data_2C37
#
_model_server_result.job_id            cRG0-wToxhKVLPStgJNtRw 
_model_server_result.datetime_utc      '2024-10-19 08:21:11' 
_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          2c37 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"MA","auth_seq_id":302}' 
#
_entry.id    2C37 
#
_exptl.entry_id    2C37 
_exptl.method      'X-RAY DIFFRACTION' 
#
_entity.details                     ? 
_entity.formula_weight              324.181 
_entity.id                          3 
_entity.src_method                  syn 
_entity.type                        non-polymer 
_entity.pdbx_description            "URIDINE-5'-MONOPHOSPHATE" 
_entity.pdbx_number_of_molecules    25 
_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            2C37 
_cell.length_a            207.02 
_cell.length_b            212.94 
_cell.length_c            433.09 
_cell.Z_PDB               96 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 2C37 
_symmetry.cell_setting             ? 
_symmetry.Int_Tables_number        20 
_symmetry.space_group_name_Hall    . 
_symmetry.space_group_name_H-M     'C 2 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
PQS hexameric 6 author_and_software_defined_assembly 1 
PQS hexameric 6 author_and_software_defined_assembly 2 
PQS hexameric 6 author_and_software_defined_assembly 3 
PQS hexameric 6 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,C,D,E,F,Y,Z,AA,BA,CA,DA,EA,FA,GA,HA,IA 1 1 
G,H,I,J,K,L,JA,KA,LA,MA,NA,OA,PA,QA,RA 2 1 
M,N,O,P,Q,R,SA,TA,UA,VA,WA,XA,YA 3 1 
S,T,U,V,W,X,ZA,AB,BB,CB,DB,EB,FB,GB,HB,IB,JB,KB 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
? 3 Y N N 
? 3 Z N N 
? 3 BA N N 
? 3 CA N N 
? 3 EA N N 
? 3 FA N N 
? 3 GA N N 
? 3 IA N N 
? 3 JA N N 
? 3 KA N N 
? 3 MA N N 
? 3 NA N N 
? 3 OA N N 
? 3 QA N N 
? 3 SA N N 
? 3 TA N N 
? 3 VA N N 
? 3 AB N N 
? 3 BB N N 
? 3 CB N N 
? 3 EB N N 
? 3 GB N N 
? 3 HB N N 
? 3 IB N N 
? 3 KB 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
covale ? covale1 Y O3' U5P . A U5P 401 1_555 BA P U5P . B U5P 302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.613 ? 
covale ? covale2 Z P U5P . A U5P 402 1_555 BA O3' U5P . B U5P 302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.624 ? 
covale ? covale3 Z O3' U5P . A U5P 402 1_555 CA P U5P . B U5P 303 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.613 ? 
covale ? covale4 EA O3' U5P . E U5P 401 1_555 FA P U5P . E U5P 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.617 ? 
covale ? covale5 FA O3' U5P . E U5P 402 1_555 GA P U5P . E U5P 403 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.61 ? 
covale ? covale6 GA O3' U5P . E U5P 403 1_555 IA P U5P . F U5P 302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.621 ? 
covale ? covale7 JA O3' U5P . G U5P 401 1_555 MA P U5P . H U5P 302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.619 ? 
covale ? covale8 KA P U5P . G U5P 402 1_555 MA O3' U5P . H U5P 302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.611 ? 
covale ? covale9 NA O3' U5P . I U5P 401 1_555 QA P U5P . J U5P 302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.623 ? 
covale ? covale10 OA P U5P . I U5P 402 1_555 QA O3' U5P . J U5P 302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.611 ? 
covale ? covale11 SA O3' U5P . M U5P 401 1_555 VA P U5P . N U5P 302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.62 ? 
covale ? covale12 TA P U5P . M U5P 402 1_555 VA O3' U5P . N U5P 302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.613 ? 
covale ? covale13 AB O3' U5P . U U5P 401 1_555 BB P U5P . U U5P 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.599 ? 
covale ? covale14 BB O3' U5P . U U5P 402 1_555 CB P U5P . U U5P 403 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.609 ? 
covale ? covale15 CB O3' U5P . U U5P 403 1_555 EB P U5P . V U5P 302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.613 ? 
covale ? covale16 GB O3' U5P . W U5P 401 1_555 HB P U5P . W U5P 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.617 ? 
covale ? covale17 HB O3' U5P . W U5P 402 1_555 IB P U5P . W U5P 403 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.603 ? 
covale ? covale18 IB O3' U5P . W U5P 403 1_555 KB P U5P . X U5P 302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.621 ? 
metalc ? metalc1 CB O1P U5P . U U5P 403 1_555 FB NA NA . V NA 303 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.693 ? 
metalc ? metalc2 EB O2P U5P . V U5P 302 1_555 FB NA NA . V NA 303 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.287 ? 
#
_chem_comp.formula           'C9 H13 N2 O9 P' 
_chem_comp.formula_weight    324.181 
_chem_comp.id                U5P 
_chem_comp.mon_nstd_flag     . 
_chem_comp.name              "URIDINE-5'-MONOPHOSPHATE" 
_chem_comp.type              non-polymer 
_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 U5P sing 381 n n 
N1 C6 U5P sing 382 n n 
N1 C1' U5P sing 383 n n 
C2 N3 U5P sing 384 n n 
C2 O2 U5P doub 385 n n 
N3 C4 U5P sing 386 n n 
N3 HN3 U5P sing 387 n n 
C4 C5 U5P sing 388 n n 
C4 O4 U5P doub 389 n n 
C5 C6 U5P doub 390 n n 
C5 H5 U5P sing 391 n n 
C6 H6 U5P sing 392 n n 
C1' C2' U5P sing 393 n n 
C1' O4' U5P sing 394 n n 
C1' H1' U5P sing 395 n n 
C2' O2' U5P sing 396 n n 
C2' C3' U5P sing 397 n n 
C2' H2' U5P sing 398 n n 
O2' HO2' U5P sing 399 n n 
C3' C4' U5P sing 400 n n 
C3' O3' U5P sing 401 n n 
C3' H3' U5P sing 402 n n 
C4' O4' U5P sing 403 n n 
C4' C5' U5P sing 404 n n 
C4' H4' U5P sing 405 n n 
O3' HO3' U5P sing 406 n n 
C5' O5' U5P sing 407 n n 
C5' "H5'1" U5P sing 408 n n 
C5' "H5'2" U5P sing 409 n n 
O5' P U5P sing 410 n n 
P O1P U5P doub 411 n n 
P O2P U5P sing 412 n n 
P O3P U5P sing 413 n n 
O2P HOP2 U5P sing 414 n n 
O3P HOP3 U5P sing 415 n n 
#
_atom_sites.entry_id                     2C37 
_atom_sites.fract_transf_matrix[1][1]    0.00483 
_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]    0.004696 
_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]    0.002309 
_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
Y 3 U5P A 1 401 401 U5P U5P . 
Z 3 U5P A 1 402 403 U5P U5P . 
AA 4 CL B 1 301 301 CL CL . 
BA 3 U5P B 1 302 402 U5P U5P . 
CA 3 U5P B 1 303 404 U5P U5P . 
DA 4 CL D 1 301 301 CL CL . 
EA 3 U5P E 1 401 401 U5P U5P . 
FA 3 U5P E 1 402 402 U5P U5P . 
GA 3 U5P E 1 403 403 U5P U5P . 
HA 4 CL F 1 301 301 CL CL . 
IA 3 U5P F 1 302 404 U5P U5P . 
JA 3 U5P G 1 401 401 U5P U5P . 
KA 3 U5P G 1 402 403 U5P U5P . 
LA 4 CL H 1 301 301 CL CL . 
MA 3 U5P H 1 302 402 U5P U5P . 
NA 3 U5P I 1 401 401 U5P U5P . 
OA 3 U5P I 1 402 403 U5P U5P . 
PA 4 CL J 1 301 301 CL CL . 
QA 3 U5P J 1 302 402 U5P U5P . 
RA 4 CL L 1 301 301 CL CL . 
SA 3 U5P M 1 401 401 U5P U5P . 
TA 3 U5P M 1 402 403 U5P U5P . 
UA 4 CL N 1 301 301 CL CL . 
VA 3 U5P N 1 302 402 U5P U5P . 
WA 5 RP5 N 1 303 405 RP5 RP5 . 
XA 4 CL P 1 301 301 CL CL . 
YA 4 CL R 1 301 301 CL CL . 
ZA 4 CL T 1 301 301 CL CL . 
AB 3 U5P U 1 401 401 U5P U5P . 
BB 3 U5P U 1 402 402 U5P U5P . 
CB 3 U5P U 1 403 403 U5P U5P . 
DB 4 CL V 1 301 301 CL CL . 
EB 3 U5P V 1 302 404 U5P U5P . 
FB 6 NA V 1 303 501 NA NA . 
GB 3 U5P W 1 401 401 U5P U5P . 
HB 3 U5P W 1 402 402 U5P U5P . 
IB 3 U5P W 1 403 403 U5P U5P . 
JB 4 CL X 1 301 301 CL CL . 
KB 3 U5P X 1 302 404 U5P U5P . 
#
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 U5P . . . MA 3 -73.051 -94.216 -13.94 1 101.23 ? N1 U5P 302 H 1 
HETATM 2 C C2 U5P . . . MA 3 -73.638 -95.474 -14.108 1 100.68 ? C2 U5P 302 H 1 
HETATM 3 N N3 U5P . . . MA 3 -74.582 -95.538 -15.107 1 100.41 ? N3 U5P 302 H 1 
HETATM 4 C C4 U5P . . . MA 3 -74.994 -94.51 -15.937 1 100.39 ? C4 U5P 302 H 1 
HETATM 5 C C5 U5P . . . MA 3 -74.353 -93.239 -15.716 1 100.26 ? C5 U5P 302 H 1 
HETATM 6 C C6 U5P . . . MA 3 -73.432 -93.15 -14.75 1 100.59 ? C6 U5P 302 H 1 
HETATM 7 O O2 U5P . . . MA 3 -73.371 -96.468 -13.449 1 99.96 ? O2 U5P 302 H 1 
HETATM 8 O O4 U5P . . . MA 3 -75.847 -94.731 -16.785 1 100.89 ? O4 U5P 302 H 1 
HETATM 9 C C1' U5P . . . MA 3 -71.972 -93.992 -12.875 1 101.37 ? C1' U5P 302 H 1 
HETATM 10 C C2' U5P . . . MA 3 -70.646 -94.701 -13.18 1 101.55 ? C2' U5P 302 H 1 
HETATM 11 O O2' U5P . . . MA 3 -69.896 -94.947 -11.999 1 101.26 ? O2' U5P 302 H 1 
HETATM 12 C C3' U5P . . . MA 3 -70.012 -93.659 -14.101 1 101.71 ? C3' U5P 302 H 1 
HETATM 13 C C4' U5P . . . MA 3 -70.259 -92.405 -13.26 1 101.92 ? C4' U5P 302 H 1 
HETATM 14 O O3' U5P . . . MA 3 -68.635 -93.934 -14.4 1 101.93 ? O3' U5P 302 H 1 
HETATM 15 O O4' U5P . . . MA 3 -71.633 -92.613 -12.791 1 101.57 ? O4' U5P 302 H 1 
HETATM 16 C C5' U5P . . . MA 3 -70.046 -91.023 -13.902 1 101.57 ? C5' U5P 302 H 1 
HETATM 17 O O5' U5P . . . MA 3 -70.849 -90.743 -15.085 1 100.91 ? O5' U5P 302 H 1 
HETATM 18 P P U5P . . . MA 3 -71.237 -89.253 -15.56 1 99.31 ? P U5P 302 H 1 
HETATM 19 O O1P U5P . . . MA 3 -70.007 -88.431 -15.633 1 98.98 ? O1P U5P 302 H 1 
HETATM 20 O O2P U5P . . . MA 3 -72.095 -89.368 -16.765 1 98.59 ? O2P U5P 302 H 1 
#
_model_server_stats.io_time_ms              79 
_model_server_stats.parse_time_ms           8 
_model_server_stats.create_model_time_ms    65 
_model_server_stats.query_time_ms           307 
_model_server_stats.encode_time_ms          2 
_model_server_stats.element_count           20 
#