data_2YAZ
#
_model_server_result.job_id            de0aIcONYYbLU63Kx_vwjw 
_model_server_result.datetime_utc      '2024-11-25 20:40:07' 
_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          2yaz 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"J","auth_seq_id":1265}' 
#
_entry.id    2YAZ 
#
_exptl.entry_id    2YAZ 
_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    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         120 
_cell.entry_id            2YAZ 
_cell.length_a            109.11 
_cell.length_b            109.11 
_cell.length_c            309.311 
_cell.Z_PDB               24 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 2YAZ 
_symmetry.cell_setting             ? 
_symmetry.Int_Tables_number        152 
_symmetry.space_group_name_Hall    . 
_symmetry.space_group_name_H-M     'P 31 2 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 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,E,F,G,H,I,P,Q 1 1 
C,D,J,K,L,M,N,O,R,S 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 E N N 
? 2 I N N 
? 2 J N N 
? 2 N 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
metalc ? metalc1 A OE1 GLU 51 A GLU 48 1_555 G MG MG . A MG 1267 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.649 ? 
metalc ? metalc2 A OE1 GLU 79 A GLU 76 1_555 G MG MG . A MG 1267 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.808 ? 
metalc ? metalc3 A OE2 GLU 79 A GLU 76 1_555 G MG MG . A MG 1267 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.644 ? 
metalc ? metalc4 A OD2 ASP 82 A ASP 79 1_555 G MG MG . A MG 1267 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.367 ? 
metalc ? metalc5 C OD2 ASP 82 D ASP 79 1_555 K MG MG . D MG 1266 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.131 ? 
metalc ? metalc6 D OE1 GLU 51 E GLU 48 1_555 O MG MG . E MG 1267 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.698 ? 
metalc ? metalc7 D OE2 GLU 79 E GLU 76 1_555 O MG MG . E MG 1267 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.96 ? 
metalc ? metalc8 N OP3 UMP . E UMP 1266 1_555 O MG MG . E MG 1267 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.588 ? 
#
_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 362 n n 
N1 C6 UMP sing 363 n n 
N1 C1' UMP sing 364 n n 
C2 N3 UMP sing 365 n n 
C2 O2 UMP doub 366 n n 
N3 C4 UMP sing 367 n n 
N3 HN3 UMP sing 368 n n 
C4 C5 UMP sing 369 n n 
C4 O4 UMP doub 370 n n 
C5 C6 UMP doub 371 n n 
C5 H5 UMP sing 372 n n 
C6 H6 UMP sing 373 n n 
C1' C2' UMP sing 374 n n 
C1' O4' UMP sing 375 n n 
C1' H1' UMP sing 376 n n 
C2' C3' UMP sing 377 n n 
C2' H2' UMP sing 378 n n 
C2' "H2''" UMP sing 379 n n 
C3' C4' UMP sing 380 n n 
C3' O3' UMP sing 381 n n 
C3' H3' UMP sing 382 n n 
C4' O4' UMP sing 383 n n 
C4' C5' UMP sing 384 n n 
C4' H4' UMP sing 385 n n 
O3' HO3' UMP sing 386 n n 
C5' O5' UMP sing 387 n n 
C5' H5' UMP sing 388 n n 
C5' "H5''" UMP sing 389 n n 
O5' P UMP sing 390 n n 
P OP1 UMP doub 391 n n 
P OP2 UMP sing 392 n n 
P OP3 UMP sing 393 n n 
OP2 HOP2 UMP sing 394 n n 
OP3 HOP3 UMP sing 395 n n 
#
_atom_sites.entry_id                     2YAZ 
_atom_sites.fract_transf_matrix[1][1]    0.009165 
_atom_sites.fract_transf_matrix[1][2]    0.005291 
_atom_sites.fract_transf_matrix[1][3]    0 
_atom_sites.fract_transf_matrix[2][1]    0 
_atom_sites.fract_transf_matrix[2][2]    0.010583 
_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]    0.003233 
_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 UMP A 1 1265 1265 UMP UMP . 
F 3 SO4 A 1 1266 1266 SO4 SO4 . 
G 4 MG A 1 1267 1267 MG MG . 
H 3 SO4 A 1 1268 1268 SO4 SO4 . 
I 2 UMP B 1 1265 1265 UMP UMP . 
J 2 UMP D 1 1265 1265 UMP UMP . 
K 4 MG D 1 1266 1266 MG MG . 
L 3 SO4 D 1 1267 1267 SO4 SO4 . 
M 3 SO4 E 1 1265 1265 SO4 SO4 . 
N 2 UMP E 1 1266 1266 UMP UMP . 
O 4 MG E 1 1267 1267 MG MG . 
P 5 HOH A 1 2001 2001 HOH HOH . 
P 5 HOH A 2 2002 2002 HOH HOH . 
P 5 HOH A 3 2003 2003 HOH HOH . 
P 5 HOH A 4 2004 2004 HOH HOH . 
P 5 HOH A 5 2005 2005 HOH HOH . 
P 5 HOH A 6 2006 2006 HOH HOH . 
P 5 HOH A 7 2007 2007 HOH HOH . 
P 5 HOH A 8 2008 2008 HOH HOH . 
P 5 HOH A 9 2009 2009 HOH HOH . 
P 5 HOH A 10 2010 2010 HOH HOH . 
P 5 HOH A 11 2011 2011 HOH HOH . 
P 5 HOH A 12 2012 2012 HOH HOH . 
Q 5 HOH B 1 2001 2001 HOH HOH . 
Q 5 HOH B 2 2002 2002 HOH HOH . 
Q 5 HOH B 3 2003 2003 HOH HOH . 
Q 5 HOH B 4 2004 2004 HOH HOH . 
Q 5 HOH B 5 2005 2005 HOH HOH . 
Q 5 HOH B 6 2006 2006 HOH HOH . 
R 5 HOH D 1 2001 2001 HOH HOH . 
R 5 HOH D 2 2002 2002 HOH HOH . 
R 5 HOH D 3 2003 2003 HOH HOH . 
R 5 HOH D 4 2004 2004 HOH HOH . 
R 5 HOH D 5 2005 2005 HOH HOH . 
R 5 HOH D 6 2006 2006 HOH HOH . 
R 5 HOH D 7 2007 2007 HOH HOH . 
R 5 HOH D 8 2008 2008 HOH HOH . 
R 5 HOH D 9 2009 2009 HOH HOH . 
R 5 HOH D 10 2010 2010 HOH HOH . 
R 5 HOH D 11 2011 2011 HOH HOH . 
S 5 HOH E 1 2001 2001 HOH HOH . 
S 5 HOH E 2 2002 2002 HOH HOH . 
S 5 HOH E 3 2003 2003 HOH HOH . 
S 5 HOH E 4 2004 2004 HOH HOH . 
S 5 HOH E 5 2005 2005 HOH HOH . 
S 5 HOH E 6 2006 2006 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 UMP . . . J 2 -22.208 30.535 -49.15 1 58.51 ? N1 UMP 1265 D 1 
HETATM 2 C C2 UMP . . . J 2 -21.266 31.036 -50.045 1 55.5 ? C2 UMP 1265 D 1 
HETATM 3 N N3 UMP . . . J 2 -21.411 30.831 -51.408 1 56.75 ? N3 UMP 1265 D 1 
HETATM 4 C C4 UMP . . . J 2 -22.489 30.105 -51.889 1 63.15 ? C4 UMP 1265 D 1 
HETATM 5 C C5 UMP . . . J 2 -23.435 29.598 -50.992 1 53.6 ? C5 UMP 1265 D 1 
HETATM 6 C C6 UMP . . . J 2 -23.281 29.814 -49.617 1 52.32 ? C6 UMP 1265 D 1 
HETATM 7 O O2 UMP . . . J 2 -20.295 31.683 -49.64 1 57.61 ? O2 UMP 1265 D 1 
HETATM 8 O O4 UMP . . . J 2 -22.606 29.922 -53.106 1 52.1 ? O4 UMP 1265 D 1 
HETATM 9 C C1' UMP . . . J 2 -22.009 30.765 -47.698 1 45.73 ? C1' UMP 1265 D 1 
HETATM 10 C C2' UMP . . . J 2 -22.351 32.186 -47.297 1 39.38 ? C2' UMP 1265 D 1 
HETATM 11 C C3' UMP . . . J 2 -22.702 32.035 -45.819 1 52.79 ? C3' UMP 1265 D 1 
HETATM 12 C C4' UMP . . . J 2 -23.103 30.589 -45.638 1 57 ? C4' UMP 1265 D 1 
HETATM 13 O O3' UMP . . . J 2 -21.606 32.292 -44.955 1 51.52 ? O3' UMP 1265 D 1 
HETATM 14 O O4' UMP . . . J 2 -22.766 29.916 -46.843 1 51.81 ? O4' UMP 1265 D 1 
HETATM 15 C C5' UMP . . . J 2 -24.599 30.553 -45.344 1 64.11 ? C5' UMP 1265 D 1 
HETATM 16 O O5' UMP . . . J 2 -24.998 29.235 -45.064 1 68.98 ? O5' UMP 1265 D 1 
HETATM 17 P P UMP . . . J 2 -26.211 28.987 -44.047 1 65.66 ? P UMP 1265 D 1 
HETATM 18 O OP1 UMP . . . J 2 -25.689 29.436 -42.699 1 77.93 ? OP1 UMP 1265 D 1 
HETATM 19 O OP2 UMP . . . J 2 -26.543 27.514 -44.065 1 56.93 ? OP2 UMP 1265 D 1 
HETATM 20 O OP3 UMP . . . J 2 -27.38 29.797 -44.47 1 66.02 ? OP3 UMP 1265 D 1 
#
_model_server_stats.io_time_ms              21 
_model_server_stats.parse_time_ms           11 
_model_server_stats.create_model_time_ms    20 
_model_server_stats.query_time_ms           319 
_model_server_stats.encode_time_ms          6 
_model_server_stats.element_count           20 
#