data_4CDR
#
_model_server_result.job_id            3LR2MF_6fJ3I7J2deIws4Q 
_model_server_result.datetime_utc      '2024-11-14 04:25:57' 
_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          4cdr 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"PA","auth_seq_id":1001}' 
#
_entry.id    4CDR 
#
_exptl.entry_id    4CDR 
_exptl.method      'X-RAY DIFFRACTION' 
#
_entity.details                     ? 
_entity.formula_weight              404.161 
_entity.id                          4 
_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         120 
_cell.entry_id            4CDR 
_cell.length_a            273.728 
_cell.length_b            273.728 
_cell.length_c            142.581 
_cell.Z_PDB               24 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 4CDR 
_symmetry.cell_setting             ? 
_symmetry.Int_Tables_number        150 
_symmetry.space_group_name_Hall    . 
_symmetry.space_group_name_H-M     'P 3 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 software_defined_assembly 1 
PISA dimeric 2 software_defined_assembly 2 
PISA dimeric 2 software_defined_assembly 3 
PISA dimeric 2 software_defined_assembly 4 
#
loop_
_pdbx_struct_assembly_gen.asym_id_list
_pdbx_struct_assembly_gen.assembly_id
_pdbx_struct_assembly_gen.oper_expression
D,H,DA,EA,FA,GA,HA,IA,JA,PA,QA 1 1 
C,G,X,Y,Z,AA,BA,CA,OA 2 1 
B,F,Q,R,S,T,U,V,W,MA,NA 3 1 
A,E,I,J,K,L,M,N,O,P,KA,LA 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
? 4 KA N N 
? 4 MA N N 
? 4 OA N N 
? 4 PA 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 E C ACE 1 E ACE 1 1_555 E N VAL 2 E VAL 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.391 ? 
covale ? covale2 E C VAL 5 E VAL 5 1_555 E N SRZ 6 E SRZ 6 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.355 ? 
covale ? covale3 E C SRZ 6 E SRZ 6 1_555 E N THR 7 E THR 7 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.334 ? 
covale ? covale4 E CZ SRZ 6 E SRZ 6 1_555 KA O3B UDP . E UDP 1001 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.423 ? 
covale ? covale5 E C ALA 8 E ALA 8 1_555 E N NH2 9 E NH2 9 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.322 ? 
covale ? covale6 F C ACE 1 F ACE 1 1_555 F N VAL 2 F VAL 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.416 ? 
covale ? covale7 F C VAL 5 F VAL 5 1_555 F N SRZ 6 F SRZ 6 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.366 ? 
covale ? covale8 F C SRZ 6 F SRZ 6 1_555 F N THR 7 F THR 7 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.346 ? 
covale ? covale9 F CZ SRZ 6 F SRZ 6 1_555 MA O3B UDP . F UDP 1001 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.411 ? 
covale ? covale10 F C ALA 8 F ALA 8 1_555 F N NH2 9 F NH2 9 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.328 ? 
covale ? covale11 G C ACE 1 G ACE 1 1_555 G N VAL 2 G VAL 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.417 ? 
covale ? covale12 G C VAL 5 G VAL 5 1_555 G N SRZ 6 G SRZ 6 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.347 ? 
covale ? covale13 G C SRZ 6 G SRZ 6 1_555 G N THR 7 G THR 7 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.325 ? 
covale ? covale14 G CZ SRZ 6 G SRZ 6 1_555 OA O3B UDP . G UDP 1001 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.422 ? 
covale ? covale15 G C ALA 8 G ALA 8 1_555 G N NH2 9 G NH2 9 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.34 ? 
covale ? covale16 H C ACE 1 H ACE 1 1_555 H N VAL 2 H VAL 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.403 ? 
covale ? covale17 H C VAL 5 H VAL 5 1_555 H N SRZ 6 H SRZ 6 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.354 ? 
covale ? covale18 H C SRZ 6 H SRZ 6 1_555 H N THR 7 H THR 7 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.34 ? 
covale ? covale19 H CZ SRZ 6 H SRZ 6 1_555 PA O3B UDP . H UDP 1001 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.429 ? 
covale ? covale20 H C ALA 8 H ALA 8 1_555 H N NH2 9 H NH2 9 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.337 ? 
#
_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 391 n n 
N1 C6 UDP sing 392 n n 
N1 C1' UDP sing 393 n n 
C2 N3 UDP sing 394 n n 
C2 O2 UDP doub 395 n n 
N3 C4 UDP sing 396 n n 
N3 HN3 UDP sing 397 n n 
C4 C5 UDP sing 398 n n 
C4 O4 UDP doub 399 n n 
C5 C6 UDP doub 400 n n 
C5 H5 UDP sing 401 n n 
C6 H6 UDP sing 402 n n 
C1' C2' UDP sing 403 n n 
C1' O4' UDP sing 404 n n 
C1' H1' UDP sing 405 n n 
C2' O2' UDP sing 406 n n 
C2' C3' UDP sing 407 n n 
C2' H2' UDP sing 408 n n 
O2' HO2' UDP sing 409 n n 
C3' C4' UDP sing 410 n n 
C3' O3' UDP sing 411 n n 
C3' H3' UDP sing 412 n n 
C4' O4' UDP sing 413 n n 
C4' C5' UDP sing 414 n n 
C4' H4' UDP sing 415 n n 
O3' HO3' UDP sing 416 n n 
C5' O5' UDP sing 417 n n 
C5' "H5'1" UDP sing 418 n n 
C5' "H5'2" UDP sing 419 n n 
O5' PA UDP sing 420 n n 
PA O1A UDP doub 421 n n 
PA O2A UDP sing 422 n n 
PA O3A UDP sing 423 n n 
O2A HOA2 UDP sing 424 n n 
O3A PB UDP sing 425 n n 
PB O1B UDP doub 426 n n 
PB O2B UDP sing 427 n n 
PB O3B UDP sing 428 n n 
O2B HOB2 UDP sing 429 n n 
O3B HOB3 UDP sing 430 n n 
#
_atom_sites.entry_id                     4CDR 
_atom_sites.fract_transf_matrix[1][1]    0.003653 
_atom_sites.fract_transf_matrix[1][2]    0.002109 
_atom_sites.fract_transf_matrix[1][3]    0 
_atom_sites.fract_transf_matrix[2][1]    0 
_atom_sites.fract_transf_matrix[2][2]    0.004218 
_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]    0.007014 
_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 3 SO4 A 1 2029 2029 SO4 SO4 . 
J 3 SO4 A 1 2030 2030 SO4 SO4 . 
K 3 SO4 A 1 2031 2031 SO4 SO4 . 
L 3 SO4 A 1 2032 2032 SO4 SO4 . 
M 3 SO4 A 1 2033 2033 SO4 SO4 . 
N 3 SO4 A 1 2034 2034 SO4 SO4 . 
O 3 SO4 A 1 2035 2035 SO4 SO4 . 
P 3 SO4 A 1 2036 2036 SO4 SO4 . 
Q 3 SO4 B 1 2029 2029 SO4 SO4 . 
R 3 SO4 B 1 2030 2030 SO4 SO4 . 
S 3 SO4 B 1 2031 2031 SO4 SO4 . 
T 3 SO4 B 1 2032 2032 SO4 SO4 . 
U 3 SO4 B 1 2033 2033 SO4 SO4 . 
V 3 SO4 B 1 2034 2034 SO4 SO4 . 
W 3 SO4 B 1 2035 2035 SO4 SO4 . 
X 3 SO4 C 1 2029 2029 SO4 SO4 . 
Y 3 SO4 C 1 2030 2030 SO4 SO4 . 
Z 3 SO4 C 1 2031 2031 SO4 SO4 . 
AA 3 SO4 C 1 2032 2032 SO4 SO4 . 
BA 3 SO4 C 1 2033 2033 SO4 SO4 . 
CA 3 SO4 C 1 2034 2034 SO4 SO4 . 
DA 3 SO4 D 1 2029 2029 SO4 SO4 . 
EA 3 SO4 D 1 2030 2030 SO4 SO4 . 
FA 3 SO4 D 1 2031 2031 SO4 SO4 . 
GA 3 SO4 D 1 2032 2032 SO4 SO4 . 
HA 3 SO4 D 1 2033 2033 SO4 SO4 . 
IA 3 SO4 D 1 2034 2034 SO4 SO4 . 
JA 3 SO4 D 1 2035 2035 SO4 SO4 . 
KA 4 UDP E 1 1001 1001 UDP UDP . 
LA 3 SO4 E 1 1009 1009 SO4 SO4 . 
MA 4 UDP F 1 1001 1001 UDP UDP . 
NA 3 SO4 F 1 1009 1009 SO4 SO4 . 
OA 4 UDP G 1 1001 1001 UDP UDP . 
PA 4 UDP H 1 1001 1001 UDP UDP . 
QA 3 SO4 H 1 1009 1009 SO4 SO4 . 
#
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 . . . PA 4 177.9 -40.247 28.998 1 49.27 ? N1 UDP 1001 H 1 
HETATM 2 C C2 UDP . . . PA 4 177.037 -41.027 29.632 1 50.82 ? C2 UDP 1001 H 1 
HETATM 3 N N3 UDP . . . PA 4 177.333 -41.64 30.831 1 50.9 ? N3 UDP 1001 H 1 
HETATM 4 C C4 UDP . . . PA 4 178.569 -41.491 31.387 1 50.06 ? C4 UDP 1001 H 1 
HETATM 5 C C5 UDP . . . PA 4 179.496 -40.691 30.732 1 49.13 ? C5 UDP 1001 H 1 
HETATM 6 C C6 UDP . . . PA 4 179.168 -40.071 29.533 1 48.89 ? C6 UDP 1001 H 1 
HETATM 7 O O2 UDP . . . PA 4 175.921 -41.195 29.162 1 54.04 ? O2 UDP 1001 H 1 
HETATM 8 O O4 UDP . . . PA 4 178.798 -42.065 32.454 1 50.95 ? O4 UDP 1001 H 1 
HETATM 9 C C1' UDP . . . PA 4 177.457 -39.69 27.688 1 49.81 ? C1' UDP 1001 H 1 
HETATM 10 C C2' UDP . . . PA 4 177.738 -38.268 27.501 1 50.17 ? C2' UDP 1001 H 1 
HETATM 11 O O2' UDP . . . PA 4 176.684 -37.587 28.138 1 50.3 ? O2' UDP 1001 H 1 
HETATM 12 C C3' UDP . . . PA 4 177.618 -38.137 25.974 1 50.55 ? C3' UDP 1001 H 1 
HETATM 13 C C4' UDP . . . PA 4 178.133 -39.445 25.451 1 50.26 ? C4' UDP 1001 H 1 
HETATM 14 O O4' UDP . . . PA 4 178.133 -40.328 26.572 1 50.64 ? O4' UDP 1001 H 1 
HETATM 15 O O3' UDP . . . PA 4 176.244 -37.993 25.554 1 51.31 ? O3' UDP 1001 H 1 
HETATM 16 C C5' UDP . . . PA 4 179.601 -39.294 25.129 1 51.76 ? C5' UDP 1001 H 1 
HETATM 17 O O5' UDP . . . PA 4 179.849 -39.633 23.779 1 54.02 ? O5' UDP 1001 H 1 
HETATM 18 P PA UDP . . . PA 4 181.045 -38.879 23.018 1 56.24 ? PA UDP 1001 H 1 
HETATM 19 O O1A UDP . . . PA 4 182.36 -39.425 23.459 1 56.2 ? O1A UDP 1001 H 1 
HETATM 20 O O2A UDP . . . PA 4 180.691 -38.824 21.583 1 56.15 ? O2A UDP 1001 H 1 
HETATM 21 O O3A UDP . . . PA 4 180.931 -37.389 23.59 1 58.33 ? O3A UDP 1001 H 1 
HETATM 22 P PB UDP . . . PA 4 181.575 -36.117 22.825 1 61.39 ? PB UDP 1001 H 1 
HETATM 23 O O1B UDP . . . PA 4 181.798 -35.091 23.885 1 62.3 ? O1B UDP 1001 H 1 
HETATM 24 O O2B UDP . . . PA 4 182.694 -36.516 21.936 1 60.18 ? O2B UDP 1001 H 1 
HETATM 25 O O3B UDP . . . PA 4 180.353 -35.608 21.883 1 60.04 ? O3B UDP 1001 H 1 
#
_model_server_stats.io_time_ms              15 
_model_server_stats.parse_time_ms           9 
_model_server_stats.create_model_time_ms    31 
_model_server_stats.query_time_ms           286 
_model_server_stats.encode_time_ms          6 
_model_server_stats.element_count           25 
#