data_6PF9
#
_model_server_result.job_id            ldJbAW_XWNWqNOsIvxvMRA 
_model_server_result.datetime_utc      '2024-11-29 00:16:22' 
_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          6pf9 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"Q","auth_seq_id":602}' 
#
_entry.id    6PF9 
#
_exptl.entry_id    6PF9 
_exptl.method      'X-RAY DIFFRACTION' 
#
_entity.details                     ? 
_entity.formula_weight              326.172 
_entity.id                          3 
_entity.src_method                  syn 
_entity.type                        non-polymer 
_entity.pdbx_description            "5-FLUORO-2'-DEOXYURIDINE-5'-MONOPHOSPHATE" 
_entity.pdbx_number_of_molecules    5 
_entity.pdbx_parent_entity_id       . 
_entity.pdbx_mutation               ? 
_entity.pdbx_fragment               ? 
_entity.pdbx_ec                     ? 
#
_cell.angle_alpha         90 
_cell.angle_beta          94.87 
_cell.angle_gamma         90 
_cell.entry_id            6PF9 
_cell.length_a            214.201 
_cell.length_b            116.51 
_cell.length_c            221.439 
_cell.Z_PDB               20 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 6PF9 
_symmetry.cell_setting             ? 
_symmetry.Int_Tables_number        5 
_symmetry.space_group_name_Hall    ? 
_symmetry.space_group_name_H-M     'C 1 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 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,F,G,H,I,J 1 1,2 
B,C,K,L,M,N,O,P,Q,R,S,T,EA,FA 2 1 
D,U,V,W,X,Y,GA 3 1 
E,Z,AA,BA,CA,DA,HA 3 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' 2_555 -x,y,-z -1 0 0 0 1 0 0 0 -1 0 0 0 
3 'crystal symmetry operation' 3_555 x+1/2,y+1/2,z 1 0 0 0 1 0 0 0 1 107.1005 58.255 0 
#
loop_
_struct_asym.details
_struct_asym.entity_id
_struct_asym.id
_struct_asym.pdbx_modified
_struct_asym.pdbx_blank_PDB_chainid_flag
? 3 G N N 
? 3 L N N 
? 3 Q N N 
? 3 V N N 
? 3 AA N N 
#
_chem_comp.formula           'C9 H12 F N2 O8 P' 
_chem_comp.formula_weight    326.172 
_chem_comp.id                UFP 
_chem_comp.mon_nstd_flag     . 
_chem_comp.name              "5-FLUORO-2'-DEOXYURIDINE-5'-MONOPHOSPHATE" 
_chem_comp.type              'dna 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 UFP sing 554 n n 
N1 C6 UFP sing 555 n n 
N1 C1' UFP sing 556 n n 
C2 N3 UFP sing 557 n n 
C2 O2 UFP doub 558 n n 
N3 C4 UFP sing 559 n n 
N3 HN3 UFP sing 560 n n 
C4 C5 UFP sing 561 n n 
C4 O4 UFP doub 562 n n 
C5 C6 UFP doub 563 n n 
C5 F5 UFP sing 564 n n 
C6 H6 UFP sing 565 n n 
C1' C2' UFP sing 566 n n 
C1' O4' UFP sing 567 n n 
C1' H1' UFP sing 568 n n 
C2' C3' UFP sing 569 n n 
C2' "H2'1" UFP sing 570 n n 
C2' "H2'2" UFP sing 571 n n 
C3' C4' UFP sing 572 n n 
C3' O3' UFP sing 573 n n 
C3' H3' UFP sing 574 n n 
C4' O4' UFP sing 575 n n 
C4' C5' UFP sing 576 n n 
C4' H4' UFP sing 577 n n 
O3' HO3' UFP sing 578 n n 
C5' O5' UFP sing 579 n n 
C5' "H5'1" UFP sing 580 n n 
C5' "H5'2" UFP sing 581 n n 
O5' P UFP sing 582 n n 
P O1P UFP doub 583 n n 
P O2P UFP sing 584 n n 
P O3P UFP sing 585 n n 
O2P HOP2 UFP sing 586 n n 
O3P HOP3 UFP sing 587 n n 
#
_atom_sites.entry_id                     6PF9 
_atom_sites.fract_transf_matrix[1][1]    0.004669 
_atom_sites.fract_transf_matrix[1][2]    0 
_atom_sites.fract_transf_matrix[1][3]    0.000398 
_atom_sites.fract_transf_matrix[2][1]    0 
_atom_sites.fract_transf_matrix[2][2]    0.008583 
_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]    0.004532 
_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
F 2 NDP A 1 601 601 NDP NDP . 
G 3 UFP A 1 602 602 UFP UFP . 
H 4 OF7 A 1 603 603 OF7 M80 . 
I 5 MTX A 1 604 604 MTX MTX . 
J 6 SO4 A 1 605 5 SO4 SO4 . 
K 2 NDP B 1 601 601 NDP NDP . 
L 3 UFP B 1 602 602 UFP UFP . 
M 4 OF7 B 1 603 603 OF7 M80 . 
N 5 MTX B 1 604 604 MTX MTX . 
O 6 SO4 B 1 605 1 SO4 SO4 . 
P 2 NDP C 1 601 601 NDP NDP . 
Q 3 UFP C 1 602 602 UFP UFP . 
R 4 OF7 C 1 603 603 OF7 M80 . 
S 5 MTX C 1 604 604 MTX MTX . 
T 6 SO4 C 1 605 4 SO4 SO4 . 
U 2 NDP D 1 601 601 NDP NDP . 
V 3 UFP D 1 602 602 UFP UFP . 
W 4 OF7 D 1 603 603 OF7 M80 . 
X 5 MTX D 1 604 604 MTX MTX . 
Y 6 SO4 D 1 605 2 SO4 SO4 . 
Z 2 NDP E 1 601 601 NDP NDP . 
AA 3 UFP E 1 602 602 UFP UFP . 
BA 4 OF7 E 1 603 603 OF7 M80 . 
CA 5 MTX E 1 604 604 MTX MTX . 
DA 6 SO4 E 1 605 3 SO4 SO4 . 
EA 7 HOH B 1 701 3 HOH HOH . 
FA 7 HOH C 1 701 9 HOH HOH . 
FA 7 HOH C 2 702 7 HOH HOH . 
FA 7 HOH C 3 703 6 HOH HOH . 
FA 7 HOH C 4 704 12 HOH HOH . 
GA 7 HOH D 1 701 5 HOH HOH . 
GA 7 HOH D 2 702 10 HOH HOH . 
GA 7 HOH D 3 703 4 HOH HOH . 
GA 7 HOH D 4 704 1 HOH HOH . 
GA 7 HOH D 5 705 11 HOH HOH . 
HA 7 HOH E 1 701 8 HOH HOH . 
HA 7 HOH E 2 702 2 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 UFP . . . Q 3 21.266 -15.088 67.062 1 85.39 ? N1 UFP 602 C 1 
HETATM 2 C C2 UFP . . . Q 3 21.07 -14.33 65.946 1 87.68 ? C2 UFP 602 C 1 
HETATM 3 N N3 UFP . . . Q 3 19.903 -14.392 65.274 1 99.66 ? N3 UFP 602 C 1 
HETATM 4 C C4 UFP . . . Q 3 18.901 -15.198 65.677 1 95.98 ? C4 UFP 602 C 1 
HETATM 5 C C5 UFP . . . Q 3 19.088 -15.994 66.834 1 92.81 ? C5 UFP 602 C 1 
HETATM 6 C C6 UFP . . . Q 3 20.263 -15.92 67.487 1 88.58 ? C6 UFP 602 C 1 
HETATM 7 O O2 UFP . . . Q 3 21.912 -13.57 65.496 1 87.98 ? O2 UFP 602 C 1 
HETATM 8 O O4 UFP . . . Q 3 17.856 -15.238 65.055 1 87.55 ? O4 UFP 602 C 1 
HETATM 9 F F5 UFP . . . Q 3 18.115 -16.821 67.283 1 87.71 ? F5 UFP 602 C 1 
HETATM 10 C C1' UFP . . . Q 3 22.489 -15.124 67.895 1 87.97 ? C1' UFP 602 C 1 
HETATM 11 C C2' UFP . . . Q 3 23.061 -13.746 68.31 1 81.08 ? C2' UFP 602 C 1 
HETATM 12 C C3' UFP . . . Q 3 23.886 -14.143 69.545 1 70.75 ? C3' UFP 602 C 1 
HETATM 13 C C4' UFP . . . Q 3 22.929 -15.13 70.232 1 69.3 ? C4' UFP 602 C 1 
HETATM 14 O O3' UFP . . . Q 3 25.081 -14.826 69.172 1 74.69 ? O3' UFP 602 C 1 
HETATM 15 O O4' UFP . . . Q 3 22.17 -15.756 69.161 1 86.2 ? O4' UFP 602 C 1 
HETATM 16 C C5' UFP . . . Q 3 22.003 -14.37 71.18 1 73.88 ? C5' UFP 602 C 1 
HETATM 17 O O5' UFP . . . Q 3 22.743 -13.312 71.787 1 69.47 ? O5' UFP 602 C 1 
HETATM 18 P P UFP . . . Q 3 22.351 -13.319 73.341 1 67.16 ? P UFP 602 C 1 
HETATM 19 O O1P UFP . . . Q 3 20.993 -12.496 73.557 1 50.61 ? O1P UFP 602 C 1 
HETATM 20 O O2P UFP . . . Q 3 22.126 -14.838 73.806 1 77.79 ? O2P UFP 602 C 1 
HETATM 21 O O3P UFP . . . Q 3 23.432 -12.697 74.133 1 83.45 ? O3P UFP 602 C 1 
#
_model_server_stats.io_time_ms              15 
_model_server_stats.parse_time_ms           11 
_model_server_stats.create_model_time_ms    24 
_model_server_stats.query_time_ms           286 
_model_server_stats.encode_time_ms          2 
_model_server_stats.element_count           21 
#