data_4KYA
#
_model_server_result.job_id            fSg5zuEw-4EE58tvO50Sjg 
_model_server_result.datetime_utc      '2024-11-12 21:14:44' 
_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          4kya 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"U","auth_seq_id":701}' 
#
_entry.id    4KYA 
#
_exptl.entry_id    4KYA 
_exptl.method      'X-RAY DIFFRACTION' 
#
_entity.details                     ? 
_entity.formula_weight              308.182 
_entity.id                          2 
_entity.src_method                  syn 
_entity.type                        non-polymer 
_entity.pdbx_description            "2'-DEOXYURIDINE 5'-MONOPHOSPHATE" 
_entity.pdbx_number_of_molecules    8 
_entity.pdbx_parent_entity_id       . 
_entity.pdbx_mutation               ? 
_entity.pdbx_fragment               ? 
_entity.pdbx_ec                     ? 
#
_cell.angle_alpha         90.07 
_cell.angle_beta          89.96 
_cell.angle_gamma         90.07 
_cell.entry_id            4KYA 
_cell.length_a            53.531 
_cell.length_b            145.079 
_cell.length_c            176.614 
_cell.Z_PDB               8 
_cell.pdbx_unique_axis    ? 
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_symmetry.entry_id                 4KYA 
_symmetry.cell_setting             ? 
_symmetry.Int_Tables_number        1 
_symmetry.space_group_name_Hall    ? 
_symmetry.space_group_name_H-M     'P 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,B,I,J,K,L,M,N,O,P 1 1 
C,D,Q,R,S,T,U,V,W,X 2 1 
E,F,Y,Z,AA,BA,CA,DA,EA,FA 3 1 
G,H,GA,HA,IA,JA,KA,LA,MA,NA 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
? 2 I N N 
? 2 M N N 
? 2 Q N N 
? 2 U N N 
? 2 Y N N 
? 2 CA N N 
? 2 GA N N 
? 2 KA N N 
#
_chem_comp.formula           'C9 H13 N2 O8 P' 
_chem_comp.formula_weight    308.182 
_chem_comp.id                UMP 
_chem_comp.mon_nstd_flag     . 
_chem_comp.name              "2'-DEOXYURIDINE 5'-MONOPHOSPHATE" 
_chem_comp.type              non-polymer 
_chem_comp.pdbx_synonyms     DUMP 
#
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 UMP sing 535 n n 
N1 C6 UMP sing 536 n n 
N1 C1' UMP sing 537 n n 
C2 N3 UMP sing 538 n n 
C2 O2 UMP doub 539 n n 
N3 C4 UMP sing 540 n n 
N3 HN3 UMP sing 541 n n 
C4 C5 UMP sing 542 n n 
C4 O4 UMP doub 543 n n 
C5 C6 UMP doub 544 n n 
C5 H5 UMP sing 545 n n 
C6 H6 UMP sing 546 n n 
C1' C2' UMP sing 547 n n 
C1' O4' UMP sing 548 n n 
C1' H1' UMP sing 549 n n 
C2' C3' UMP sing 550 n n 
C2' H2' UMP sing 551 n n 
C2' "H2''" UMP sing 552 n n 
C3' C4' UMP sing 553 n n 
C3' O3' UMP sing 554 n n 
C3' H3' UMP sing 555 n n 
C4' O4' UMP sing 556 n n 
C4' C5' UMP sing 557 n n 
C4' H4' UMP sing 558 n n 
O3' HO3' UMP sing 559 n n 
C5' O5' UMP sing 560 n n 
C5' H5' UMP sing 561 n n 
C5' "H5''" UMP sing 562 n n 
O5' P UMP sing 563 n n 
P OP1 UMP doub 564 n n 
P OP2 UMP sing 565 n n 
P OP3 UMP sing 566 n n 
OP2 HOP2 UMP sing 567 n n 
OP3 HOP3 UMP sing 568 n n 
#
_atom_sites.entry_id                     4KYA 
_atom_sites.fract_transf_matrix[1][1]    0.018681 
_atom_sites.fract_transf_matrix[1][2]    0.000023 
_atom_sites.fract_transf_matrix[1][3]    -0.000013 
_atom_sites.fract_transf_matrix[2][1]    0 
_atom_sites.fract_transf_matrix[2][2]    0.006893 
_atom_sites.fract_transf_matrix[2][3]    0.000008 
_atom_sites.fract_transf_matrix[3][1]    0 
_atom_sites.fract_transf_matrix[3][2]    0 
_atom_sites.fract_transf_matrix[3][3]    0.005662 
_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 2 UMP A 1 701 701 UMP UMP . 
J 3 1UG A 1 702 702 1UG 1UG . 
K 4 FOL A 1 703 703 FOL FOL . 
L 5 NDP A 1 704 704 NDP NDP . 
M 2 UMP B 1 701 701 UMP UMP . 
N 3 1UG B 1 702 702 1UG 1UG . 
O 4 FOL B 1 703 703 FOL FOL . 
P 5 NDP B 1 704 704 NDP NDP . 
Q 2 UMP C 1 701 701 UMP UMP . 
R 3 1UG C 1 702 702 1UG 1UG . 
S 4 FOL C 1 703 703 FOL FOL . 
T 5 NDP C 1 704 704 NDP NDP . 
U 2 UMP D 1 701 701 UMP UMP . 
V 3 1UG D 1 702 702 1UG 1UG . 
W 4 FOL D 1 703 703 FOL FOL . 
X 5 NDP D 1 704 704 NDP NDP . 
Y 2 UMP E 1 701 701 UMP UMP . 
Z 3 1UG E 1 702 702 1UG 1UG . 
AA 4 FOL E 1 703 703 FOL FOL . 
BA 5 NDP E 1 704 704 NDP NDP . 
CA 2 UMP F 1 701 701 UMP UMP . 
DA 3 1UG F 1 702 702 1UG 1UG . 
EA 4 FOL F 1 703 703 FOL FOL . 
FA 5 NDP F 1 704 704 NDP NDP . 
GA 2 UMP G 1 701 701 UMP UMP . 
HA 3 1UG G 1 702 702 1UG 1UG . 
IA 4 FOL G 1 703 703 FOL FOL . 
JA 5 NDP G 1 704 704 NDP NDP . 
KA 2 UMP H 1 701 701 UMP UMP . 
LA 3 1UG H 1 702 702 1UG 1UG . 
MA 4 FOL H 1 703 703 FOL FOL . 
NA 5 NDP H 1 704 704 NDP NDP . 
#
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 UMP . . . U 2 -37.729 -15.081 -135.512 1 62.53 ? N1 UMP 701 D 1 
HETATM 2 C C2 UMP . . . U 2 -36.382 -15.03 -135.023 1 53.98 ? C2 UMP 701 D 1 
HETATM 3 N N3 UMP . . . U 2 -35.383 -15.406 -135.796 1 53.52 ? N3 UMP 701 D 1 
HETATM 4 C C4 UMP . . . U 2 -35.596 -15.838 -137.037 1 58.04 ? C4 UMP 701 D 1 
HETATM 5 C C5 UMP . . . U 2 -36.909 -15.904 -137.56 1 73.52 ? C5 UMP 701 D 1 
HETATM 6 C C6 UMP . . . U 2 -37.972 -15.516 -136.755 1 67.28 ? C6 UMP 701 D 1 
HETATM 7 O O2 UMP . . . U 2 -36.071 -14.64 -133.871 1 44.68 ? O2 UMP 701 D 1 
HETATM 8 O O4 UMP . . . U 2 -34.64 -16.18 -137.729 1 49.79 ? O4 UMP 701 D 1 
HETATM 9 C C1' UMP . . . U 2 -38.881 -14.684 -134.72 1 60.5 ? C1' UMP 701 D 1 
HETATM 10 C C2' UMP . . . U 2 -38.838 -13.257 -134.223 1 44.6 ? C2' UMP 701 D 1 
HETATM 11 C C3' UMP . . . U 2 -40.305 -12.874 -134.16 1 39.99 ? C3' UMP 701 D 1 
HETATM 12 C C4' UMP . . . U 2 -40.897 -13.633 -135.308 1 46.48 ? C4' UMP 701 D 1 
HETATM 13 O O3' UMP . . . U 2 -40.866 -13.527 -133.045 1 44.21 ? O3' UMP 701 D 1 
HETATM 14 O O4' UMP . . . U 2 -40.076 -14.796 -135.522 1 66.53 ? O4' UMP 701 D 1 
HETATM 15 C C5' UMP . . . U 2 -41.247 -12.797 -136.551 1 42.42 ? C5' UMP 701 D 1 
HETATM 16 O O5' UMP . . . U 2 -42.44 -12.098 -136.492 1 43.06 ? O5' UMP 701 D 1 
HETATM 17 P P UMP . . . U 2 -42.548 -10.541 -136.98 1 43.86 ? P UMP 701 D 1 
HETATM 18 O OP1 UMP . . . U 2 -42.525 -10.79 -138.437 1 51.32 ? OP1 UMP 701 D 1 
HETATM 19 O OP2 UMP . . . U 2 -41.276 -9.934 -136.373 1 25.14 ? OP2 UMP 701 D 1 
HETATM 20 O OP3 UMP . . . U 2 -43.797 -9.887 -136.538 1 46.08 ? OP3 UMP 701 D 1 
#
_model_server_stats.io_time_ms              17 
_model_server_stats.parse_time_ms           9 
_model_server_stats.create_model_time_ms    65 
_model_server_stats.query_time_ms           330 
_model_server_stats.encode_time_ms          4 
_model_server_stats.element_count           20 
#