data_2VP6
#
_model_server_result.job_id            yJmJ_ZcxEZmNgVSFF-Xn0Q 
_model_server_result.datetime_utc      '2024-11-23 12:11:02' 
_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          2vp6 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"Q","auth_seq_id":1210}' 
#
_entry.id    2VP6 
#
_exptl.entry_id    2VP6 
_exptl.method      'X-RAY DIFFRACTION' 
#
_entity.details                     ? 
_entity.formula_weight              342.172 
_entity.id                          3 
_entity.src_method                  syn 
_entity.type                        non-polymer 
_entity.pdbx_description            "5-FLUORO-URIDINE-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 
_cell.angle_beta          90.29 
_cell.angle_gamma         90 
_cell.entry_id            2VP6 
_cell.length_a            70.352 
_cell.length_b            70.714 
_cell.length_c            225.396 
_cell.Z_PDB               16 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 2VP6 
_symmetry.cell_setting             ? 
_symmetry.Int_Tables_number        4 
_symmetry.space_group_name_Hall    . 
_symmetry.space_group_name_H-M     'P 1 21 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
PQS dimeric 2 author_and_software_defined_assembly 1 
PQS dimeric 2 author_and_software_defined_assembly 2 
PQS dimeric 2 author_and_software_defined_assembly 3 
PQS 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 1 1 
C,D,N,O,P,Q 2 1 
E,F,R,S,T,U 3 1 
G,H,V,W,X,Y 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 K N N 
? 3 M N N 
? 3 O N N 
? 3 Q N N 
? 3 S N N 
? 3 U N N 
? 3 W N N 
? 3 Y N N 
#
_chem_comp.formula           'C9 H12 F N2 O9 P' 
_chem_comp.formula_weight    342.172 
_chem_comp.id                5FU 
_chem_comp.mon_nstd_flag     n 
_chem_comp.name              "5-FLUORO-URIDINE-5'-MONOPHOSPHATE" 
_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
F5 C5 5FU sing 1 n n 
C5 C6 5FU doub 2 n n 
C5 C4 5FU sing 3 n n 
C4 O4 5FU doub 4 n n 
C4 N3 5FU sing 5 n n 
N3 H3 5FU sing 6 n n 
N3 C2 5FU sing 7 n n 
C2 N1 5FU sing 8 n n 
C2 O2 5FU doub 9 n n 
C6 N1 5FU sing 10 n n 
C6 H6 5FU sing 11 n n 
N1 C1' 5FU sing 12 n n 
C1' C2' 5FU sing 13 n n 
C1' H1' 5FU sing 14 n n 
C1' O4' 5FU sing 15 n n 
O4' C4' 5FU sing 16 n n 
C2' O2' 5FU sing 17 n n 
C2' H2' 5FU sing 18 n n 
C2' C3' 5FU sing 19 n n 
O2' "HO'2" 5FU sing 20 n n 
C3' C4' 5FU sing 21 n n 
C3' H3' 5FU sing 22 n n 
C3' O3' 5FU sing 23 n n 
O3' H3T 5FU sing 24 n n 
C4' H4' 5FU sing 25 n n 
C4' C5' 5FU sing 26 n n 
C5' "H5'1" 5FU sing 27 n n 
C5' "H5'2" 5FU sing 28 n n 
C5' O5' 5FU sing 29 n n 
O5' P 5FU sing 30 n n 
P O1P 5FU doub 31 n n 
P O2P 5FU sing 32 n n 
P O3P 5FU sing 33 n n 
O2P HOP2 5FU sing 34 n n 
O3P HOP3 5FU sing 35 n n 
#
_atom_sites.entry_id                     2VP6 
_atom_sites.fract_transf_matrix[1][1]    0.014214 
_atom_sites.fract_transf_matrix[1][2]    0 
_atom_sites.fract_transf_matrix[1][3]    0.000072 
_atom_sites.fract_transf_matrix[2][1]    0 
_atom_sites.fract_transf_matrix[2][2]    0.014141 
_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]    0.004437 
_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 SO4 A 1 1209 1209 SO4 SO4 . 
J 2 SO4 A 1 1210 1210 SO4 SO4 . 
K 3 5FU A 1 1211 1211 5FU 5FU . 
L 2 SO4 B 1 1209 1209 SO4 SO4 . 
M 3 5FU B 1 1210 1210 5FU 5FU . 
N 2 SO4 C 1 1209 1209 SO4 SO4 . 
O 3 5FU C 1 1210 1210 5FU 5FU . 
P 2 SO4 D 1 1209 1209 SO4 SO4 . 
Q 3 5FU D 1 1210 1210 5FU 5FU . 
R 2 SO4 E 1 1209 1209 SO4 SO4 . 
S 3 5FU E 1 1210 1210 5FU 5FU . 
T 2 SO4 F 1 1209 1209 SO4 SO4 . 
U 3 5FU F 1 1210 1210 5FU 5FU . 
V 2 SO4 G 1 1209 1209 SO4 SO4 . 
W 3 5FU G 1 1210 1210 5FU 5FU . 
X 2 SO4 H 1 1209 1209 SO4 SO4 . 
Y 3 5FU H 1 1210 1210 5FU 5FU . 
#
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 F F5 5FU . . . Q 3 56.435 29.732 72.855 1 58.76 ? F5 5FU 1210 D 1 
HETATM 2 C C5 5FU . . . Q 3 55.086 29.565 72.942 1 57.78 ? C5 5FU 1210 D 1 
HETATM 3 C C4 5FU . . . Q 3 54.356 30.58 73.712 1 57.76 ? C4 5FU 1210 D 1 
HETATM 4 O O4 5FU . . . Q 3 55.021 31.519 74.23 1 58.55 ? O4 5FU 1210 D 1 
HETATM 5 N N3 5FU . . . Q 3 53.028 30.477 73.811 1 57.39 ? N3 5FU 1210 D 1 
HETATM 6 C C2 5FU . . . Q 3 52.345 29.467 73.244 1 58.29 ? C2 5FU 1210 D 1 
HETATM 7 O O2 5FU . . . Q 3 51.087 29.443 73.389 1 57.67 ? O2 5FU 1210 D 1 
HETATM 8 C C6 5FU . . . Q 3 54.361 28.516 72.358 1 57.12 ? C6 5FU 1210 D 1 
HETATM 9 N N1 5FU . . . Q 3 53.02 28.452 72.494 1 58.54 ? N1 5FU 1210 D 1 
HETATM 10 C C1' 5FU . . . Q 3 52.196 27.356 71.88 1 59.63 ? C1' 5FU 1210 D 1 
HETATM 11 O O4' 5FU . . . Q 3 52.513 26.025 72.344 1 60.61 ? O4' 5FU 1210 D 1 
HETATM 12 C C2' 5FU . . . Q 3 52.222 27.283 70.343 1 60.43 ? C2' 5FU 1210 D 1 
HETATM 13 C C3' 5FU . . . Q 3 52.17 25.783 70.062 1 60.23 ? C3' 5FU 1210 D 1 
HETATM 14 O O3' 5FU . . . Q 3 50.829 25.344 70.153 1 62.79 ? O3' 5FU 1210 D 1 
HETATM 15 C C4' 5FU . . . Q 3 52.741 25.097 71.267 1 58.96 ? C4' 5FU 1210 D 1 
HETATM 16 C C5' 5FU . . . Q 3 54.214 24.784 71.061 1 56.77 ? C5' 5FU 1210 D 1 
HETATM 17 O O5' 5FU . . . Q 3 54.962 26.006 70.943 1 53.93 ? O5' 5FU 1210 D 1 
#
_model_server_stats.io_time_ms              72 
_model_server_stats.parse_time_ms           9 
_model_server_stats.create_model_time_ms    33 
_model_server_stats.query_time_ms           282 
_model_server_stats.encode_time_ms          4 
_model_server_stats.element_count           17 
#