data_6PFF
#
_model_server_result.job_id            nVhwz6YRmK5qKtaKnuzMJw 
_model_server_result.datetime_utc      '2024-11-25 08:35:31' 
_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          6pff 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"AA","auth_seq_id":602}' 
#
_entry.id    6PFF 
#
_exptl.entry_id    6PFF 
_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          95.69 
_cell.angle_gamma         90 
_cell.entry_id            6PFF 
_cell.length_a            213.424 
_cell.length_b            116.794 
_cell.length_c            221.76 
_cell.Z_PDB               20 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 6PFF 
_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,N,O,EA,FA 1 1 
C,D,P,Q,R,S,T,U,V,W,X,Y,GA,HA 2 1 
E,Z,AA,BA,CA,DA 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_455 -x-1,y,-z -1 0 0 0 1 0 0 0 -1 -213.424 0 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 552 n n 
N1 C6 UFP sing 553 n n 
N1 C1' UFP sing 554 n n 
C2 N3 UFP sing 555 n n 
C2 O2 UFP doub 556 n n 
N3 C4 UFP sing 557 n n 
N3 HN3 UFP sing 558 n n 
C4 C5 UFP sing 559 n n 
C4 O4 UFP doub 560 n n 
C5 C6 UFP doub 561 n n 
C5 F5 UFP sing 562 n n 
C6 H6 UFP sing 563 n n 
C1' C2' UFP sing 564 n n 
C1' O4' UFP sing 565 n n 
C1' H1' UFP sing 566 n n 
C2' C3' UFP sing 567 n n 
C2' "H2'1" UFP sing 568 n n 
C2' "H2'2" UFP sing 569 n n 
C3' C4' UFP sing 570 n n 
C3' O3' UFP sing 571 n n 
C3' H3' UFP sing 572 n n 
C4' O4' UFP sing 573 n n 
C4' C5' UFP sing 574 n n 
C4' H4' UFP sing 575 n n 
O3' HO3' UFP sing 576 n n 
C5' O5' UFP sing 577 n n 
C5' "H5'1" UFP sing 578 n n 
C5' "H5'2" UFP sing 579 n n 
O5' P UFP sing 580 n n 
P O1P UFP doub 581 n n 
P O2P UFP sing 582 n n 
P O3P UFP sing 583 n n 
O2P HOP2 UFP sing 584 n n 
O3P HOP3 UFP sing 585 n n 
#
_atom_sites.entry_id                     6PFF 
_atom_sites.fract_transf_matrix[1][1]    0.004686 
_atom_sites.fract_transf_matrix[1][2]    0 
_atom_sites.fract_transf_matrix[1][3]    0.000467 
_atom_sites.fract_transf_matrix[2][1]    0 
_atom_sites.fract_transf_matrix[2][2]    0.008562 
_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 OG1 A 1 603 603 OG1 T13 . 
I 5 MTX A 1 604 604 MTX MTX . 
J 6 SO4 A 1 605 2 SO4 SO4 . 
K 2 NDP B 1 601 601 NDP NDP . 
L 3 UFP B 1 602 602 UFP UFP . 
M 4 OG1 B 1 603 603 OG1 T13 . 
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 OG1 C 1 603 603 OG1 T13 . 
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 OG1 D 1 603 603 OG1 T13 . 
X 5 MTX D 1 604 604 MTX MTX . 
Y 6 SO4 D 1 605 3 SO4 SO4 . 
Z 2 NDP E 1 601 601 NDP NDP . 
AA 3 UFP E 1 602 602 UFP UFP . 
BA 4 OG1 E 1 603 603 OG1 T13 . 
CA 5 MTX E 1 604 604 MTX MTX . 
DA 6 SO4 E 1 605 5 SO4 SO4 . 
EA 7 HOH A 1 701 6 HOH HOH . 
EA 7 HOH A 2 702 1 HOH HOH . 
EA 7 HOH A 3 703 8 HOH HOH . 
FA 7 HOH B 1 701 11 HOH HOH . 
FA 7 HOH B 2 702 13 HOH HOH . 
FA 7 HOH B 3 703 10 HOH HOH . 
FA 7 HOH B 4 704 5 HOH HOH . 
FA 7 HOH B 5 705 7 HOH HOH . 
FA 7 HOH B 6 706 4 HOH HOH . 
GA 7 HOH C 1 701 3 HOH HOH . 
HA 7 HOH D 1 701 12 HOH HOH . 
HA 7 HOH D 2 702 14 HOH HOH . 
HA 7 HOH D 3 703 2 HOH HOH . 
HA 7 HOH D 4 704 9 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 . . . AA 3 -121.34 -94.408 5.402 1 116.24 ? N1 UFP 602 E 1 
HETATM 2 C C2 UFP . . . AA 3 -120.44 -93.488 5.852 1 105.48 ? C2 UFP 602 E 1 
HETATM 3 N N3 UFP . . . AA 3 -119.525 -93.826 6.783 1 111.2 ? N3 UFP 602 E 1 
HETATM 4 C C4 UFP . . . AA 3 -119.471 -95.071 7.296 1 114.65 ? C4 UFP 602 E 1 
HETATM 5 C C5 UFP . . . AA 3 -120.398 -96.039 6.843 1 114.5 ? C5 UFP 602 E 1 
HETATM 6 C C6 UFP . . . AA 3 -121.306 -95.681 5.916 1 115.89 ? C6 UFP 602 E 1 
HETATM 7 O O2 UFP . . . AA 3 -120.401 -92.334 5.456 1 96.63 ? O2 UFP 602 E 1 
HETATM 8 O O4 UFP . . . AA 3 -118.639 -95.36 8.136 1 117.02 ? O4 UFP 602 E 1 
HETATM 9 F F5 UFP . . . AA 3 -120.377 -97.301 7.333 1 121.02 ? F5 UFP 602 E 1 
HETATM 10 C C1' UFP . . . AA 3 -122.395 -94.178 4.387 1 118.54 ? C1' UFP 602 E 1 
HETATM 11 C C2' UFP . . . AA 3 -121.93 -93.467 3.094 1 107.56 ? C2' UFP 602 E 1 
HETATM 12 C C3' UFP . . . AA 3 -123.097 -93.811 2.152 1 103.26 ? C3' UFP 602 E 1 
HETATM 13 C C4' UFP . . . AA 3 -123.405 -95.269 2.541 1 118.51 ? C4' UFP 602 E 1 
HETATM 14 O O3' UFP . . . AA 3 -124.232 -92.989 2.426 1 96.28 ? O3' UFP 602 E 1 
HETATM 15 O O4' UFP . . . AA 3 -122.867 -95.455 3.883 1 123.53 ? O4' UFP 602 E 1 
HETATM 16 C C5' UFP . . . AA 3 -122.761 -96.24 1.546 1 115.11 ? C5' UFP 602 E 1 
HETATM 17 O O5' UFP . . . AA 3 -123.389 -96.111 0.269 1 95.53 ? O5' UFP 602 E 1 
HETATM 18 P P UFP . . . AA 3 -122.559 -97.013 -0.774 1 98.27 ? P UFP 602 E 1 
HETATM 19 O O1P UFP . . . AA 3 -123.102 -96.838 -2.14 1 108.23 ? O1P UFP 602 E 1 
HETATM 20 O O2P UFP . . . AA 3 -122.67 -98.56 -0.353 1 101.46 ? O2P UFP 602 E 1 
HETATM 21 O O3P UFP . . . AA 3 -121.019 -96.559 -0.745 1 91.52 ? O3P UFP 602 E 1 
#
_model_server_stats.io_time_ms              17 
_model_server_stats.parse_time_ms           13 
_model_server_stats.create_model_time_ms    36 
_model_server_stats.query_time_ms           457 
_model_server_stats.encode_time_ms          4 
_model_server_stats.element_count           21 
#