data_7Y8D
#
_model_server_result.job_id            sXzXDPTuv1GRL3FZQ_ZKkg 
_model_server_result.datetime_utc      '2025-08-01 19:37:17' 
_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          7y8d 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"C","auth_seq_id":101}' 
#
_entry.id    7Y8D 
#
_exptl.entry_id    7Y8D 
_exptl.method      'X-RAY DIFFRACTION' 
#
_entity.details                     ? 
_entity.formula_weight              487.958 
_entity.id                          3 
_entity.src_method                  syn 
_entity.type                        non-polymer 
_entity.pdbx_description            '(2R)-3-[2-(aminomethyl)-3-azanyl-1-[4-[2-(2-chloranylethanoylamino)ethylcarbamoyl]phenyl]prop-1-enyl]sulfanyl-2-(carboxyamino)propanoic acid' 
_entity.pdbx_number_of_molecules    1 
_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            7Y8D 
_cell.length_a            69.803 
_cell.length_b            99.366 
_cell.length_c            51.359 
_cell.Z_PDB               8 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 7Y8D 
_symmetry.cell_setting             ? 
_symmetry.Int_Tables_number        20 
_symmetry.space_group_name_Hall    ? 
_symmetry.space_group_name_H-M     'C 2 2 21' 
#
_pdbx_struct_assembly.method_details        PISA 
_pdbx_struct_assembly.oligomeric_details    dimeric 
_pdbx_struct_assembly.oligomeric_count      2 
_pdbx_struct_assembly.details               author_and_software_defined_assembly 
_pdbx_struct_assembly.id                    1 
#
_pdbx_struct_assembly_gen.asym_id_list       A,B,C,D,E 
_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    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 
#
_struct_asym.details                        ? 
_struct_asym.entity_id                      3 
_struct_asym.id                             C 
_struct_asym.pdbx_modified                  N 
_struct_asym.pdbx_blank_PDB_chainid_flag    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
covale ? covale1 B N CYS 1 B CYS 1 1_555 C C1 JFF . B JFF 101 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.399 doub 
covale ? covale2 B SG CYS 1 B CYS 1 1_555 C C1 JFF . B JFF 101 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.623 ? 
covale ? covale3 B C CYS 11 B CYS 11 1_555 B N NH2 12 B NH2 12 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.441 ? 
covale ? covale4 B SG CYS 11 B CYS 11 1_555 C C19 JFF . B JFF 101 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.857 ? 
#
_chem_comp.formula           'C19 H26 Cl N5 O6 S' 
_chem_comp.formula_weight    487.958 
_chem_comp.id                JFF 
_chem_comp.mon_nstd_flag     . 
_chem_comp.name              '(2R)-3-[2-(aminomethyl)-3-azanyl-1-[4-[2-(2-chloranylethanoylamino)ethylcarbamoyl]phenyl]prop-1-enyl]sulfanyl-2-(carboxyamino)propanoic acid' 
_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
C14 C13 JFF doub 173 n y 
C14 C9 JFF sing 174 n y 
C13 C12 JFF sing 175 n y 
O5 C15 JFF doub 176 n n 
C9 C1 JFF sing 177 n n 
C9 C10 JFF doub 178 n y 
C12 C15 JFF sing 179 n n 
C12 C11 JFF doub 180 n y 
C15 N4 JFF sing 181 n n 
C16 N4 JFF sing 182 n n 
C16 C17 JFF sing 183 n n 
C10 C11 JFF sing 184 n y 
C17 N5 JFF sing 185 n n 
N5 C18 JFF sing 186 n n 
C18 C19 JFF sing 187 n n 
C18 O6 JFF doub 188 n n 
C10 H4 JFF sing 189 n n 
C11 H5 JFF sing 190 n n 
C13 H6 JFF sing 191 n n 
C14 H7 JFF sing 192 n n 
N4 H8 JFF sing 193 n n 
C16 H9 JFF sing 194 n n 
C16 H10 JFF sing 195 n n 
C17 H11 JFF sing 196 n n 
C17 H12 JFF sing 197 n n 
N5 H13 JFF sing 198 n n 
C19 H14 JFF sing 199 n n 
C19 H15 JFF sing 200 n n 
C1 S1 JFF sing 201 n n 
C1 C2 JFF doub 202 n n 
C2 C3 JFF sing 203 n n 
C2 C4 JFF sing 204 n n 
C3 N2 JFF sing 205 n n 
C4 N3 JFF sing 206 n n 
S1 C5 JFF sing 207 n n 
C5 C6 JFF sing 208 n n 
C6 C7 JFF sing 209 n n 
C7 O4 JFF doub 210 n n 
C7 O3 JFF sing 211 n n 
C6 N1 JFF sing 212 n n 
N1 C8 JFF sing 213 n n 
C8 O1 JFF sing 214 n n 
C8 O2 JFF doub 215 n n 
C19 CL1 JFF sing 216 n n 
C3 H1 JFF sing 217 n n 
C3 H2 JFF sing 218 n n 
C4 H3 JFF sing 219 n n 
C4 H16 JFF sing 220 n n 
N2 H17 JFF sing 221 n n 
N2 H18 JFF sing 222 n n 
N3 H19 JFF sing 223 n n 
N3 H20 JFF sing 224 n n 
C5 H21 JFF sing 225 n n 
C5 H22 JFF sing 226 n n 
C6 H23 JFF sing 227 n n 
O3 H24 JFF sing 228 n n 
N1 H25 JFF sing 229 n n 
O1 H26 JFF sing 230 n n 
#
_atom_sites.entry_id                     7Y8D 
_atom_sites.fract_transf_matrix[1][1]    0.014326 
_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]    0.010064 
_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]    0.019471 
_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 3 JFF B 1 101 1 JFF LIG . 
D 4 HOH A 1 201 47 HOH HOH . 
D 4 HOH A 2 202 54 HOH HOH . 
D 4 HOH A 3 203 40 HOH HOH . 
D 4 HOH A 4 204 19 HOH HOH . 
D 4 HOH A 5 205 55 HOH HOH . 
D 4 HOH A 6 206 15 HOH HOH . 
D 4 HOH A 7 207 59 HOH HOH . 
D 4 HOH A 8 208 36 HOH HOH . 
D 4 HOH A 9 209 31 HOH HOH . 
D 4 HOH A 10 210 64 HOH HOH . 
D 4 HOH A 11 211 12 HOH HOH . 
D 4 HOH A 12 212 58 HOH HOH . 
D 4 HOH A 13 213 63 HOH HOH . 
D 4 HOH A 14 214 25 HOH HOH . 
D 4 HOH A 15 215 41 HOH HOH . 
D 4 HOH A 16 216 39 HOH HOH . 
D 4 HOH A 17 217 21 HOH HOH . 
D 4 HOH A 18 218 32 HOH HOH . 
D 4 HOH A 19 219 51 HOH HOH . 
D 4 HOH A 20 220 70 HOH HOH . 
D 4 HOH A 21 221 17 HOH HOH . 
D 4 HOH A 22 222 29 HOH HOH . 
D 4 HOH A 23 223 66 HOH HOH . 
D 4 HOH A 24 224 69 HOH HOH . 
D 4 HOH A 25 225 18 HOH HOH . 
D 4 HOH A 26 226 4 HOH HOH . 
D 4 HOH A 27 227 57 HOH HOH . 
D 4 HOH A 28 228 50 HOH HOH . 
D 4 HOH A 29 229 53 HOH HOH . 
D 4 HOH A 30 230 2 HOH HOH . 
D 4 HOH A 31 231 60 HOH HOH . 
D 4 HOH A 32 232 1 HOH HOH . 
D 4 HOH A 33 233 13 HOH HOH . 
D 4 HOH A 34 234 65 HOH HOH . 
D 4 HOH A 35 235 6 HOH HOH . 
D 4 HOH A 36 236 35 HOH HOH . 
D 4 HOH A 37 237 23 HOH HOH . 
D 4 HOH A 38 238 61 HOH HOH . 
D 4 HOH A 39 239 11 HOH HOH . 
D 4 HOH A 40 240 49 HOH HOH . 
D 4 HOH A 41 241 42 HOH HOH . 
D 4 HOH A 42 242 38 HOH HOH . 
D 4 HOH A 43 243 27 HOH HOH . 
D 4 HOH A 44 244 3 HOH HOH . 
D 4 HOH A 45 245 37 HOH HOH . 
D 4 HOH A 46 246 22 HOH HOH . 
D 4 HOH A 47 247 26 HOH HOH . 
D 4 HOH A 48 248 62 HOH HOH . 
D 4 HOH A 49 249 68 HOH HOH . 
D 4 HOH A 50 250 14 HOH HOH . 
D 4 HOH A 51 251 8 HOH HOH . 
D 4 HOH A 52 252 7 HOH HOH . 
D 4 HOH A 53 253 24 HOH HOH . 
D 4 HOH A 54 254 33 HOH HOH . 
D 4 HOH A 55 255 10 HOH HOH . 
D 4 HOH A 56 256 56 HOH HOH . 
D 4 HOH A 57 257 16 HOH HOH . 
D 4 HOH A 58 258 5 HOH HOH . 
D 4 HOH A 59 259 52 HOH HOH . 
D 4 HOH A 60 260 20 HOH HOH . 
D 4 HOH A 61 261 44 HOH HOH . 
D 4 HOH A 62 262 72 HOH HOH . 
D 4 HOH A 63 263 43 HOH HOH . 
D 4 HOH A 64 264 46 HOH HOH . 
D 4 HOH A 65 265 30 HOH HOH . 
D 4 HOH A 66 266 71 HOH HOH . 
D 4 HOH A 67 267 73 HOH HOH . 
E 4 HOH B 1 201 28 HOH HOH . 
E 4 HOH B 2 202 45 HOH HOH . 
E 4 HOH B 3 203 34 HOH HOH . 
E 4 HOH B 4 204 9 HOH HOH . 
E 4 HOH B 5 205 48 HOH HOH . 
E 4 HOH B 6 206 67 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 C C1 JFF . . . C 3 46.896 19.293 -42.211 1 34.98 ? C1 JFF 101 B 1 
HETATM 2 C C9 JFF . . . C 3 45.515 18.651 -42.212 1 32.9 ? C9 JFF 101 B 1 
HETATM 3 C C10 JFF . . . C 3 44.564 19.033 -41.13 1 32.6 ? C10 JFF 101 B 1 
HETATM 4 C C11 JFF . . . C 3 43.204 18.395 -41.067 1 36.43 ? C11 JFF 101 B 1 
HETATM 5 C C12 JFF . . . C 3 42.812 17.435 -42.17 1 34.92 ? C12 JFF 101 B 1 
HETATM 6 C C13 JFF . . . C 3 43.791 17.011 -43.258 1 32.89 ? C13 JFF 101 B 1 
HETATM 7 C C14 JFF . . . C 3 45.146 17.659 -43.296 1 32.62 ? C14 JFF 101 B 1 
HETATM 8 C C15 JFF . . . C 3 41.518 16.673 -42.062 1 41.98 ? C15 JFF 101 B 1 
HETATM 9 O O5 JFF . . . C 3 41.578 15.604 -42.502 1 53.92 ? O5 JFF 101 B 1 
HETATM 10 N N4 JFF . . . C 3 40.33 16.889 -41.305 1 49.14 ? N4 JFF 101 B 1 
HETATM 11 C C16 JFF . . . C 3 39.341 15.778 -41.348 1 43.98 ? C16 JFF 101 B 1 
HETATM 12 C C17 JFF . . . C 3 39.63 14.535 -40.452 1 43.26 ? C17 JFF 101 B 1 
HETATM 13 N N5 JFF . . . C 3 40.653 14.946 -39.599 1 42.62 ? N5 JFF 101 B 1 
HETATM 14 C C18 JFF . . . C 3 41.777 14.35 -38.919 1 33.48 ? C18 JFF 101 B 1 
HETATM 15 O O6 JFF . . . C 3 42.343 15.292 -38.414 1 29.66 ? O6 JFF 101 B 1 
HETATM 16 C C19 JFF . . . C 3 42.294 12.919 -38.737 1 28.89 ? C19 JFF 101 B 1 
#
_model_server_stats.io_time_ms              73 
_model_server_stats.parse_time_ms           105 
_model_server_stats.create_model_time_ms    43 
_model_server_stats.query_time_ms           315 
_model_server_stats.encode_time_ms          8 
_model_server_stats.element_count           16 
#