data_3P8E
#
_model_server_result.job_id            -c4xDEopenIjuKOUNRg-Iw 
_model_server_result.datetime_utc      '2024-10-18 16:20:40' 
_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          3p8e 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"C","auth_seq_id":286}' 
#
_entry.id    3P8E 
#
_exptl.entry_id    3P8E 
_exptl.method      'X-RAY DIFFRACTION' 
#
_entity.details                     ? 
_entity.formula_weight              217.309 
_entity.id                          2 
_entity.src_method                  syn 
_entity.type                        non-polymer 
_entity.pdbx_description            N~5~-[(1S)-1-aminopentyl]-L-ornithine 
_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          90.13 
_cell.angle_gamma         90 
_cell.entry_id            3P8E 
_cell.length_a            47.21 
_cell.length_b            80.9 
_cell.length_c            74.09 
_cell.Z_PDB               4 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 3P8E 
_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,E 1 1 
B,D,F 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
? 2 C N N 
? 2 D 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
covale ? covale1 A SG CYS 297 A CYS 274 1_555 C CZ LN7 . A LN7 286 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.987 ? 
covale ? covale2 B SG CYS 297 B CYS 274 1_555 D CZ LN7 . B LN7 286 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.994 ? 
#
_chem_comp.formula           'C10 H23 N3 O2' 
_chem_comp.formula_weight    217.309 
_chem_comp.id                LN7 
_chem_comp.mon_nstd_flag     . 
_chem_comp.name              N~5~-[(1S)-1-aminopentyl]-L-ornithine 
_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
OA2 C LN7 doub 194 n n 
CA C LN7 sing 195 n n 
C OA1 LN7 sing 196 n n 
N CA LN7 sing 197 n n 
N HN LN7 sing 198 n n 
N HNA LN7 sing 199 n n 
CA CB LN7 sing 200 n n 
CA HA LN7 sing 201 n n 
CB CG LN7 sing 202 n n 
CB HB LN7 sing 203 n n 
CB HBA LN7 sing 204 n n 
CG CD LN7 sing 205 n n 
CD NE LN7 sing 206 n n 
CD HD LN7 sing 207 n n 
CD HDA LN7 sing 208 n n 
NE CZ LN7 sing 209 n n 
NE HNE LN7 sing 210 n n 
CG HG LN7 sing 211 n n 
CG HGA LN7 sing 212 n n 
CH1 CZ LN7 sing 213 n n 
CZ NH2 LN7 sing 214 n n 
CZ HZ LN7 sing 215 n n 
OA1 HOA1 LN7 sing 216 n n 
CH1 CT1 LN7 sing 217 n n 
CH1 HH1 LN7 sing 218 n n 
CH1 HH1A LN7 sing 219 n n 
NH2 HNH2 LN7 sing 220 n n 
NH2 HNHA LN7 sing 221 n n 
CT1 CI1 LN7 sing 222 n n 
CI1 CK1 LN7 sing 223 n n 
CI1 HI1 LN7 sing 224 n n 
CI1 HI1A LN7 sing 225 n n 
CK1 HK1 LN7 sing 226 n n 
CK1 HK1A LN7 sing 227 n n 
CK1 HK1B LN7 sing 228 n n 
CT1 HT1 LN7 sing 229 n n 
CT1 HT1A LN7 sing 230 n n 
#
_atom_sites.entry_id                     3P8E 
_atom_sites.fract_transf_matrix[1][1]    0.021182 
_atom_sites.fract_transf_matrix[1][2]    0 
_atom_sites.fract_transf_matrix[1][3]    0.000048 
_atom_sites.fract_transf_matrix[2][1]    0 
_atom_sites.fract_transf_matrix[2][2]    0.012361 
_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]    0.013497 
_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 LN7 A 1 286 1 LN7 LN7 . 
D 2 LN7 B 1 286 1 LN7 LN7 . 
E 3 HOH A 1 287 1 HOH HOH . 
E 3 HOH A 2 288 5 HOH HOH . 
E 3 HOH A 3 289 9 HOH HOH . 
E 3 HOH A 4 290 10 HOH HOH . 
E 3 HOH A 5 291 11 HOH HOH . 
E 3 HOH A 6 292 12 HOH HOH . 
E 3 HOH A 7 293 14 HOH HOH . 
E 3 HOH A 8 294 16 HOH HOH . 
E 3 HOH A 9 295 19 HOH HOH . 
E 3 HOH A 10 296 21 HOH HOH . 
E 3 HOH A 11 297 22 HOH HOH . 
E 3 HOH A 12 298 23 HOH HOH . 
E 3 HOH A 13 299 27 HOH HOH . 
E 3 HOH A 14 300 29 HOH HOH . 
E 3 HOH A 15 301 30 HOH HOH . 
E 3 HOH A 16 302 32 HOH HOH . 
E 3 HOH A 17 303 33 HOH HOH . 
E 3 HOH A 18 304 36 HOH HOH . 
E 3 HOH A 19 305 37 HOH HOH . 
E 3 HOH A 20 306 41 HOH HOH . 
E 3 HOH A 21 307 45 HOH HOH . 
E 3 HOH A 22 308 46 HOH HOH . 
E 3 HOH A 23 309 47 HOH HOH . 
E 3 HOH A 24 310 48 HOH HOH . 
E 3 HOH A 25 311 49 HOH HOH . 
E 3 HOH A 26 312 51 HOH HOH . 
F 3 HOH B 1 287 2 HOH HOH . 
F 3 HOH B 2 288 3 HOH HOH . 
F 3 HOH B 3 289 4 HOH HOH . 
F 3 HOH B 4 290 6 HOH HOH . 
F 3 HOH B 5 291 7 HOH HOH . 
F 3 HOH B 6 292 8 HOH HOH . 
F 3 HOH B 7 293 13 HOH HOH . 
F 3 HOH B 8 294 15 HOH HOH . 
F 3 HOH B 9 295 17 HOH HOH . 
F 3 HOH B 10 296 20 HOH HOH . 
F 3 HOH B 11 297 24 HOH HOH . 
F 3 HOH B 12 298 25 HOH HOH . 
F 3 HOH B 13 299 26 HOH HOH . 
F 3 HOH B 14 300 28 HOH HOH . 
F 3 HOH B 15 301 31 HOH HOH . 
F 3 HOH B 16 302 34 HOH HOH . 
F 3 HOH B 17 303 35 HOH HOH . 
F 3 HOH B 18 304 38 HOH HOH . 
F 3 HOH B 19 305 39 HOH HOH . 
F 3 HOH B 20 306 40 HOH HOH . 
F 3 HOH B 21 307 43 HOH HOH . 
F 3 HOH B 22 308 50 HOH HOH . 
F 3 HOH B 23 309 52 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 C LN7 . . . C 2 -28.611 19.324 -21.637 1 43.61 ? C LN7 286 A 1 
HETATM 2 N N LN7 . . . C 2 -26.99 19.321 -23.491 1 37.11 ? N LN7 286 A 1 
HETATM 3 C CA LN7 . . . C 2 -27.187 18.941 -22.073 1 42.88 ? CA LN7 286 A 1 
HETATM 4 C CB LN7 . . . C 2 -26.186 19.695 -21.196 1 37.36 ? CB LN7 286 A 1 
HETATM 5 C CD LN7 . . . C 2 -25.28 20.117 -18.876 1 31.54 ? CD LN7 286 A 1 
HETATM 6 N NE LN7 . . . C 2 -25.448 19.749 -17.461 1 35.63 ? NE LN7 286 A 1 
HETATM 7 C CG LN7 . . . C 2 -26.297 19.321 -19.717 1 32.46 ? CG LN7 286 A 1 
HETATM 8 C CZ LN7 . . . C 2 -24.645 20.556 -16.519 1 35.97 ? CZ LN7 286 A 1 
HETATM 9 O OA1 LN7 . . . C 2 -29.12 18.668 -20.696 1 40.83 ? OA1 LN7 286 A 1 
HETATM 10 O OA2 LN7 . . . C 2 -29.149 20.279 -22.251 1 44.79 ? OA2 LN7 286 A 1 
HETATM 11 C CH1 LN7 . . . C 2 -25.028 22.026 -16.791 1 41.42 ? CH1 LN7 286 A 1 
HETATM 12 N NH2 LN7 . . . C 2 -25.013 20.092 -15.175 1 35.19 ? NH2 LN7 286 A 1 
HETATM 13 C CI1 LN7 . . . C 2 -26.758 22.131 -15.076 1 37.47 ? CI1 LN7 286 A 1 
HETATM 14 C CK1 LN7 . . . C 2 -25.819 22.992 -14.223 1 32.82 ? CK1 LN7 286 A 1 
HETATM 15 C CT1 LN7 . . . C 2 -26.494 22.372 -16.556 1 34.1 ? CT1 LN7 286 A 1 
#
_model_server_stats.io_time_ms              0 
_model_server_stats.parse_time_ms           6 
_model_server_stats.create_model_time_ms    4 
_model_server_stats.query_time_ms           310 
_model_server_stats.encode_time_ms          1 
_model_server_stats.element_count           15 
#