data_5FUY
#
_model_server_result.job_id            i8G8N2CEOVru4Pg8j207FA 
_model_server_result.datetime_utc      '2024-11-24 05:49:48' 
_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          5fuy 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"Q","auth_seq_id":1384}' 
#
_entry.id    5FUY 
#
_exptl.entry_id    5FUY 
_exptl.method      'X-RAY DIFFRACTION' 
#
_entity.details                     ? 
_entity.formula_weight              324.224 
_entity.id                          3 
_entity.src_method                  syn 
_entity.type                        non-polymer 
_entity.pdbx_description            '[(2R,3S,5R)-3-HYDROXY-5-[(5S)-5-METHYL-2,4-DIOXO-1,3-DIAZINAN-1-YL]OXOLAN-2-YL]METHYL DIHYDROGEN PHOSPHATE' 
_entity.pdbx_number_of_molecules    6 
_entity.pdbx_parent_entity_id       . 
_entity.pdbx_mutation               ? 
_entity.pdbx_fragment               ? 
_entity.pdbx_ec                     ? 
#
_cell.angle_alpha         90 
_cell.angle_beta          90 
_cell.angle_gamma         90 
_cell.entry_id            5FUY 
_cell.length_a            87.614 
_cell.length_b            96.999 
_cell.length_c            304.431 
_cell.Z_PDB               48 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 5FUY 
_symmetry.cell_setting             ? 
_symmetry.Int_Tables_number        20 
_symmetry.space_group_name_Hall    . 
_symmetry.space_group_name_H-M     'C 2 2 21' 
#
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 tetrameric 4 author_and_software_defined_assembly 1 
PISA tetrameric 4 author_and_software_defined_assembly 2 
#
loop_
_pdbx_struct_assembly_gen.asym_id_list
_pdbx_struct_assembly_gen.assembly_id
_pdbx_struct_assembly_gen.oper_expression
A,B,C,D,G,H,I,J,K,L,M,N,O,P,Q,R,Y,Z,AA,BA 1 1 
E,F,S,T,U,V,W,X,CA,DA 2 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' 3_555 -x,y,-z+1/2 -1 0 0 0 1 0 0 0 -1 0 0 152.2155 
#
loop_
_struct_asym.details
_struct_asym.entity_id
_struct_asym.id
_struct_asym.pdbx_modified
_struct_asym.pdbx_blank_PDB_chainid_flag
? 3 H N N 
? 3 K N N 
? 3 N N N 
? 3 Q N N 
? 3 T N N 
? 3 W N N 
#
loop_
_struct_conn.conn_type_id
_struct_conn.details
_struct_conn.id
_struct_conn.ptnr1_label_asym_id
_struct_conn.ptnr1_label_atom_id
_struct_conn.ptnr1_label_comp_id
_struct_conn.ptnr1_label_seq_id
_struct_conn.ptnr1_auth_asym_id
_struct_conn.ptnr1_auth_comp_id
_struct_conn.ptnr1_auth_seq_id
_struct_conn.ptnr1_symmetry
_struct_conn.ptnr2_label_asym_id
_struct_conn.ptnr2_label_atom_id
_struct_conn.ptnr2_label_comp_id
_struct_conn.ptnr2_label_seq_id
_struct_conn.ptnr2_auth_asym_id
_struct_conn.ptnr2_auth_comp_id
_struct_conn.ptnr2_auth_seq_id
_struct_conn.ptnr2_symmetry
_struct_conn.pdbx_ptnr1_PDB_ins_code
_struct_conn.pdbx_ptnr1_label_alt_id
_struct_conn.pdbx_ptnr1_standard_comp_id
_struct_conn.pdbx_ptnr2_PDB_ins_code
_struct_conn.pdbx_ptnr2_label_alt_id
_struct_conn.pdbx_ptnr3_PDB_ins_code
_struct_conn.pdbx_ptnr3_label_alt_id
_struct_conn.pdbx_ptnr3_label_asym_id
_struct_conn.pdbx_ptnr3_label_atom_id
_struct_conn.pdbx_ptnr3_label_comp_id
_struct_conn.pdbx_ptnr3_label_seq_id
_struct_conn.pdbx_PDB_id
_struct_conn.pdbx_dist_value
_struct_conn.pdbx_value_order
disulf ? disulf1 B SG CYS 123 B CYS 325 1_555 C SG CYS 123 C CYS 325 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.887 ? 
metalc ? metalc1 A SG CYS 139 A CYS 341 1_555 I ZN ZN . A ZN 1387 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.319 ? 
metalc ? metalc2 A SG CYS 142 A CYS 344 1_555 I ZN ZN . A ZN 1387 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.296 ? 
metalc ? metalc3 A SG CYS 172 A CYS 374 1_555 I ZN ZN . A ZN 1387 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.365 ? 
metalc ? metalc4 A SG CYS 175 A CYS 377 1_555 I ZN ZN . A ZN 1387 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.282 ? 
metalc ? metalc5 B SG CYS 139 B CYS 341 1_555 L ZN ZN . B ZN 1386 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.359 ? 
metalc ? metalc6 B SG CYS 142 B CYS 344 1_555 L ZN ZN . B ZN 1386 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.297 ? 
metalc ? metalc7 B SG CYS 172 B CYS 374 1_555 L ZN ZN . B ZN 1386 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.34 ? 
metalc ? metalc8 B SG CYS 175 B CYS 377 1_555 L ZN ZN . B ZN 1386 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.318 ? 
metalc ? metalc9 C SG CYS 139 C CYS 341 1_555 O ZN ZN . C ZN 1387 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.292 ? 
metalc ? metalc10 C SG CYS 142 C CYS 344 1_555 O ZN ZN . C ZN 1387 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.326 ? 
metalc ? metalc11 C SG CYS 172 C CYS 374 1_555 O ZN ZN . C ZN 1387 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.363 ? 
metalc ? metalc12 C SG CYS 175 C CYS 377 1_555 O ZN ZN . C ZN 1387 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.295 ? 
metalc ? metalc13 D SG CYS 139 D CYS 341 1_555 R ZN ZN . D ZN 1385 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.325 ? 
metalc ? metalc14 D SG CYS 142 D CYS 344 1_555 R ZN ZN . D ZN 1385 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.319 ? 
metalc ? metalc15 D SG CYS 172 D CYS 374 1_555 R ZN ZN . D ZN 1385 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.336 ? 
metalc ? metalc16 D SG CYS 175 D CYS 377 1_555 R ZN ZN . D ZN 1385 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.337 ? 
metalc ? metalc17 E SG CYS 139 E CYS 341 1_555 U ZN ZN . E ZN 1388 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.344 ? 
metalc ? metalc18 E SG CYS 142 E CYS 344 1_555 U ZN ZN . E ZN 1388 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.299 ? 
metalc ? metalc19 E SG CYS 172 E CYS 374 1_555 U ZN ZN . E ZN 1388 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.347 ? 
metalc ? metalc20 E SG CYS 175 E CYS 377 1_555 U ZN ZN . E ZN 1388 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.293 ? 
metalc ? metalc21 F SG CYS 139 F CYS 341 1_555 X ZN ZN . F ZN 1387 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.309 ? 
metalc ? metalc22 F SG CYS 142 F CYS 344 1_555 X ZN ZN . F ZN 1387 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.308 ? 
metalc ? metalc23 F SG CYS 172 F CYS 374 1_555 X ZN ZN . F ZN 1387 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.355 ? 
metalc ? metalc24 F SG CYS 175 F CYS 377 1_555 X ZN ZN . F ZN 1387 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.291 ? 
#
_chem_comp.formula           'C10 H17 N2 O8 P' 
_chem_comp.formula_weight    324.224 
_chem_comp.id                QBT 
_chem_comp.mon_nstd_flag     . 
_chem_comp.name              '[(2R,3S,5R)-3-HYDROXY-5-[(5S)-5-METHYL-2,4-DIOXO-1,3-DIAZINAN-1-YL]OXOLAN-2-YL]METHYL DIHYDROGEN PHOSPHATE' 
_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
P O1P QBT sing 281 n n 
P O2P QBT doub 282 n n 
P O5' QBT sing 283 n n 
P O3P QBT sing 284 n n 
O5' C5' QBT sing 285 n n 
C5' C4' QBT sing 286 n n 
C4' O4' QBT sing 287 n n 
C4' C3' QBT sing 288 n n 
O4' C1' QBT sing 289 n n 
C3' O3' QBT sing 290 n n 
C3' C2' QBT sing 291 n n 
C2' C1' QBT sing 292 n n 
C1' N1 QBT sing 293 n n 
N1 C2 QBT sing 294 n n 
N1 C6 QBT sing 295 n n 
C2 O2 QBT doub 296 n n 
C2 N3 QBT sing 297 n n 
N3 C4 QBT sing 298 n n 
C4 O4 QBT doub 299 n n 
C4 C5 QBT sing 300 n n 
C5 C5M QBT sing 301 n n 
O1P H1P QBT sing 302 n n 
C5' "H5'1" QBT sing 303 n n 
C5' "H5'2" QBT sing 304 n n 
C4' H4' QBT sing 305 n n 
C3' H3' QBT sing 306 n n 
C1' H1' QBT sing 307 n n 
O3' HA QBT sing 308 n n 
C2' "H2'1" QBT sing 309 n n 
C2' "H2'2" QBT sing 310 n n 
C6 H61C QBT sing 311 n n 
C6 H62C QBT sing 312 n n 
N3 H3 QBT sing 313 n n 
C5 C6 QBT sing 314 n n 
C5 H5M QBT sing 315 n n 
C5M H52 QBT sing 316 n n 
C5M H53 QBT sing 317 n n 
C5M H54 QBT sing 318 n n 
O3P H3P QBT sing 319 n n 
#
_atom_sites.entry_id                     5FUY 
_atom_sites.fract_transf_matrix[1][1]    0.011414 
_atom_sites.fract_transf_matrix[1][2]    0 
_atom_sites.fract_transf_matrix[1][3]    0 
_atom_sites.fract_transf_matrix[2][1]    0 
_atom_sites.fract_transf_matrix[2][2]    0.010309 
_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]    0.003285 
_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
G 2 PO4 A 1 1385 1385 PO4 PO4 . 
H 3 QBT A 1 1386 1386 QBT QBT . 
I 4 ZN A 1 1387 1387 ZN ZN . 
J 2 PO4 B 1 1384 1384 PO4 PO4 . 
K 3 QBT B 1 1385 1385 QBT QBT . 
L 4 ZN B 1 1386 1386 ZN ZN . 
M 2 PO4 C 1 1385 1385 PO4 PO4 . 
N 3 QBT C 1 1386 1386 QBT QBT . 
O 4 ZN C 1 1387 1387 ZN ZN . 
P 2 PO4 D 1 1383 1383 PO4 PO4 . 
Q 3 QBT D 1 1384 1384 QBT QBT . 
R 4 ZN D 1 1385 1385 ZN ZN . 
S 2 PO4 E 1 1386 1386 PO4 PO4 . 
T 3 QBT E 1 1387 1387 QBT QBT . 
U 4 ZN E 1 1388 1388 ZN ZN . 
V 2 PO4 F 1 1385 1385 PO4 PO4 . 
W 3 QBT F 1 1386 1386 QBT QBT . 
X 4 ZN F 1 1387 1387 ZN ZN . 
Y 5 HOH A 1 2001 2001 HOH HOH . 
Y 5 HOH A 2 2002 2002 HOH HOH . 
Y 5 HOH A 3 2003 2003 HOH HOH . 
Y 5 HOH A 4 2004 2004 HOH HOH . 
Y 5 HOH A 5 2005 2005 HOH HOH . 
Y 5 HOH A 6 2006 2006 HOH HOH . 
Y 5 HOH A 7 2007 2007 HOH HOH . 
Y 5 HOH A 8 2008 2008 HOH HOH . 
Z 5 HOH B 1 2001 2001 HOH HOH . 
Z 5 HOH B 2 2002 2002 HOH HOH . 
Z 5 HOH B 3 2003 2003 HOH HOH . 
Z 5 HOH B 4 2004 2004 HOH HOH . 
Z 5 HOH B 5 2005 2005 HOH HOH . 
Z 5 HOH B 6 2006 2006 HOH HOH . 
Z 5 HOH B 7 2007 2007 HOH HOH . 
AA 5 HOH C 1 2001 2001 HOH HOH . 
BA 5 HOH D 1 2001 2001 HOH HOH . 
BA 5 HOH D 2 2002 2002 HOH HOH . 
BA 5 HOH D 3 2003 2003 HOH HOH . 
CA 5 HOH E 1 2001 2001 HOH HOH . 
CA 5 HOH E 2 2002 2002 HOH HOH . 
CA 5 HOH E 3 2003 2003 HOH HOH . 
CA 5 HOH E 4 2004 2004 HOH HOH . 
CA 5 HOH E 5 2005 2005 HOH HOH . 
CA 5 HOH E 6 2006 2006 HOH HOH . 
CA 5 HOH E 7 2007 2007 HOH HOH . 
CA 5 HOH E 8 2008 2008 HOH HOH . 
CA 5 HOH E 9 2009 2009 HOH HOH . 
CA 5 HOH E 10 2010 2010 HOH HOH . 
CA 5 HOH E 11 2011 2011 HOH HOH . 
DA 5 HOH F 1 2001 2001 HOH HOH . 
DA 5 HOH F 2 2002 2002 HOH HOH . 
DA 5 HOH F 3 2003 2003 HOH HOH . 
DA 5 HOH F 4 2004 2004 HOH HOH . 
DA 5 HOH F 5 2005 2005 HOH HOH . 
DA 5 HOH F 6 2006 2006 HOH HOH . 
DA 5 HOH F 7 2007 2007 HOH HOH . 
DA 5 HOH F 8 2008 2008 HOH HOH . 
DA 5 HOH F 9 2009 2009 HOH HOH . 
DA 5 HOH F 10 2010 2010 HOH HOH . 
DA 5 HOH F 11 2011 2011 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 P P QBT . . . Q 3 31.045 -36.401 36.711 1 105.67 ? P QBT 1384 D 1 
HETATM 2 O O1P QBT . . . Q 3 30.254 -35.525 35.757 1 82.96 ? O1P QBT 1384 D 1 
HETATM 3 O O2P QBT . . . Q 3 32.172 -35.628 37.394 1 99.51 ? O2P QBT 1384 D 1 
HETATM 4 O O5' QBT . . . Q 3 29.97 -36.621 37.897 1 83.78 ? O5' QBT 1384 D 1 
HETATM 5 C C5' QBT . . . Q 3 28.735 -37.274 37.643 1 77.06 ? C5' QBT 1384 D 1 
HETATM 6 C C4' QBT . . . Q 3 28.202 -37.929 38.911 1 74.36 ? C4' QBT 1384 D 1 
HETATM 7 O O4' QBT . . . Q 3 27.398 -37.028 39.652 1 72.02 ? O4' QBT 1384 D 1 
HETATM 8 C C3' QBT . . . Q 3 27.284 -39.099 38.611 1 73.9 ? C3' QBT 1384 D 1 
HETATM 9 O O3' QBT . . . Q 3 27.541 -40.098 39.597 1 72.26 ? O3' QBT 1384 D 1 
HETATM 10 C C2' QBT . . . Q 3 25.876 -38.562 38.717 1 71.43 ? C2' QBT 1384 D 1 
HETATM 11 C C1' QBT . . . Q 3 26.06 -37.53 39.807 1 72.65 ? C1' QBT 1384 D 1 
HETATM 12 N N1 QBT . . . Q 3 25.157 -36.377 39.812 1 81.39 ? N1 QBT 1384 D 1 
HETATM 13 C C2 QBT . . . Q 3 24.571 -35.979 41.037 1 87.07 ? C2 QBT 1384 D 1 
HETATM 14 O O2 QBT . . . Q 3 24.794 -36.654 42.061 1 85.85 ? O2 QBT 1384 D 1 
HETATM 15 N N3 QBT . . . Q 3 23.762 -34.901 41.11 1 92.22 ? N3 QBT 1384 D 1 
HETATM 16 C C4 QBT . . . Q 3 23.492 -34.164 40.027 1 87.35 ? C4 QBT 1384 D 1 
HETATM 17 O O4 QBT . . . Q 3 22.743 -33.179 40.118 1 93.46 ? O4 QBT 1384 D 1 
HETATM 18 C C5 QBT . . . Q 3 24.108 -34.54 38.733 1 84.36 ? C5 QBT 1384 D 1 
HETATM 19 C C6 QBT . . . Q 3 24.943 -35.649 38.697 1 86.54 ? C6 QBT 1384 D 1 
HETATM 20 C C5M QBT . . . Q 3 23.869 -33.747 37.485 1 86.39 ? C5M QBT 1384 D 1 
HETATM 21 O O3P QBT . . . Q 3 31.412 -37.81 36.211 1 81.55 ? O3P QBT 1384 D 1 
#
_model_server_stats.io_time_ms              8 
_model_server_stats.parse_time_ms           8 
_model_server_stats.create_model_time_ms    7 
_model_server_stats.query_time_ms           237 
_model_server_stats.encode_time_ms          15 
_model_server_stats.element_count           21 
#