data_2ZI6
#
_model_server_result.job_id            wyZIY2S4EKSHCPAm2CsXlw 
_model_server_result.datetime_utc      '2024-11-13 04:00:37' 
_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          2zi6 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"E","auth_seq_id":1301}' 
#
_entry.id    2ZI6 
#
_exptl.entry_id    2ZI6 
_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            2ZI6 
_cell.length_a            138.25 
_cell.length_b            138.51 
_cell.length_c            118.67 
_cell.Z_PDB               32 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 2ZI6 
_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
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 
#
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,J,M,N 1 1 
C,K,O 2 1,2 
D,L,P 3 1,3 
#
loop_
_pdbx_struct_oper_list.id
_pdbx_struct_oper_list.type
_pdbx_struct_oper_list.name
_pdbx_struct_oper_list.symmetry_operation
_pdbx_struct_oper_list.matrix[1][1]
_pdbx_struct_oper_list.matrix[1][2]
_pdbx_struct_oper_list.matrix[1][3]
_pdbx_struct_oper_list.matrix[2][1]
_pdbx_struct_oper_list.matrix[2][2]
_pdbx_struct_oper_list.matrix[2][3]
_pdbx_struct_oper_list.matrix[3][1]
_pdbx_struct_oper_list.matrix[3][2]
_pdbx_struct_oper_list.matrix[3][3]
_pdbx_struct_oper_list.vector[1]
_pdbx_struct_oper_list.vector[2]
_pdbx_struct_oper_list.vector[3]
1 'identity operation' 1_555 x,y,z 1 0 0 0 1 0 0 0 1 0 0 0 
2 'crystal symmetry operation' 3_655 -x+1,y,-z+1/2 -1 0 0 0 1 0 0 0 -1 138.25 0 59.335 
3 'crystal symmetry operation' 3_654 -x+1,y,-z-1/2 -1 0 0 0 1 0 0 0 -1 138.25 0 -59.335 
#
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 F N N 
? 2 G N N 
? 2 H 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 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                     2ZI6 
_atom_sites.fract_transf_matrix[1][1]    0.007233 
_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]    0.00722 
_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]    0.008427 
_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 1301 1301 UDP UDP . 
F 2 UDP A 1 2301 2301 UDP UDP . 
G 2 UDP A 1 3301 3301 UDP UDP . 
H 2 UDP A 1 4301 4301 UDP UDP . 
I 3 3D1 A 1 1302 1302 3D1 DAD . 
J 3 3D1 B 1 2302 2302 3D1 DAD . 
K 3 3D1 C 1 3302 3302 3D1 DAD . 
L 3 3D1 D 1 4302 4302 3D1 DAD . 
M 4 HOH A 1 7002 7002 HOH HOH . 
M 4 HOH A 2 7009 7009 HOH HOH . 
M 4 HOH A 3 7015 7015 HOH HOH . 
M 4 HOH A 4 7017 7017 HOH HOH . 
M 4 HOH A 5 7030 7030 HOH HOH . 
M 4 HOH A 6 7034 7034 HOH HOH . 
M 4 HOH A 7 7042 7042 HOH HOH . 
M 4 HOH A 8 7043 7043 HOH HOH . 
M 4 HOH A 9 7045 7045 HOH HOH . 
M 4 HOH A 10 7046 7046 HOH HOH . 
M 4 HOH A 11 7049 7049 HOH HOH . 
M 4 HOH A 12 7051 7051 HOH HOH . 
M 4 HOH A 13 7052 7052 HOH HOH . 
M 4 HOH A 14 7055 7055 HOH HOH . 
M 4 HOH A 15 7056 7056 HOH HOH . 
M 4 HOH A 16 7063 7063 HOH HOH . 
M 4 HOH A 17 7070 7070 HOH HOH . 
M 4 HOH A 18 7072 7072 HOH HOH . 
M 4 HOH A 19 7074 7074 HOH HOH . 
M 4 HOH A 20 7076 7076 HOH HOH . 
M 4 HOH A 21 7081 7081 HOH HOH . 
M 4 HOH A 22 7085 7085 HOH HOH . 
M 4 HOH A 23 7092 7092 HOH HOH . 
M 4 HOH A 24 7098 7098 HOH HOH . 
M 4 HOH A 25 7099 7099 HOH HOH . 
M 4 HOH A 26 7100 7100 HOH HOH . 
M 4 HOH A 27 7101 7101 HOH HOH . 
M 4 HOH A 28 7104 7104 HOH HOH . 
M 4 HOH A 29 7105 7105 HOH HOH . 
M 4 HOH A 30 7106 7106 HOH HOH . 
M 4 HOH A 31 7112 7112 HOH HOH . 
M 4 HOH A 32 7113 7113 HOH HOH . 
M 4 HOH A 33 7114 7114 HOH HOH . 
M 4 HOH A 34 7115 7115 HOH HOH . 
M 4 HOH A 35 7117 7117 HOH HOH . 
M 4 HOH A 36 7129 7129 HOH HOH . 
M 4 HOH A 37 7130 7130 HOH HOH . 
M 4 HOH A 38 7131 7131 HOH HOH . 
M 4 HOH A 39 7132 7132 HOH HOH . 
M 4 HOH A 40 7133 7133 HOH HOH . 
M 4 HOH A 41 7136 7136 HOH HOH . 
M 4 HOH A 42 7141 7141 HOH HOH . 
M 4 HOH A 43 7148 7148 HOH HOH . 
M 4 HOH A 44 7149 7149 HOH HOH . 
M 4 HOH A 45 7151 7151 HOH HOH . 
M 4 HOH A 46 7155 7155 HOH HOH . 
M 4 HOH A 47 7156 7156 HOH HOH . 
M 4 HOH A 48 7158 7158 HOH HOH . 
M 4 HOH A 49 7160 7160 HOH HOH . 
M 4 HOH A 50 7164 7164 HOH HOH . 
N 4 HOH B 1 7003 7003 HOH HOH . 
N 4 HOH B 2 7006 7006 HOH HOH . 
N 4 HOH B 3 7007 7007 HOH HOH . 
N 4 HOH B 4 7012 7012 HOH HOH . 
N 4 HOH B 5 7013 7013 HOH HOH . 
N 4 HOH B 6 7019 7019 HOH HOH . 
N 4 HOH B 7 7020 7020 HOH HOH . 
N 4 HOH B 8 7022 7022 HOH HOH . 
N 4 HOH B 9 7023 7023 HOH HOH . 
N 4 HOH B 10 7028 7028 HOH HOH . 
N 4 HOH B 11 7029 7029 HOH HOH . 
N 4 HOH B 12 7031 7031 HOH HOH . 
N 4 HOH B 13 7033 7033 HOH HOH . 
N 4 HOH B 14 7038 7038 HOH HOH . 
N 4 HOH B 15 7041 7041 HOH HOH . 
N 4 HOH B 16 7047 7047 HOH HOH . 
N 4 HOH B 17 7050 7050 HOH HOH . 
N 4 HOH B 18 7057 7057 HOH HOH . 
N 4 HOH B 19 7060 7060 HOH HOH . 
N 4 HOH B 20 7061 7061 HOH HOH . 
N 4 HOH B 21 7062 7062 HOH HOH . 
N 4 HOH B 22 7068 7068 HOH HOH . 
N 4 HOH B 23 7069 7069 HOH HOH . 
N 4 HOH B 24 7071 7071 HOH HOH . 
N 4 HOH B 25 7078 7078 HOH HOH . 
N 4 HOH B 26 7080 7080 HOH HOH . 
N 4 HOH B 27 7083 7083 HOH HOH . 
N 4 HOH B 28 7087 7087 HOH HOH . 
N 4 HOH B 29 7088 7088 HOH HOH . 
N 4 HOH B 30 7089 7089 HOH HOH . 
N 4 HOH B 31 7093 7093 HOH HOH . 
N 4 HOH B 32 7094 7094 HOH HOH . 
N 4 HOH B 33 7096 7096 HOH HOH . 
N 4 HOH B 34 7102 7102 HOH HOH . 
N 4 HOH B 35 7103 7103 HOH HOH . 
N 4 HOH B 36 7107 7107 HOH HOH . 
N 4 HOH B 37 7108 7108 HOH HOH . 
N 4 HOH B 38 7137 7137 HOH HOH . 
N 4 HOH B 39 7143 7143 HOH HOH . 
N 4 HOH B 40 7150 7150 HOH HOH . 
N 4 HOH B 41 7152 7152 HOH HOH . 
N 4 HOH B 42 7162 7162 HOH HOH . 
O 4 HOH C 1 7004 7004 HOH HOH . 
O 4 HOH C 2 7005 7005 HOH HOH . 
O 4 HOH C 3 7010 7010 HOH HOH . 
O 4 HOH C 4 7016 7016 HOH HOH . 
O 4 HOH C 5 7021 7021 HOH HOH . 
O 4 HOH C 6 7032 7032 HOH HOH . 
O 4 HOH C 7 7035 7035 HOH HOH . 
O 4 HOH C 8 7037 7037 HOH HOH . 
O 4 HOH C 9 7039 7039 HOH HOH . 
O 4 HOH C 10 7040 7040 HOH HOH . 
O 4 HOH C 11 7044 7044 HOH HOH . 
O 4 HOH C 12 7053 7053 HOH HOH . 
O 4 HOH C 13 7054 7054 HOH HOH . 
O 4 HOH C 14 7059 7059 HOH HOH . 
O 4 HOH C 15 7064 7064 HOH HOH . 
O 4 HOH C 16 7067 7067 HOH HOH . 
O 4 HOH C 17 7075 7075 HOH HOH . 
O 4 HOH C 18 7079 7079 HOH HOH . 
O 4 HOH C 19 7084 7084 HOH HOH . 
O 4 HOH C 20 7090 7090 HOH HOH . 
O 4 HOH C 21 7097 7097 HOH HOH . 
O 4 HOH C 22 7109 7109 HOH HOH . 
O 4 HOH C 23 7110 7110 HOH HOH . 
O 4 HOH C 24 7120 7120 HOH HOH . 
O 4 HOH C 25 7121 7121 HOH HOH . 
O 4 HOH C 26 7123 7123 HOH HOH . 
O 4 HOH C 27 7124 7124 HOH HOH . 
O 4 HOH C 28 7125 7125 HOH HOH . 
O 4 HOH C 29 7126 7126 HOH HOH . 
O 4 HOH C 30 7127 7127 HOH HOH . 
O 4 HOH C 31 7139 7139 HOH HOH . 
O 4 HOH C 32 7142 7142 HOH HOH . 
O 4 HOH C 33 7144 7144 HOH HOH . 
O 4 HOH C 34 7154 7154 HOH HOH . 
O 4 HOH C 35 7157 7157 HOH HOH . 
O 4 HOH C 36 7159 7159 HOH HOH . 
O 4 HOH C 37 7161 7161 HOH HOH . 
O 4 HOH C 38 7165 7165 HOH HOH . 
P 4 HOH D 1 7001 7001 HOH HOH . 
P 4 HOH D 2 7008 7008 HOH HOH . 
P 4 HOH D 3 7011 7011 HOH HOH . 
P 4 HOH D 4 7014 7014 HOH HOH . 
P 4 HOH D 5 7018 7018 HOH HOH . 
P 4 HOH D 6 7024 7024 HOH HOH . 
P 4 HOH D 7 7025 7025 HOH HOH . 
P 4 HOH D 8 7026 7026 HOH HOH . 
P 4 HOH D 9 7027 7027 HOH HOH . 
P 4 HOH D 10 7036 7036 HOH HOH . 
P 4 HOH D 11 7048 7048 HOH HOH . 
P 4 HOH D 12 7058 7058 HOH HOH . 
P 4 HOH D 13 7065 7065 HOH HOH . 
P 4 HOH D 14 7066 7066 HOH HOH . 
P 4 HOH D 15 7073 7073 HOH HOH . 
P 4 HOH D 16 7077 7077 HOH HOH . 
P 4 HOH D 17 7082 7082 HOH HOH . 
P 4 HOH D 18 7086 7086 HOH HOH . 
P 4 HOH D 19 7091 7091 HOH HOH . 
P 4 HOH D 20 7095 7095 HOH HOH . 
P 4 HOH D 21 7111 7111 HOH HOH . 
P 4 HOH D 22 7116 7116 HOH HOH . 
P 4 HOH D 23 7118 7118 HOH HOH . 
P 4 HOH D 24 7119 7119 HOH HOH . 
P 4 HOH D 25 7122 7122 HOH HOH . 
P 4 HOH D 26 7128 7128 HOH HOH . 
P 4 HOH D 27 7134 7134 HOH HOH . 
P 4 HOH D 28 7135 7135 HOH HOH . 
P 4 HOH D 29 7138 7138 HOH HOH . 
P 4 HOH D 30 7140 7140 HOH HOH . 
P 4 HOH D 31 7145 7145 HOH HOH . 
P 4 HOH D 32 7146 7146 HOH HOH . 
P 4 HOH D 33 7147 7147 HOH HOH . 
P 4 HOH D 34 7153 7153 HOH HOH . 
P 4 HOH D 35 7163 7163 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 UDP . . . E 2 113.465 5.801 -15.402 1 28.04 ? N1 UDP 1301 A 1 
HETATM 2 C C2 UDP . . . E 2 113.29 4.644 -16.172 1 29.43 ? C2 UDP 1301 A 1 
HETATM 3 N N3 UDP . . . E 2 114.046 4.378 -17.279 1 30.03 ? N3 UDP 1301 A 1 
HETATM 4 C C4 UDP . . . E 2 115.086 5.244 -17.538 1 31.79 ? C4 UDP 1301 A 1 
HETATM 5 C C5 UDP . . . E 2 115.231 6.446 -16.837 1 30.23 ? C5 UDP 1301 A 1 
HETATM 6 C C6 UDP . . . E 2 114.428 6.699 -15.729 1 28.51 ? C6 UDP 1301 A 1 
HETATM 7 O O2 UDP . . . E 2 112.423 3.84 -15.905 1 33.17 ? O2 UDP 1301 A 1 
HETATM 8 O O4 UDP . . . E 2 115.782 5.006 -18.521 1 36.29 ? O4 UDP 1301 A 1 
HETATM 9 C C1' UDP . . . E 2 112.575 6.035 -14.274 1 25.91 ? C1' UDP 1301 A 1 
HETATM 10 C C2' UDP . . . E 2 113.124 6.017 -12.888 1 25.99 ? C2' UDP 1301 A 1 
HETATM 11 O O2' UDP . . . E 2 113.221 4.72 -12.363 1 26.31 ? O2' UDP 1301 A 1 
HETATM 12 C C3' UDP . . . E 2 112.082 6.759 -12.081 1 26.73 ? C3' UDP 1301 A 1 
HETATM 13 C C4' UDP . . . E 2 111.484 7.692 -13.108 1 25.24 ? C4' UDP 1301 A 1 
HETATM 14 O O4' UDP . . . E 2 111.877 7.248 -14.404 1 25.72 ? O4' UDP 1301 A 1 
HETATM 15 O O3' UDP . . . E 2 111.081 5.873 -11.687 1 34.78 ? O3' UDP 1301 A 1 
HETATM 16 C C5' UDP . . . E 2 112.088 9.086 -12.818 1 26.11 ? C5' UDP 1301 A 1 
HETATM 17 O O5' UDP . . . E 2 113.538 8.927 -12.933 1 23.86 ? O5' UDP 1301 A 1 
HETATM 18 P PA UDP . . . E 2 114.464 10.01 -12.241 1 20.42 ? PA UDP 1301 A 1 
HETATM 19 O O1A UDP . . . E 2 114.298 10.209 -10.798 1 16.59 ? O1A UDP 1301 A 1 
HETATM 20 O O2A UDP . . . E 2 115.843 9.744 -12.663 1 17.23 ? O2A UDP 1301 A 1 
HETATM 21 O O3A UDP . . . E 2 114.04 11.373 -13.01 1 19.68 ? O3A UDP 1301 A 1 
HETATM 22 P PB UDP . . . E 2 114.665 12.877 -12.652 1 17.98 ? PB UDP 1301 A 1 
HETATM 23 O O1B UDP . . . E 2 115.695 12.605 -11.614 1 9.82 ? O1B UDP 1301 A 1 
HETATM 24 O O2B UDP . . . E 2 113.569 13.684 -12.052 1 7.8 ? O2B UDP 1301 A 1 
HETATM 25 O O3B UDP . . . E 2 114.999 13.363 -13.943 1 4.1 ? O3B UDP 1301 A 1 
#
_model_server_stats.io_time_ms              14 
_model_server_stats.parse_time_ms           8 
_model_server_stats.create_model_time_ms    16 
_model_server_stats.query_time_ms           250 
_model_server_stats.encode_time_ms          3 
_model_server_stats.element_count           25 
#