data_6PFA
#
_model_server_result.job_id            1H7BoFm162uSEUGpGK1Pgw 
_model_server_result.datetime_utc      '2024-12-01 00:09:17' 
_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          6pfa 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"AA","auth_seq_id":602}' 
#
_entry.id    6PFA 
#
_exptl.entry_id    6PFA 
_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          95.72 
_cell.angle_gamma         90 
_cell.entry_id            6PFA 
_cell.length_a            213.21 
_cell.length_b            117.294 
_cell.length_c            222.817 
_cell.Z_PDB               20 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 6PFA 
_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,IA 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 -213.21 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 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                     6PFA 
_atom_sites.fract_transf_matrix[1][1]    0.00469 
_atom_sites.fract_transf_matrix[1][2]    0 
_atom_sites.fract_transf_matrix[1][3]    0.00047 
_atom_sites.fract_transf_matrix[2][1]    0 
_atom_sites.fract_transf_matrix[2][2]    0.008526 
_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]    0.00451 
_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 OF4 A 1 603 603 OF4 M85 . 
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 OF4 B 1 603 603 OF4 M85 . 
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 OF4 C 1 603 603 OF4 M85 . 
S 5 MTX C 1 604 604 MTX MTX . 
T 6 SO4 C 1 605 3 SO4 SO4 . 
U 2 NDP D 1 601 601 NDP NDP . 
V 3 UFP D 1 602 602 UFP UFP . 
W 4 OF4 D 1 603 603 OF4 M85 . 
X 5 MTX D 1 604 604 MTX MTX . 
Y 6 SO4 D 1 605 4 SO4 SO4 . 
Z 2 NDP E 1 601 601 NDP NDP . 
AA 3 UFP E 1 602 602 UFP UFP . 
BA 4 OF4 E 1 603 603 OF4 M85 . 
CA 5 MTX E 1 604 604 MTX MTX . 
DA 6 SO4 E 1 605 5 SO4 SO4 . 
EA 7 HOH A 1 701 98 HOH HOH . 
EA 7 HOH A 2 702 59 HOH HOH . 
EA 7 HOH A 3 703 95 HOH HOH . 
EA 7 HOH A 4 704 63 HOH HOH . 
EA 7 HOH A 5 705 54 HOH HOH . 
EA 7 HOH A 6 706 4 HOH HOH . 
EA 7 HOH A 7 707 65 HOH HOH . 
EA 7 HOH A 8 708 100 HOH HOH . 
EA 7 HOH A 9 709 23 HOH HOH . 
EA 7 HOH A 10 710 6 HOH HOH . 
EA 7 HOH A 11 711 36 HOH HOH . 
EA 7 HOH A 12 712 45 HOH HOH . 
EA 7 HOH A 13 713 19 HOH HOH . 
EA 7 HOH A 14 714 72 HOH HOH . 
EA 7 HOH A 15 715 81 HOH HOH . 
EA 7 HOH A 16 716 62 HOH HOH . 
EA 7 HOH A 17 717 28 HOH HOH . 
EA 7 HOH A 18 718 70 HOH HOH . 
EA 7 HOH A 19 719 33 HOH HOH . 
EA 7 HOH A 20 720 110 HOH HOH . 
EA 7 HOH A 21 721 76 HOH HOH . 
EA 7 HOH A 22 722 96 HOH HOH . 
EA 7 HOH A 23 723 109 HOH HOH . 
EA 7 HOH A 24 724 69 HOH HOH . 
FA 7 HOH B 1 701 44 HOH HOH . 
FA 7 HOH B 2 702 1 HOH HOH . 
FA 7 HOH B 3 703 73 HOH HOH . 
FA 7 HOH B 4 704 3 HOH HOH . 
FA 7 HOH B 5 705 56 HOH HOH . 
FA 7 HOH B 6 706 67 HOH HOH . 
FA 7 HOH B 7 707 22 HOH HOH . 
FA 7 HOH B 8 708 13 HOH HOH . 
FA 7 HOH B 9 709 16 HOH HOH . 
FA 7 HOH B 10 710 55 HOH HOH . 
FA 7 HOH B 11 711 41 HOH HOH . 
FA 7 HOH B 12 712 99 HOH HOH . 
FA 7 HOH B 13 713 71 HOH HOH . 
FA 7 HOH B 14 714 27 HOH HOH . 
FA 7 HOH B 15 715 25 HOH HOH . 
FA 7 HOH B 16 716 2 HOH HOH . 
FA 7 HOH B 17 717 86 HOH HOH . 
FA 7 HOH B 18 718 50 HOH HOH . 
FA 7 HOH B 19 719 8 HOH HOH . 
FA 7 HOH B 20 720 12 HOH HOH . 
FA 7 HOH B 21 721 35 HOH HOH . 
FA 7 HOH B 22 722 11 HOH HOH . 
FA 7 HOH B 23 723 39 HOH HOH . 
FA 7 HOH B 24 724 32 HOH HOH . 
FA 7 HOH B 25 725 88 HOH HOH . 
FA 7 HOH B 26 726 40 HOH HOH . 
FA 7 HOH B 27 727 66 HOH HOH . 
FA 7 HOH B 28 728 101 HOH HOH . 
FA 7 HOH B 29 729 9 HOH HOH . 
FA 7 HOH B 30 730 43 HOH HOH . 
FA 7 HOH B 31 731 14 HOH HOH . 
FA 7 HOH B 32 732 105 HOH HOH . 
FA 7 HOH B 33 733 10 HOH HOH . 
FA 7 HOH B 34 734 18 HOH HOH . 
FA 7 HOH B 35 735 38 HOH HOH . 
FA 7 HOH B 36 736 57 HOH HOH . 
FA 7 HOH B 37 737 107 HOH HOH . 
GA 7 HOH C 1 701 15 HOH HOH . 
GA 7 HOH C 2 702 104 HOH HOH . 
GA 7 HOH C 3 703 48 HOH HOH . 
GA 7 HOH C 4 704 68 HOH HOH . 
GA 7 HOH C 5 705 29 HOH HOH . 
GA 7 HOH C 6 706 58 HOH HOH . 
GA 7 HOH C 7 707 30 HOH HOH . 
GA 7 HOH C 8 708 80 HOH HOH . 
GA 7 HOH C 9 709 78 HOH HOH . 
GA 7 HOH C 10 710 20 HOH HOH . 
GA 7 HOH C 11 711 90 HOH HOH . 
GA 7 HOH C 12 712 97 HOH HOH . 
GA 7 HOH C 13 713 24 HOH HOH . 
GA 7 HOH C 14 714 17 HOH HOH . 
GA 7 HOH C 15 715 64 HOH HOH . 
HA 7 HOH D 1 701 51 HOH HOH . 
HA 7 HOH D 2 702 77 HOH HOH . 
HA 7 HOH D 3 703 74 HOH HOH . 
HA 7 HOH D 4 704 42 HOH HOH . 
HA 7 HOH D 5 705 5 HOH HOH . 
HA 7 HOH D 6 706 83 HOH HOH . 
HA 7 HOH D 7 707 37 HOH HOH . 
HA 7 HOH D 8 708 92 HOH HOH . 
HA 7 HOH D 9 709 52 HOH HOH . 
HA 7 HOH D 10 710 61 HOH HOH . 
HA 7 HOH D 11 711 85 HOH HOH . 
HA 7 HOH D 12 712 94 HOH HOH . 
HA 7 HOH D 13 713 79 HOH HOH . 
HA 7 HOH D 14 714 26 HOH HOH . 
HA 7 HOH D 15 715 106 HOH HOH . 
HA 7 HOH D 16 716 102 HOH HOH . 
HA 7 HOH D 17 717 47 HOH HOH . 
HA 7 HOH D 18 718 82 HOH HOH . 
IA 7 HOH E 1 701 31 HOH HOH . 
IA 7 HOH E 2 702 7 HOH HOH . 
IA 7 HOH E 3 703 21 HOH HOH . 
IA 7 HOH E 4 704 84 HOH HOH . 
IA 7 HOH E 5 705 111 HOH HOH . 
IA 7 HOH E 6 706 46 HOH HOH . 
IA 7 HOH E 7 707 91 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 -121.254 -95.177 5.394 1 117.06 ? N1 UFP 602 E 1 
HETATM 2 C C2 UFP . . . AA 3 -120.307 -94.304 5.839 1 109.26 ? C2 UFP 602 E 1 
HETATM 3 N N3 UFP . . . AA 3 -119.469 -94.655 6.834 1 113.88 ? N3 UFP 602 E 1 
HETATM 4 C C4 UFP . . . AA 3 -119.54 -95.868 7.418 1 119.71 ? C4 UFP 602 E 1 
HETATM 5 C C5 UFP . . . AA 3 -120.518 -96.786 6.97 1 116.47 ? C5 UFP 602 E 1 
HETATM 6 C C6 UFP . . . AA 3 -121.347 -96.415 5.977 1 118.29 ? C6 UFP 602 E 1 
HETATM 7 O O2 UFP . . . AA 3 -120.164 -93.184 5.376 1 98.49 ? O2 UFP 602 E 1 
HETATM 8 O O4 UFP . . . AA 3 -118.775 -96.17 8.316 1 127.8 ? O4 UFP 602 E 1 
HETATM 9 F F5 UFP . . . AA 3 -120.626 -98.015 7.529 1 120.33 ? F5 UFP 602 E 1 
HETATM 10 C C1' UFP . . . AA 3 -122.232 -94.915 4.315 1 117.75 ? C1' UFP 602 E 1 
HETATM 11 C C2' UFP . . . AA 3 -121.629 -94.429 2.978 1 108.64 ? C2' UFP 602 E 1 
HETATM 12 C C3' UFP . . . AA 3 -122.828 -94.661 2.04 1 110.92 ? C3' UFP 602 E 1 
HETATM 13 C C4' UFP . . . AA 3 -123.441 -95.966 2.59 1 123.64 ? C4' UFP 602 E 1 
HETATM 14 O O3' UFP . . . AA 3 -123.778 -93.602 2.167 1 101.63 ? O3' UFP 602 E 1 
HETATM 15 O O4' UFP . . . AA 3 -122.87 -96.154 3.917 1 125.1 ? O4' UFP 602 E 1 
HETATM 16 C C5' UFP . . . AA 3 -123.138 -97.16 1.674 1 120.4 ? C5' UFP 602 E 1 
HETATM 17 O O5' UFP . . . AA 3 -122.041 -96.858 0.81 1 118.22 ? O5' UFP 602 E 1 
HETATM 18 P P UFP . . . AA 3 -122.256 -97.647 -0.579 1 102.45 ? P UFP 602 E 1 
HETATM 19 O O1P UFP . . . AA 3 -121.29 -97.014 -1.696 1 87.03 ? O1P UFP 602 E 1 
HETATM 20 O O2P UFP . . . AA 3 -121.885 -99.198 -0.385 1 99.06 ? O2P UFP 602 E 1 
HETATM 21 O O3P UFP . . . AA 3 -123.668 -97.528 -1.009 1 94.69 ? O3P UFP 602 E 1 
#
_model_server_stats.io_time_ms              21 
_model_server_stats.parse_time_ms           34 
_model_server_stats.create_model_time_ms    33 
_model_server_stats.query_time_ms           454 
_model_server_stats.encode_time_ms          5 
_model_server_stats.element_count           21 
#