 D 1 
HETATM 18 P PA UDP . . . P 2 10.504 42.119 123.409 1 63.71 ? PA UDP 801 D 1 
HETATM 19 O O1A UDP . . . P 2 10.548 43.57 123.838 1 66.3 ? O1A UDP 801 D 1 
HETATM 20 O O2A UDP . . . P 2 9.519 41.659 122.354 1 57.34 ? O2A UDP 801 D 1 
HETATM 21 O O3A UDP . . . P 2 10.362 41.225 124.753 1 65.68 ? O3A UDP 801 D 1 
HETATM 22 P PB UDP . . . P 2 11.269 41.483 126.07 1 66.67 ? PB UDP 801 D 1 
HETATM 23 O O1B UDP . . . P 2 11.561 40.106 126.601 1 71.95 ? O1B UDP 801 D 1 
HETATM 24 O O2B UDP . . . P 2 10.382 42.335 126.945 1 70.43 ? O2B UDP 801 D 1 
HETATM 25 O O3B UDP . . . P 2 12.521 42.164 125.601 1 70.29 ? O3B UDP 801 D 1 
#
_model_server_stats.io_time_ms              77 
_model_server_stats.parse_time_ms           11 
_model_server_stats.create_model_time_ms    46 
_model_server_stats.query_time_ms           344 
_model_server_stats.encode_time_ms          2 
_model_server_stats.element_count           25 
#