data_7XS6
#
_model_server_result.job_id            NNGo16elc8RECyZGQF6C9A 
_model_server_result.datetime_utc      '2024-11-15 19:49:49' 
_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          7xs6 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"X","auth_seq_id":1222}' 
#
_entry.id    7XS6 
#
_exptl.entry_id    7XS6 
_exptl.method      'ELECTRON MICROSCOPY' 
#
_entity.details                     ? 
_entity.formula_weight              495.44 
_entity.id                          5 
_entity.src_method                  syn 
_entity.type                        non-polymer 
_entity.pdbx_description            '(2S)-{[(2S,3S,4S)-2-amino-4-hydroxy-4-(5-hydroxypyridin-2-yl)-3-methylbutanoyl]amino}[(2R,3S,4R,5R)-5-(2,4-dioxo-3,4-dihydropyrimidin-1(2H)-yl)-3,4-dihydroxyoxolan-2-yl]acetic acid (non-preferred name)' 
_entity.pdbx_number_of_molecules    2 
_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            7XS6 
_cell.length_a            1 
_cell.length_b            1 
_cell.length_c            1 
_cell.Z_PDB               ? 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 7XS6 
_symmetry.cell_setting             ? 
_symmetry.Int_Tables_number        1 
_symmetry.space_group_name_Hall    ? 
_symmetry.space_group_name_H-M     'P 1' 
#
_pdbx_struct_assembly.method_details        ? 
_pdbx_struct_assembly.oligomeric_details    dimeric 
_pdbx_struct_assembly.oligomeric_count      2 
_pdbx_struct_assembly.details               author_defined_assembly 
_pdbx_struct_assembly.id                    1 
#
_pdbx_struct_assembly_gen.asym_id_list       A,B,C,D,E,F,G,H,I,J,K,L,M,N,O,P,Q,R,S,T,U,V,W,X,Y,Z,AA,BA,CA,DA,EA,FA,GA,HA,IA,JA,KA,LA,MA,NA,OA,PA,QA,RA,SA,TA 
_pdbx_struct_assembly_gen.assembly_id        1 
_pdbx_struct_assembly_gen.oper_expression    1 
#
_pdbx_struct_oper_list.id                    1 
_pdbx_struct_oper_list.type                  'identity operation' 
_pdbx_struct_oper_list.name                  1_555 
_pdbx_struct_oper_list.symmetry_operation    ? 
_pdbx_struct_oper_list.matrix[1][1]          1 
_pdbx_struct_oper_list.matrix[1][2]          0 
_pdbx_struct_oper_list.matrix[1][3]          0 
_pdbx_struct_oper_list.matrix[2][1]          0 
_pdbx_struct_oper_list.matrix[2][2]          1 
_pdbx_struct_oper_list.matrix[2][3]          0 
_pdbx_struct_oper_list.matrix[3][1]          0 
_pdbx_struct_oper_list.matrix[3][2]          0 
_pdbx_struct_oper_list.matrix[3][3]          1 
_pdbx_struct_oper_list.vector[1]             0 
_pdbx_struct_oper_list.vector[2]             0 
_pdbx_struct_oper_list.vector[3]             0 
#
loop_
_struct_asym.details
_struct_asym.entity_id
_struct_asym.id
_struct_asym.pdbx_modified
_struct_asym.pdbx_blank_PDB_chainid_flag
? 5 X N N 
? 5 TA N N 
#
_chem_comp.formula           'C20 H25 N5 O10' 
_chem_comp.formula_weight    495.44 
_chem_comp.id                BGI 
_chem_comp.mon_nstd_flag     . 
_chem_comp.name              '(2S)-{[(2S,3S,4S)-2-amino-4-hydroxy-4-(5-hydroxypyridin-2-yl)-3-methylbutanoyl]amino}[(2R,3S,4R,5R)-5-(2,4-dioxo-3,4-dihydropyrimidin-1(2H)-yl)-3,4-dihydroxyoxolan-2-yl]acetic acid (non-preferred name)' 
_chem_comp.type              non-polymer 
_chem_comp.pdbx_synonyms     'Nikkomycin Z' 
#
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
O29 C28 BGI doub 188 n n 
N27 C28 BGI sing 189 n n 
N27 C25 BGI sing 190 n n 
C28 N22 BGI sing 191 n n 
O26 C25 BGI doub 192 n n 
C25 C24 BGI sing 193 n n 
O30 C19 BGI sing 194 n n 
N22 C20 BGI sing 195 n n 
N22 C23 BGI sing 196 n n 
C20 C19 BGI sing 197 n n 
C20 O21 BGI sing 198 n n 
O31 C18 BGI sing 199 n n 
C24 C23 BGI doub 200 n n 
C19 C18 BGI sing 201 n n 
C18 C17 BGI sing 202 n n 
O21 C17 BGI sing 203 n n 
C17 C16 BGI sing 204 n n 
C16 C32 BGI sing 205 n n 
C16 N15 BGI sing 206 n n 
O34 C32 BGI doub 207 n n 
C32 O33 BGI sing 208 n n 
N15 C13 BGI sing 209 n n 
O14 C13 BGI doub 210 n n 
C13 C12 BGI sing 211 n n 
C12 N35 BGI sing 212 n n 
C12 C02 BGI sing 213 n n 
C02 C01 BGI sing 214 n n 
C02 C03 BGI sing 215 n n 
O11 C03 BGI sing 216 n n 
C03 C04 BGI sing 217 n n 
C09 C04 BGI doub 218 n y 
C09 C08 BGI sing 219 n y 
C04 N05 BGI sing 220 n y 
C08 C07 BGI doub 221 n y 
N05 C06 BGI doub 222 n y 
C07 C06 BGI sing 223 n y 
C07 O10 BGI sing 224 n n 
C17 H171 BGI sing 225 n n 
C20 H201 BGI sing 226 n n 
C24 H241 BGI sing 227 n n 
C01 H011 BGI sing 228 n n 
C01 H013 BGI sing 229 n n 
C01 H012 BGI sing 230 n n 
C02 H021 BGI sing 231 n n 
C03 H031 BGI sing 232 n n 
C06 H061 BGI sing 233 n n 
C08 H081 BGI sing 234 n n 
C09 H091 BGI sing 235 n n 
C12 H121 BGI sing 236 n n 
C16 H161 BGI sing 237 n n 
C18 H181 BGI sing 238 n n 
C19 H191 BGI sing 239 n n 
C23 H231 BGI sing 240 n n 
N15 H151 BGI sing 241 n n 
N27 H271 BGI sing 242 n n 
N35 H351 BGI sing 243 n n 
N35 H352 BGI sing 244 n n 
O10 H101 BGI sing 245 n n 
O11 H111 BGI sing 246 n n 
O30 H301 BGI sing 247 n n 
O31 H311 BGI sing 248 n n 
O33 H2 BGI sing 249 n n 
#
_atom_sites.entry_id                     7XS6 
_atom_sites.fract_transf_matrix[1][1]    1 
_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]    1 
_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]    1 
_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
C 2 C14 B 1 1201 2002 C14 C14 . 
D 2 C14 B 1 1202 2003 C14 C14 . 
E 2 C14 B 1 1203 2004 C14 C14 . 
F 2 C14 B 1 1204 2005 C14 C14 . 
G 2 C14 B 1 1205 2006 C14 C14 . 
H 2 C14 B 1 1206 2007 C14 C14 . 
I 2 C14 B 1 1207 2008 C14 C14 . 
J 2 C14 B 1 1208 2009 C14 C14 . 
K 3 D12 B 1 1209 2010 D12 D12 . 
L 3 D12 B 1 1210 2011 D12 D12 . 
M 3 D12 B 1 1211 2012 D12 D12 . 
N 3 D12 B 1 1212 2013 D12 D12 . 
O 4 HP6 B 1 1213 2014 HP6 HP6 . 
P 4 HP6 B 1 1214 2015 HP6 HP6 . 
Q 4 HP6 B 1 1215 2016 HP6 HP6 . 
R 4 HP6 B 1 1216 2017 HP6 HP6 . 
S 4 HP6 B 1 1217 2018 HP6 HP6 . 
T 4 HP6 B 1 1218 2019 HP6 HP6 . 
U 4 HP6 B 1 1219 2020 HP6 HP6 . 
V 3 D12 B 1 1220 2021 D12 D12 . 
W 2 C14 B 1 1221 2002 C14 C14 . 
X 5 BGI B 1 1222 1 BGI LIG . 
Y 6 0V9 A 1 2001 2001 0V9 6OU . 
Z 6 0V9 A 1 2002 2001 0V9 6OU . 
AA 2 C14 A 1 2003 2003 C14 C14 . 
BA 2 C14 A 1 2004 2004 C14 C14 . 
CA 2 C14 A 1 2005 2005 C14 C14 . 
DA 2 C14 A 1 2006 2006 C14 C14 . 
EA 2 C14 A 1 2007 2007 C14 C14 . 
FA 2 C14 A 1 2008 2008 C14 C14 . 
GA 2 C14 A 1 2009 2009 C14 C14 . 
HA 3 D12 A 1 2010 2010 D12 D12 . 
IA 3 D12 A 1 2011 2011 D12 D12 . 
JA 3 D12 A 1 2012 2012 D12 D12 . 
KA 3 D12 A 1 2013 2013 D12 D12 . 
LA 4 HP6 A 1 2014 2014 HP6 HP6 . 
MA 4 HP6 A 1 2015 2015 HP6 HP6 . 
NA 4 HP6 A 1 2016 2016 HP6 HP6 . 
OA 4 HP6 A 1 2017 2017 HP6 HP6 . 
PA 4 HP6 A 1 2018 2018 HP6 HP6 . 
QA 4 HP6 A 1 2019 2019 HP6 HP6 . 
RA 4 HP6 A 1 2020 2020 HP6 HP6 . 
SA 3 D12 A 1 2021 2021 D12 D12 . 
TA 5 BGI A 1 2022 2 BGI LIG . 
#
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 C C13 BGI . . . X 5 108.989 143.758 104.675 1 20 ? C13 BGI 1222 B 1 
HETATM 2 C C17 BGI . . . X 5 110.6 144.6 101.639 1 20 ? C17 BGI 1222 B 1 
HETATM 3 C C20 BGI . . . X 5 111.657 144.502 99.653 1 20 ? C20 BGI 1222 B 1 
HETATM 4 C C24 BGI . . . X 5 114.106 141.527 99.753 1 20 ? C24 BGI 1222 B 1 
HETATM 5 C C28 BGI . . . X 5 113.483 143.828 98.046 1 20 ? C28 BGI 1222 B 1 
HETATM 6 C C01 BGI . . . X 5 109.338 143.981 107.579 1 20 ? C01 BGI 1222 B 1 
HETATM 7 C C02 BGI . . . X 5 108.492 144.979 106.797 1 20 ? C02 BGI 1222 B 1 
HETATM 8 C C03 BGI . . . X 5 107.383 145.51 107.673 1 20 ? C03 BGI 1222 B 1 
HETATM 9 C C04 BGI . . . X 5 107.947 146.516 108.696 1 20 ? C04 BGI 1222 B 1 
HETATM 10 C C06 BGI . . . X 5 109.697 148.279 109.343 1 20 ? C06 BGI 1222 B 1 
HETATM 11 C C07 BGI . . . X 5 109.023 148.456 110.695 1 20 ? C07 BGI 1222 B 1 
HETATM 12 C C08 BGI . . . X 5 107.814 147.661 111.036 1 20 ? C08 BGI 1222 B 1 
HETATM 13 C C09 BGI . . . X 5 107.266 146.69 110.047 1 20 ? C09 BGI 1222 B 1 
HETATM 14 C C12 BGI . . . X 5 107.872 144.275 105.582 1 20 ? C12 BGI 1222 B 1 
HETATM 15 C C16 BGI . . . X 5 110.874 144.214 102.977 1 20 ? C16 BGI 1222 B 1 
HETATM 16 C C18 BGI . . . X 5 110 143.393 100.795 1 20 ? C18 BGI 1222 B 1 
HETATM 17 C C19 BGI . . . X 5 110.175 143.778 99.626 1 20 ? C19 BGI 1222 B 1 
HETATM 18 C C23 BGI . . . X 5 113.011 142.458 100.141 1 20 ? C23 BGI 1222 B 1 
HETATM 19 C C25 BGI . . . X 5 114.876 141.77 98.51 1 20 ? C25 BGI 1222 B 1 
HETATM 20 C C32 BGI . . . X 5 112.187 144.862 103.49 1 20 ? C32 BGI 1222 B 1 
HETATM 21 N N05 BGI . . . X 5 109.15 147.311 108.36 1 20 ? N05 BGI 1222 B 1 
HETATM 22 N N15 BGI . . . X 5 109.769 144.708 103.87 1 20 ? N15 BGI 1222 B 1 
HETATM 23 N N22 BGI . . . X 5 112.698 143.595 99.291 1 20 ? N22 BGI 1222 B 1 
HETATM 24 N N27 BGI . . . X 5 114.571 142.897 97.673 1 20 ? N27 BGI 1222 B 1 
HETATM 25 N N35 BGI . . . X 5 107.072 143.173 106.034 1 20 ? N35 BGI 1222 B 1 
HETATM 26 O O10 BGI . . . X 5 109.543 149.375 111.63 1 20 ? O10 BGI 1222 B 1 
HETATM 27 O O11 BGI . . . X 5 106.461 146.164 106.864 1 20 ? O11 BGI 1222 B 1 
HETATM 28 O O14 BGI . . . X 5 109.224 142.608 104.617 1 20 ? O14 BGI 1222 B 1 
HETATM 29 O O21 BGI . . . X 5 111.854 144.91 100.875 1 20 ? O21 BGI 1222 B 1 
HETATM 30 O O26 BGI . . . X 5 115.741 141.038 98.205 1 20 ? O26 BGI 1222 B 1 
HETATM 31 O O29 BGI . . . X 5 113.243 144.747 97.355 1 20 ? O29 BGI 1222 B 1 
HETATM 32 O O30 BGI . . . X 5 109.207 144.814 99.221 1 20 ? O30 BGI 1222 B 1 
HETATM 33 O O31 BGI . . . X 5 108.553 143.151 101.149 1 20 ? O31 BGI 1222 B 1 
HETATM 34 O O33 BGI . . . X 5 112.184 146.073 103.839 1 20 -1 O33 BGI 1222 B 1 
HETATM 35 O O34 BGI . . . X 5 113.245 144.194 103.563 1 20 ? O34 BGI 1222 B 1 
#
_model_server_stats.io_time_ms              10 
_model_server_stats.parse_time_ms           8 
_model_server_stats.create_model_time_ms    28 
_model_server_stats.query_time_ms           337 
_model_server_stats.encode_time_ms          5 
_model_server_stats.element_count           35 
#