data_5LY7
#
_model_server_result.job_id            Z5uWHweelaVUEpf-FiudhQ 
_model_server_result.datetime_utc      '2024-11-24 00:34:06' 
_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          5ly7 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"D","auth_seq_id":402}' 
#
_entry.id    5LY7 
#
_exptl.entry_id    5LY7 
_exptl.method      'X-RAY DIFFRACTION' 
#
_entity.details                     ? 
_entity.formula_weight              204.224 
_entity.id                          3 
_entity.src_method                  syn 
_entity.type                        non-polymer 
_entity.pdbx_description            2-ACETAMIDO-1,2-DIDEOXYNOJIRMYCIN 
_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          98.57 
_cell.angle_gamma         90 
_cell.entry_id            5LY7 
_cell.length_a            65.14 
_cell.length_b            66.93 
_cell.length_c            74.06 
_cell.Z_PDB               4 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 5LY7 
_symmetry.cell_setting             ? 
_symmetry.Int_Tables_number        4 
_symmetry.space_group_name_Hall    . 
_symmetry.space_group_name_H-M     'P 1 21 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 monomeric 1 author_and_software_defined_assembly 1 
PISA monomeric 1 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,C,D,G 1 1 
B,E,F,H 2 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
? 3 D N N 
? 3 F N N 
#
_chem_comp.formula           'C8 H16 N2 O4' 
_chem_comp.formula_weight    204.224 
_chem_comp.id                NOK 
_chem_comp.mon_nstd_flag     . 
_chem_comp.name              2-ACETAMIDO-1,2-DIDEOXYNOJIRMYCIN 
_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
C8 C7 NOK sing 237 n n 
C7 O7 NOK doub 238 n n 
C7 N2 NOK sing 239 n n 
N2 C2 NOK sing 240 n n 
C2 C1 NOK sing 241 n n 
C2 C3 NOK sing 242 n n 
C1 N5 NOK sing 243 n n 
N5 C5 NOK sing 244 n n 
C5 C6 NOK sing 245 n n 
C5 C4 NOK sing 246 n n 
C6 O6 NOK sing 247 n n 
C4 O4 NOK sing 248 n n 
C4 C3 NOK sing 249 n n 
C3 O3 NOK sing 250 n n 
C8 H8C1 NOK sing 251 n n 
C8 H8C2 NOK sing 252 n n 
C8 H8C3 NOK sing 253 n n 
N2 H2 NOK sing 254 n n 
C2 HA NOK sing 255 n n 
C1 H1C1 NOK sing 256 n n 
C1 H1C2 NOK sing 257 n n 
C3 H3 NOK sing 258 n n 
N5 H5 NOK sing 259 n n 
C5 HB NOK sing 260 n n 
C6 H6C1 NOK sing 261 n n 
C6 H6C2 NOK sing 262 n n 
C4 H4 NOK sing 263 n n 
O6 H6 NOK sing 264 n n 
O4 HC NOK sing 265 n n 
O3 HD NOK sing 266 n n 
#
_atom_sites.entry_id                     5LY7 
_atom_sites.fract_transf_matrix[1][1]    0.015352 
_atom_sites.fract_transf_matrix[1][2]    0 
_atom_sites.fract_transf_matrix[1][3]    0.002313 
_atom_sites.fract_transf_matrix[2][1]    0 
_atom_sites.fract_transf_matrix[2][2]    0.014941 
_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]    0.013655 
_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 PEG A 1 401 1 PEG PEG . 
D 3 NOK A 1 402 1 NOK IMI . 
E 2 PEG B 1 401 2 PEG PEG . 
F 3 NOK B 1 402 2 NOK IMI . 
G 4 HOH A 1 501 4 HOH HOH . 
G 4 HOH A 2 502 5 HOH HOH . 
G 4 HOH A 3 503 2 HOH HOH . 
G 4 HOH A 4 504 9 HOH HOH . 
G 4 HOH A 5 505 6 HOH HOH . 
G 4 HOH A 6 506 1 HOH HOH . 
G 4 HOH A 7 507 3 HOH HOH . 
G 4 HOH A 8 508 14 HOH HOH . 
G 4 HOH A 9 509 13 HOH HOH . 
G 4 HOH A 10 510 11 HOH HOH . 
G 4 HOH A 11 511 10 HOH HOH . 
H 4 HOH B 1 501 7 HOH HOH . 
H 4 HOH B 2 502 12 HOH HOH . 
H 4 HOH B 3 503 8 HOH HOH . 
H 4 HOH B 4 504 15 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 C8 NOK . . . D 3 195.157 -3.236 80.219 1 25.64 ? C8 NOK 402 A 1 
HETATM 2 C C7 NOK . . . D 3 196.35 -4.167 80.207 1 22.22 ? C7 NOK 402 A 1 
HETATM 3 O O7 NOK . . . D 3 196.906 -4.468 81.264 1 4.38 ? O7 NOK 402 A 1 
HETATM 4 N N2 NOK . . . D 3 196.717 -4.603 79 1 7.85 ? N2 NOK 402 A 1 
HETATM 5 C C2 NOK . . . D 3 197.831 -5.507 78.78 1 1 ? C2 NOK 402 A 1 
HETATM 6 C C1 NOK . . . D 3 197.201 -6.738 78.092 1 17.52 ? C1 NOK 402 A 1 
HETATM 7 N N5 NOK . . . D 3 198.192 -7.603 77.459 1 25.55 ? N5 NOK 402 A 1 
HETATM 8 C C5 NOK . . . D 3 199.007 -6.878 76.482 1 8.32 ? C5 NOK 402 A 1 
HETATM 9 C C6 NOK . . . D 3 199.87 -7.904 75.77 1 25.05 ? C6 NOK 402 A 1 
HETATM 10 O O6 NOK . . . D 3 200.534 -8.663 76.745 1 6 ? O6 NOK 402 A 1 
HETATM 11 C C4 NOK . . . D 3 199.836 -5.817 77.225 1 25.19 ? C4 NOK 402 A 1 
HETATM 12 O O4 NOK . . . D 3 200.685 -5.184 76.286 1 14.45 ? O4 NOK 402 A 1 
HETATM 13 C C3 NOK . . . D 3 198.944 -4.789 77.961 1 29.75 ? C3 NOK 402 A 1 
HETATM 14 O O3 NOK . . . D 3 199.815 -4.086 78.837 1 10.14 ? O3 NOK 402 A 1 
#
_model_server_stats.io_time_ms              24 
_model_server_stats.parse_time_ms           27 
_model_server_stats.create_model_time_ms    14 
_model_server_stats.query_time_ms           455 
_model_server_stats.encode_time_ms          5 
_model_server_stats.element_count           14 
#