data_6PFE
#
_model_server_result.job_id            ZufUKeoQF8zuO5giOdHxrg 
_model_server_result.datetime_utc      '2024-11-29 06:59:44' 
_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          6pfe 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"G","auth_seq_id":602}' 
#
_entry.id    6PFE 
#
_exptl.entry_id    6PFE 
_exptl.method      'X-RAY DIFFRACTION' 
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_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          95 
_cell.angle_gamma         90 
_cell.entry_id            6PFE 
_cell.length_a            212.859 
_cell.length_b            115.641 
_cell.length_c            219.899 
_cell.Z_PDB               20 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 6PFE 
_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,B,F,G,H,I,J,K,L,M,Z,AA 1 1 
C,E,N,O,P,Q,V,W,X,Y,BA,DA 2 1 
D,R,S,T,U,CA 3 1,2 
#
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_558 -x,y,-z+3 -1 0 0 0 1 0 0 0 -1 -57.496382 0 657.186654 
#
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 K N N 
? 3 O N N 
? 3 S N N 
? 3 W 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 551 n n 
N1 C6 UFP sing 552 n n 
N1 C1' UFP sing 553 n n 
C2 N3 UFP sing 554 n n 
C2 O2 UFP doub 555 n n 
N3 C4 UFP sing 556 n n 
N3 HN3 UFP sing 557 n n 
C4 C5 UFP sing 558 n n 
C4 O4 UFP doub 559 n n 
C5 C6 UFP doub 560 n n 
C5 F5 UFP sing 561 n n 
C6 H6 UFP sing 562 n n 
C1' C2' UFP sing 563 n n 
C1' O4' UFP sing 564 n n 
C1' H1' UFP sing 565 n n 
C2' C3' UFP sing 566 n n 
C2' "H2'1" UFP sing 567 n n 
C2' "H2'2" UFP sing 568 n n 
C3' C4' UFP sing 569 n n 
C3' O3' UFP sing 570 n n 
C3' H3' UFP sing 571 n n 
C4' O4' UFP sing 572 n n 
C4' C5' UFP sing 573 n n 
C4' H4' UFP sing 574 n n 
O3' HO3' UFP sing 575 n n 
C5' O5' UFP sing 576 n n 
C5' "H5'1" UFP sing 577 n n 
C5' "H5'2" UFP sing 578 n n 
O5' P UFP sing 579 n n 
P O1P UFP doub 580 n n 
P O2P UFP sing 581 n n 
P O3P UFP sing 582 n n 
O2P HOP2 UFP sing 583 n n 
O3P HOP3 UFP sing 584 n n 
#
_atom_sites.entry_id                     6PFE 
_atom_sites.fract_transf_matrix[1][1]    0.004698 
_atom_sites.fract_transf_matrix[1][2]    0 
_atom_sites.fract_transf_matrix[1][3]    0.000411 
_atom_sites.fract_transf_matrix[2][1]    0 
_atom_sites.fract_transf_matrix[2][2]    0.008647 
_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]    0.004565 
_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 OEA A 1 603 603 OEA T12 . 
I 5 MTX A 1 604 604 MTX MTX . 
J 2 NDP B 1 601 601 NDP NDP . 
K 3 UFP B 1 602 602 UFP UFP . 
L 4 OEA B 1 603 603 OEA T12 . 
M 5 MTX B 1 604 604 MTX MTX . 
N 2 NDP C 1 601 601 NDP NDP . 
O 3 UFP C 1 602 602 UFP UFP . 
P 4 OEA C 1 603 603 OEA T12 . 
Q 5 MTX C 1 604 604 MTX MTX . 
R 2 NDP D 1 601 601 NDP NDP . 
S 3 UFP D 1 602 602 UFP UFP . 
T 4 OEA D 1 603 603 OEA T12 . 
U 5 MTX D 1 604 604 MTX MTX . 
V 2 NDP E 1 601 601 NDP NDP . 
W 3 UFP E 1 602 602 UFP UFP . 
X 4 OEA E 1 603 603 OEA T12 . 
Y 5 MTX E 1 604 604 MTX MTX . 
Z 6 HOH A 1 701 29 HOH HOH . 
Z 6 HOH A 2 702 21 HOH HOH . 
Z 6 HOH A 3 703 40 HOH HOH . 
Z 6 HOH A 4 704 17 HOH HOH . 
Z 6 HOH A 5 705 15 HOH HOH . 
Z 6 HOH A 6 706 2 HOH HOH . 
Z 6 HOH A 7 707 20 HOH HOH . 
Z 6 HOH A 8 708 25 HOH HOH . 
Z 6 HOH A 9 709 3 HOH HOH . 
AA 6 HOH B 1 701 18 HOH HOH . 
AA 6 HOH B 2 702 31 HOH HOH . 
AA 6 HOH B 3 703 23 HOH HOH . 
AA 6 HOH B 4 704 16 HOH HOH . 
AA 6 HOH B 5 705 19 HOH HOH . 
AA 6 HOH B 6 706 8 HOH HOH . 
AA 6 HOH B 7 707 27 HOH HOH . 
AA 6 HOH B 8 708 4 HOH HOH . 
AA 6 HOH B 9 709 11 HOH HOH . 
AA 6 HOH B 10 710 30 HOH HOH . 
AA 6 HOH B 11 711 13 HOH HOH . 
AA 6 HOH B 12 712 1 HOH HOH . 
AA 6 HOH B 13 713 14 HOH HOH . 
AA 6 HOH B 14 714 34 HOH HOH . 
BA 6 HOH C 1 701 33 HOH HOH . 
BA 6 HOH C 2 702 43 HOH HOH . 
BA 6 HOH C 3 703 35 HOH HOH . 
BA 6 HOH C 4 704 39 HOH HOH . 
BA 6 HOH C 5 705 9 HOH HOH . 
CA 6 HOH D 1 701 22 HOH HOH . 
CA 6 HOH D 2 702 42 HOH HOH . 
CA 6 HOH D 3 703 5 HOH HOH . 
DA 6 HOH E 1 701 26 HOH HOH . 
DA 6 HOH E 2 702 32 HOH HOH . 
DA 6 HOH E 3 703 28 HOH HOH . 
DA 6 HOH E 4 704 36 HOH HOH . 
DA 6 HOH E 5 705 12 HOH HOH . 
DA 6 HOH E 6 706 10 HOH HOH . 
DA 6 HOH E 7 707 41 HOH HOH . 
DA 6 HOH E 8 708 24 HOH HOH . 
DA 6 HOH E 9 709 6 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 . . . G 3 20.793 95.606 215.635 1 63.56 ? N1 UFP 602 A 1 
HETATM 2 C C2 UFP . . . G 3 20.743 95.397 216.982 1 63.32 ? C2 UFP 602 A 1 
HETATM 3 N N3 UFP . . . G 3 21.771 95.776 217.767 1 69.79 ? N3 UFP 602 A 1 
HETATM 4 C C4 UFP . . . G 3 22.872 96.363 217.257 1 69.64 ? C4 UFP 602 A 1 
HETATM 5 C C5 UFP . . . G 3 22.941 96.582 215.857 1 69.67 ? C5 UFP 602 A 1 
HETATM 6 C C6 UFP . . . G 3 21.907 96.19 215.094 1 72.57 ? C6 UFP 602 A 1 
HETATM 7 O O2 UFP . . . G 3 19.801 94.874 217.554 1 65.6 ? O2 UFP 602 A 1 
HETATM 8 O O4 UFP . . . G 3 23.781 96.694 217.995 1 69.43 ? O4 UFP 602 A 1 
HETATM 9 F F5 UFP . . . G 3 24.011 97.168 215.27 1 55.13 ? F5 UFP 602 A 1 
HETATM 10 C C1' UFP . . . G 3 19.779 95.252 214.622 1 55.6 ? C1' UFP 602 A 1 
HETATM 11 C C2' UFP . . . G 3 18.297 95.504 214.99 1 58.64 ? C2' UFP 602 A 1 
HETATM 12 C C3' UFP . . . G 3 17.674 95.656 213.587 1 59.43 ? C3' UFP 602 A 1 
HETATM 13 C C4' UFP . . . G 3 18.747 96.476 212.855 1 58.03 ? C4' UFP 602 A 1 
HETATM 14 O O3' UFP . . . G 3 17.526 94.395 212.938 1 50.88 ? O3' UFP 602 A 1 
HETATM 15 O O4' UFP . . . G 3 20.013 96.094 213.462 1 66.93 ? O4' UFP 602 A 1 
HETATM 16 C C5' UFP . . . G 3 18.494 97.967 213.061 1 57.6 ? C5' UFP 602 A 1 
HETATM 17 O O5' UFP . . . G 3 18.208 98.579 211.81 1 50.05 ? O5' UFP 602 A 1 
HETATM 18 P P UFP . . . G 3 16.817 99.368 211.969 1 60.14 ? P UFP 602 A 1 
HETATM 19 O O1P UFP . . . G 3 15.699 98.624 211.087 1 55.75 ? O1P UFP 602 A 1 
HETATM 20 O O2P UFP . . . G 3 16.393 99.389 213.384 1 49.66 ? O2P UFP 602 A 1 
HETATM 21 O O3P UFP . . . G 3 17.011 100.886 211.479 1 56.39 ? O3P UFP 602 A 1 
#
_model_server_stats.io_time_ms              16 
_model_server_stats.parse_time_ms           12 
_model_server_stats.create_model_time_ms    44 
_model_server_stats.query_time_ms           289 
_model_server_stats.encode_time_ms          7 
_model_server_stats.element_count           21 
#