data_6PFD
#
_model_server_result.job_id            zitK7uelOK4eDq4uRLDwfA 
_model_server_result.datetime_utc      '2024-11-13 11:31:59' 
_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          6pfd 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"W","auth_seq_id":602}' 
#
_entry.id    6PFD 
#
_exptl.entry_id    6PFD 
_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          95.05 
_cell.angle_gamma         90 
_cell.entry_id            6PFD 
_cell.length_a            213.033 
_cell.length_b            115.887 
_cell.length_c            220.808 
_cell.Z_PDB               20 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 6PFD 
_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 1 1 
C,D,N,O,P,Q,R,S,T,U 2 1 
E,V,W,X,Y 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_858 -x+3,y,-z+3 -1 0 0 0 1 0 0 0 -1 580.789092 0 659.852643 
#
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 548 n n 
N1 C6 UFP sing 549 n n 
N1 C1' UFP sing 550 n n 
C2 N3 UFP sing 551 n n 
C2 O2 UFP doub 552 n n 
N3 C4 UFP sing 553 n n 
N3 HN3 UFP sing 554 n n 
C4 C5 UFP sing 555 n n 
C4 O4 UFP doub 556 n n 
C5 C6 UFP doub 557 n n 
C5 F5 UFP sing 558 n n 
C6 H6 UFP sing 559 n n 
C1' C2' UFP sing 560 n n 
C1' O4' UFP sing 561 n n 
C1' H1' UFP sing 562 n n 
C2' C3' UFP sing 563 n n 
C2' "H2'1" UFP sing 564 n n 
C2' "H2'2" UFP sing 565 n n 
C3' C4' UFP sing 566 n n 
C3' O3' UFP sing 567 n n 
C3' H3' UFP sing 568 n n 
C4' O4' UFP sing 569 n n 
C4' C5' UFP sing 570 n n 
C4' H4' UFP sing 571 n n 
O3' HO3' UFP sing 572 n n 
C5' O5' UFP sing 573 n n 
C5' "H5'1" UFP sing 574 n n 
C5' "H5'2" UFP sing 575 n n 
O5' P UFP sing 576 n n 
P O1P UFP doub 577 n n 
P O2P UFP sing 578 n n 
P O3P UFP sing 579 n n 
O2P HOP2 UFP sing 580 n n 
O3P HOP3 UFP sing 581 n n 
#
_atom_sites.entry_id                     6PFD 
_atom_sites.fract_transf_matrix[1][1]    0.004694 
_atom_sites.fract_transf_matrix[1][2]    0 
_atom_sites.fract_transf_matrix[1][3]    0.000414 
_atom_sites.fract_transf_matrix[2][1]    0 
_atom_sites.fract_transf_matrix[2][2]    0.008629 
_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]    0.004546 
_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 OEJ A 1 603 603 OEJ T11 . 
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 OEJ B 1 603 603 OEJ T11 . 
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 OEJ C 1 603 603 OEJ T11 . 
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 OEJ D 1 603 603 OEJ T11 . 
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 OEJ E 1 603 603 OEJ T11 . 
Y 5 MTX E 1 604 604 MTX MTX . 
#
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 . . . W 3 304.719 39.546 324.147 1 134.31 ? N1 UFP 602 E 1 
HETATM 2 C C2 UFP . . . W 3 303.71 40.355 323.711 1 124.24 ? C2 UFP 602 E 1 
HETATM 3 N N3 UFP . . . W 3 302.852 39.928 322.762 1 131.98 ? N3 UFP 602 E 1 
HETATM 4 C C4 UFP . . . W 3 302.959 38.701 322.213 1 146.3 ? C4 UFP 602 E 1 
HETATM 5 C C5 UFP . . . W 3 303.999 37.847 322.65 1 145.66 ? C5 UFP 602 E 1 
HETATM 6 C C6 UFP . . . W 3 304.849 38.294 323.596 1 139.93 ? C6 UFP 602 E 1 
HETATM 7 O O2 UFP . . . W 3 303.522 41.484 324.136 1 114.87 ? O2 UFP 602 E 1 
HETATM 8 O O4 UFP . . . W 3 302.177 38.328 321.357 1 141.63 ? O4 UFP 602 E 1 
HETATM 9 F F5 UFP . . . W 3 304.14 36.607 322.123 1 142.37 ? F5 UFP 602 E 1 
HETATM 10 C C1' UFP . . . W 3 305.727 39.885 325.18 1 138.98 ? C1' UFP 602 E 1 
HETATM 11 C C2' UFP . . . W 3 305.17 40.535 326.47 1 130.32 ? C2' UFP 602 E 1 
HETATM 12 C C3' UFP . . . W 3 306.352 40.304 327.425 1 130.02 ? C3' UFP 602 E 1 
HETATM 13 C C4' UFP . . . W 3 306.755 38.862 327.069 1 145.98 ? C4' UFP 602 E 1 
HETATM 14 O O3' UFP . . . W 3 307.425 41.193 327.117 1 116.97 ? O3' UFP 602 E 1 
HETATM 15 O O4' UFP . . . W 3 306.342 38.668 325.683 1 160.92 ? O4' UFP 602 E 1 
HETATM 16 C C5' UFP . . . W 3 306.074 37.853 328.004 1 119.72 ? C5' UFP 602 E 1 
HETATM 17 O O5' UFP . . . W 3 305.936 38.409 329.313 1 96.73 ? O5' UFP 602 E 1 
HETATM 18 P P UFP . . . W 3 306.347 37.271 330.375 1 127.98 ? P UFP 602 E 1 
HETATM 19 O O1P UFP . . . W 3 307.691 36.538 329.885 1 124.39 ? O1P UFP 602 E 1 
HETATM 20 O O2P UFP . . . W 3 306.57 37.88 331.705 1 131.04 ? O2P UFP 602 E 1 
HETATM 21 O O3P UFP . . . W 3 305.17 36.184 330.486 1 114.39 ? O3P UFP 602 E 1 
#
_model_server_stats.io_time_ms              14 
_model_server_stats.parse_time_ms           18 
_model_server_stats.create_model_time_ms    34 
_model_server_stats.query_time_ms           310 
_model_server_stats.encode_time_ms          3 
_model_server_stats.element_count           21 
#