data_1XPU
#
_model_server_result.job_id            mQ39yMJLixAfvyzXJcIMOw 
_model_server_result.datetime_utc      '2025-04-02 12:52:14' 
_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          1xpu 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"CA","auth_seq_id":6701}' 
#
_entry.id    1XPU 
#
_exptl.entry_id    1XPU 
_exptl.method      'X-RAY DIFFRACTION' 
#
_entity.details                     ? 
_entity.formula_weight              440.467 
_entity.id                          5 
_entity.src_method                  syn 
_entity.type                        non-polymer 
_entity.pdbx_description            5A-(3-FORMYLPHENYLSULFANYL)-DIHYDROBICYCLOMYCIN 
_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          96.95 
_cell.angle_gamma         90 
_cell.entry_id            1XPU 
_cell.length_a            119.477 
_cell.length_b            206.935 
_cell.length_c            148.607 
_cell.Z_PDB               24 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 1XPU 
_symmetry.cell_setting             monoclinic 
_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
? dimeric 2 author_defined_assembly 1 
? dimeric 2 author_defined_assembly 2 
? dimeric 2 author_defined_assembly 3 
? dimeric 2 author_defined_assembly 4 
? dimeric 2 author_defined_assembly 5 
? dimeric 2 author_defined_assembly 6 
#
loop_
_pdbx_struct_assembly_gen.asym_id_list
_pdbx_struct_assembly_gen.assembly_id
_pdbx_struct_assembly_gen.oper_expression
A,G,M,N,DA,FA 1 1 
B,H,O,P,Q,GA 2 1 
C,I,R,S,T,EA,HA 3 1 
D,J,U,V,W,IA 4 1 
E,K,X,Y,Z,AA,JA 5 1 
F,L,BA,CA,KA 6 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    x,y,z 
_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 Q N N 
? 5 T N N 
? 5 W N N 
? 5 Z N N 
? 5 CA 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
metalc ? metalc1 G OG1 THR 185 A THR 185 1_555 M MG MG . A MG 1601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.326 ? 
metalc ? metalc2 N O2B AGS . A AGS 1600 1_555 M MG MG . A MG 1601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.304 ? 
metalc ? metalc3 N O2G AGS . A AGS 1600 1_555 M MG MG . A MG 1601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.433 ? 
metalc ? metalc4 H NZ LYS 184 B LYS 184 1_555 O MG MG . B MG 2601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.93 ? 
metalc ? metalc5 H OG1 THR 185 B THR 185 1_555 O MG MG . B MG 2601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.244 ? 
metalc ? metalc6 P O2G AGS . B AGS 2600 1_555 O MG MG . B MG 2601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.913 ? 
metalc ? metalc7 O MG MG . B MG 2601 1_555 Q O6 FPD . B FPD 2701 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 3.132 ? 
metalc ? metalc8 O MG MG . B MG 2601 1_555 GA O HOH . B HOH 2702 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 3.098 ? 
metalc ? metalc9 I OG1 THR 185 C THR 185 1_555 R MG MG . C MG 3601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.654 ? 
metalc ? metalc10 I OD2 ASP 265 C ASP 265 1_555 R MG MG . C MG 3601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.66 ? 
metalc ? metalc11 J OG1 THR 185 D THR 185 1_555 U MG MG . D MG 4601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.351 ? 
metalc ? metalc12 V O2B AGS . D AGS 4600 1_555 U MG MG . D MG 4601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.8 ? 
metalc ? metalc13 V O2G AGS . D AGS 4600 1_555 U MG MG . D MG 4601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.193 ? 
metalc ? metalc14 K OG1 THR 185 E THR 185 1_555 X MG MG . E MG 5601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.429 ? 
metalc ? metalc15 AA O2B AGS . E AGS 6600 1_555 BA MG MG . F MG 6601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.557 ? 
metalc ? metalc16 AA O2G AGS . E AGS 6600 1_555 BA MG MG . F MG 6601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.492 ? 
metalc ? metalc17 L OG1 THR 185 F THR 185 1_555 BA MG MG . F MG 6601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.235 ? 
metalc ? metalc18 BA MG MG . F MG 6601 1_555 CA O6 FPD . F FPD 6701 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 3.145 ? 
#
_chem_comp.formula           'C19 H24 N2 O8 S' 
_chem_comp.formula_weight    440.467 
_chem_comp.id                FPD 
_chem_comp.mon_nstd_flag     . 
_chem_comp.name              5A-(3-FORMYLPHENYLSULFANYL)-DIHYDROBICYCLOMYCIN 
_chem_comp.type              non-polymer 
_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
O4 C11 FPD doub 168 n n 
C11 N2 FPD sing 169 n n 
C11 C10 FPD sing 170 n n 
N2 C5 FPD sing 171 n n 
N2 HN2 FPD sing 172 n n 
C5 C6 FPD sing 173 n n 
C5 C4 FPD sing 174 n n 
C5 O5 FPD sing 175 n n 
C6 O6 FPD doub 176 n n 
C6 N1 FPD sing 177 n n 
N1 C10 FPD sing 178 n n 
N1 HN1 FPD sing 179 n n 
C10 O7 FPD sing 180 n n 
C10 C9 FPD sing 181 n n 
O7 HO7 FPD sing 182 n n 
C4 O3 FPD sing 183 n n 
C4 C1 FPD sing 184 n n 
C4 H4 FPD sing 185 n n 
O3 HO3 FPD sing 186 n n 
C1 C3 FPD sing 187 n n 
C1 O2 FPD sing 188 n n 
C1 C2 FPD sing 189 n n 
C3 H31 FPD sing 190 n n 
C3 H32 FPD sing 191 n n 
C3 H33 FPD sing 192 n n 
O2 HO2 FPD sing 193 n n 
C2 O1 FPD sing 194 n n 
C2 H21 FPD sing 195 n n 
C2 H22 FPD sing 196 n n 
O1 HO1 FPD sing 197 n n 
O5 C7 FPD sing 198 n n 
C7 C8 FPD sing 199 n n 
C7 H71 FPD sing 200 n n 
C7 H72 FPD sing 201 n n 
C8 C9 FPD sing 202 n n 
C8 H81 FPD sing 203 n n 
C8 H82 FPD sing 204 n n 
C9 C12 FPD sing 205 n n 
C9 H9 FPD sing 206 n n 
C12 S1 FPD sing 207 n n 
C12 H121 FPD sing 208 n n 
C12 H122 FPD sing 209 n n 
S1 C FPD sing 210 n n 
C C54 FPD doub 211 n y 
C C50 FPD sing 212 n y 
C54 C53 FPD sing 213 n y 
C54 H54 FPD sing 214 n n 
C53 C13 FPD sing 215 n n 
C53 C52 FPD doub 216 n y 
C13 O8 FPD doub 217 n n 
C13 H13 FPD sing 218 n n 
C52 C51 FPD sing 219 n y 
C52 H52 FPD sing 220 n n 
C51 C50 FPD doub 221 n y 
C51 H51 FPD sing 222 n n 
C50 H50 FPD sing 223 n n 
#
_atom_sites.entry_id                     1XPU 
_atom_sites.fract_transf_matrix[1][1]    0.00837 
_atom_sites.fract_transf_matrix[1][2]    0 
_atom_sites.fract_transf_matrix[1][3]    0.00102 
_atom_sites.fract_transf_matrix[2][1]    0 
_atom_sites.fract_transf_matrix[2][2]    0.004832 
_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]    0.006779 
_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
M 3 MG A 1 1601 1601 MG MG . 
N 4 AGS A 1 1600 1600 AGS AGS . 
O 3 MG B 1 2601 2601 MG MG . 
P 4 AGS B 1 2600 2600 AGS AGS . 
Q 5 FPD B 1 2701 2701 FPD FPD . 
R 3 MG C 1 3601 3601 MG MG . 
S 4 AGS C 1 3600 3600 AGS AGS . 
T 5 FPD C 1 3701 3701 FPD FPD . 
U 3 MG D 1 4601 4601 MG MG . 
V 4 AGS D 1 4600 4600 AGS AGS . 
W 5 FPD D 1 4701 4701 FPD FPD . 
X 3 MG E 1 5601 5601 MG MG . 
Y 4 AGS E 1 5600 5600 AGS AGS . 
Z 5 FPD E 1 5701 5701 FPD FPD . 
AA 4 AGS E 1 6600 6600 AGS AGS . 
BA 3 MG F 1 6601 6601 MG MG . 
CA 5 FPD F 1 6701 6701 FPD FPD . 
DA 6 HOH G 1 12 12 HOH HOH . 
EA 6 HOH H 1 15 15 HOH HOH . 
FA 6 HOH A 1 1602 2 HOH HOH . 
FA 6 HOH A 2 1603 8 HOH HOH . 
GA 6 HOH B 1 2702 3 HOH HOH . 
GA 6 HOH B 2 2703 5 HOH HOH . 
GA 6 HOH B 3 2704 9 HOH HOH . 
GA 6 HOH B 4 2705 17 HOH HOH . 
GA 6 HOH B 5 2706 19 HOH HOH . 
HA 6 HOH C 1 3702 6 HOH HOH . 
HA 6 HOH C 2 3703 14 HOH HOH . 
HA 6 HOH C 3 3704 20 HOH HOH . 
IA 6 HOH D 1 4702 7 HOH HOH . 
IA 6 HOH D 2 4703 11 HOH HOH . 
IA 6 HOH D 3 4704 13 HOH HOH . 
IA 6 HOH D 4 4705 18 HOH HOH . 
JA 6 HOH E 1 6601 4 HOH HOH . 
JA 6 HOH E 2 6602 10 HOH HOH . 
JA 6 HOH E 3 6603 16 HOH HOH . 
KA 6 HOH F 1 6702 1 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 O O4 FPD . . . CA 5 34.251 -3.968 44.92 1 53.46 ? O4 FPD 6701 F 1 
HETATM 2 C C11 FPD . . . CA 5 35.274 -4.638 44.857 1 53.46 ? C11 FPD 6701 F 1 
HETATM 3 N N2 FPD . . . CA 5 35.604 -5.291 43.754 1 53.45 ? N2 FPD 6701 F 1 
HETATM 4 C C5 FPD . . . CA 5 36.854 -6.007 43.555 1 53.46 ? C5 FPD 6701 F 1 
HETATM 5 C C6 FPD . . . CA 5 37.751 -6.172 44.766 1 53.45 ? C6 FPD 6701 F 1 
HETATM 6 O O6 FPD . . . CA 5 38.802 -6.787 44.696 1 53.46 ? O6 FPD 6701 F 1 
HETATM 7 N N1 FPD . . . CA 5 37.418 -5.519 45.867 1 53.46 ? N1 FPD 6701 F 1 
HETATM 8 C C10 FPD . . . CA 5 36.272 -4.65 45.983 1 53.46 ? C10 FPD 6701 F 1 
HETATM 9 O O7 FPD . . . CA 5 35.641 -4.824 47.256 1 53.46 ? O7 FPD 6701 F 1 
HETATM 10 C C4 FPD . . . CA 5 36.569 -7.345 42.836 1 53.46 ? C4 FPD 6701 F 1 
HETATM 11 O O3 FPD . . . CA 5 35.366 -7.245 42.075 1 53.46 ? O3 FPD 6701 F 1 
HETATM 12 C C1 FPD . . . CA 5 37.707 -7.901 41.958 1 53.45 ? C1 FPD 6701 F 1 
HETATM 13 C C3 FPD . . . CA 5 37.177 -8.385 40.615 1 53.45 ? C3 FPD 6701 F 1 
HETATM 14 O O2 FPD . . . CA 5 38.7 -6.905 41.698 1 53.46 ? O2 FPD 6701 F 1 
HETATM 15 C C2 FPD . . . CA 5 38.396 -9.064 42.664 1 53.45 ? C2 FPD 6701 F 1 
HETATM 16 O O1 FPD . . . CA 5 37.458 -10.072 43.025 1 53.45 ? O1 FPD 6701 F 1 
HETATM 17 O O5 FPD . . . CA 5 37.612 -5.037 42.81 1 53.46 ? O5 FPD 6701 F 1 
HETATM 18 C C7 FPD . . . CA 5 37.388 -3.655 43.219 1 53.46 ? C7 FPD 6701 F 1 
HETATM 19 C C8 FPD . . . CA 5 37.939 -3.222 44.608 1 53.46 ? C8 FPD 6701 F 1 
HETATM 20 C C9 FPD . . . CA 5 36.997 -3.289 45.855 1 53.46 ? C9 FPD 6701 F 1 
HETATM 21 C C12 FPD . . . CA 5 36.102 -2.04 45.916 1 53.45 ? C12 FPD 6701 F 1 
HETATM 22 S S1 FPD . . . CA 5 35.169 -1.977 47.413 1 53.45 ? S1 FPD 6701 F 1 
HETATM 23 C C FPD . . . CA 5 35.676 -0.481 48.022 1 53.45 ? C FPD 6701 F 1 
HETATM 24 C C54 FPD . . . CA 5 37.022 -0.12 47.974 1 53.45 ? C54 FPD 6701 F 1 
HETATM 25 C C53 FPD . . . CA 5 37.432 1.109 48.481 1 53.45 ? C53 FPD 6701 F 1 
HETATM 26 C C13 FPD . . . CA 5 38.864 1.479 48.416 1 53.45 ? C13 FPD 6701 F 1 
HETATM 27 O O8 FPD . . . CA 5 39.379 1.727 47.339 1 53.45 ? O8 FPD 6701 F 1 
HETATM 28 C C52 FPD . . . CA 5 36.496 1.979 49.043 1 53.45 ? C52 FPD 6701 F 1 
HETATM 29 C C51 FPD . . . CA 5 35.149 1.622 49.095 1 53.45 ? C51 FPD 6701 F 1 
HETATM 30 C C50 FPD . . . CA 5 34.741 0.388 48.586 1 53.45 ? C50 FPD 6701 F 1 
#
_model_server_stats.io_time_ms              40 
_model_server_stats.parse_time_ms           24 
_model_server_stats.create_model_time_ms    77 
_model_server_stats.query_time_ms           812 
_model_server_stats.encode_time_ms          7 
_model_server_stats.element_count           30 
#