data_3I4A
#
_model_server_result.job_id            uSx4j5RyofJ0FuX6NUuB9g 
_model_server_result.datetime_utc      '2025-07-31 18:43:53' 
_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          3i4a 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"C","auth_seq_id":500}' 
#
_entry.id    3I4A 
#
_exptl.entry_id    3I4A 
_exptl.method      'X-RAY DIFFRACTION' 
#
_entity.details                     ? 
_entity.formula_weight              187.239 
_entity.id                          2 
_entity.src_method                  syn 
_entity.type                        non-polymer 
_entity.pdbx_description            N5-(1-iminopropyl)-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            3I4A 
_cell.length_a            47.6 
_cell.length_b            80.13 
_cell.length_c            73.9 
_cell.Z_PDB               4 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 3I4A 
_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
? monomeric 1 author_defined_assembly 1 
? monomeric 1 author_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 covalent covale1 A SG CYS 297 A CYS 274 1_555 C CZ LN5 . A LN5 500 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.982 ? 
covale covalent covale2 B SG CYS 297 B CYS 274 1_555 D CZ LN5 . B LN5 500 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.988 ? 
#
_chem_comp.formula           'C8 H17 N3 O2' 
_chem_comp.formula_weight    187.239 
_chem_comp.id                LN5 
_chem_comp.mon_nstd_flag     . 
_chem_comp.name              N5-(1-iminopropyl)-L-ornithine 
_chem_comp.type              non-polymer 
_chem_comp.pdbx_synonyms     '(2S)-2-azanyl-5-(propanimidoylamino)pentanoic acid' 
#
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
CH1 CT1 LN5 sing 194 n n 
CZ CH1 LN5 sing 195 n n 
CZ NH2 LN5 doub 196 n n 
NH2 H1H2 LN5 sing 197 n n 
NE CZ LN5 sing 198 n n 
CD NE LN5 sing 199 n n 
CG CD LN5 sing 200 n n 
CB CG LN5 sing 201 n n 
CA C LN5 sing 202 n n 
CA CB LN5 sing 203 n n 
C OA1 LN5 sing 204 n n 
OA2 C LN5 doub 205 n n 
N CA LN5 sing 206 n n 
CT1 H1T1 LN5 sing 207 n n 
CT1 H2T1 LN5 sing 208 n n 
CT1 H3T1 LN5 sing 209 n n 
CH1 H1H1 LN5 sing 210 n n 
CH1 H2H1 LN5 sing 211 n n 
NE HNE LN5 sing 212 n n 
CD H1D LN5 sing 213 n n 
CD H2D LN5 sing 214 n n 
CG H1G LN5 sing 215 n n 
CG H2G LN5 sing 216 n n 
CB H1B LN5 sing 217 n n 
CB H2B LN5 sing 218 n n 
CA HA LN5 sing 219 n n 
OA1 H15 LN5 sing 220 n n 
N H1N LN5 sing 221 n n 
N H2N LN5 sing 222 n n 
#
_atom_sites.entry_id                     3I4A 
_atom_sites.fract_transf_matrix[1][1]    0.021008 
_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]    0.01248 
_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]    0.013532 
_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 LN5 A 1 500 500 LN5 LN5 . 
D 2 LN5 B 1 500 500 LN5 LN5 . 
E 3 HOH A 1 286 1 HOH WAT . 
E 3 HOH A 2 287 3 HOH WAT . 
E 3 HOH A 3 288 6 HOH WAT . 
E 3 HOH A 4 289 9 HOH WAT . 
E 3 HOH A 5 290 10 HOH WAT . 
E 3 HOH A 6 291 11 HOH WAT . 
E 3 HOH A 7 292 12 HOH WAT . 
E 3 HOH A 8 293 14 HOH WAT . 
E 3 HOH A 9 294 15 HOH WAT . 
E 3 HOH A 10 295 16 HOH WAT . 
E 3 HOH A 11 296 18 HOH WAT . 
E 3 HOH A 12 297 20 HOH WAT . 
E 3 HOH A 13 298 21 HOH WAT . 
E 3 HOH A 14 299 27 HOH WAT . 
E 3 HOH A 15 300 28 HOH WAT . 
E 3 HOH A 16 301 29 HOH WAT . 
E 3 HOH A 17 302 32 HOH WAT . 
E 3 HOH A 18 303 56 HOH WAT . 
E 3 HOH A 19 304 57 HOH WAT . 
E 3 HOH A 20 305 58 HOH WAT . 
E 3 HOH A 21 306 60 HOH WAT . 
E 3 HOH A 22 307 61 HOH WAT . 
E 3 HOH A 23 308 63 HOH WAT . 
E 3 HOH A 24 309 64 HOH WAT . 
E 3 HOH A 25 310 65 HOH WAT . 
E 3 HOH A 26 311 66 HOH WAT . 
E 3 HOH A 27 312 67 HOH WAT . 
E 3 HOH A 28 313 68 HOH WAT . 
E 3 HOH A 29 314 69 HOH WAT . 
E 3 HOH A 30 315 70 HOH WAT . 
E 3 HOH A 31 316 71 HOH WAT . 
E 3 HOH A 32 317 72 HOH WAT . 
E 3 HOH A 33 318 73 HOH WAT . 
E 3 HOH A 34 319 74 HOH WAT . 
E 3 HOH A 35 320 75 HOH WAT . 
E 3 HOH A 36 321 76 HOH WAT . 
E 3 HOH A 37 322 77 HOH WAT . 
E 3 HOH A 38 323 78 HOH WAT . 
E 3 HOH A 39 324 79 HOH WAT . 
E 3 HOH A 40 325 80 HOH WAT . 
E 3 HOH A 41 326 88 HOH WAT . 
E 3 HOH A 42 327 89 HOH WAT . 
E 3 HOH A 43 328 92 HOH WAT . 
E 3 HOH A 44 329 94 HOH WAT . 
E 3 HOH A 45 330 96 HOH WAT . 
E 3 HOH A 46 331 97 HOH WAT . 
E 3 HOH A 47 332 98 HOH WAT . 
E 3 HOH A 48 333 100 HOH WAT . 
F 3 HOH B 1 286 2 HOH WAT . 
F 3 HOH B 2 287 4 HOH WAT . 
F 3 HOH B 3 288 5 HOH WAT . 
F 3 HOH B 4 289 7 HOH WAT . 
F 3 HOH B 5 290 8 HOH WAT . 
F 3 HOH B 6 291 13 HOH WAT . 
F 3 HOH B 7 292 17 HOH WAT . 
F 3 HOH B 8 293 19 HOH WAT . 
F 3 HOH B 9 294 22 HOH WAT . 
F 3 HOH B 10 295 23 HOH WAT . 
F 3 HOH B 11 296 24 HOH WAT . 
F 3 HOH B 12 297 25 HOH WAT . 
F 3 HOH B 13 298 26 HOH WAT . 
F 3 HOH B 14 299 30 HOH WAT . 
F 3 HOH B 15 300 31 HOH WAT . 
F 3 HOH B 16 301 33 HOH WAT . 
F 3 HOH B 17 302 35 HOH WAT . 
F 3 HOH B 18 303 36 HOH WAT . 
F 3 HOH B 19 304 37 HOH WAT . 
F 3 HOH B 20 305 38 HOH WAT . 
F 3 HOH B 21 306 39 HOH WAT . 
F 3 HOH B 22 307 40 HOH WAT . 
F 3 HOH B 23 308 41 HOH WAT . 
F 3 HOH B 24 309 42 HOH WAT . 
F 3 HOH B 25 310 43 HOH WAT . 
F 3 HOH B 26 311 44 HOH WAT . 
F 3 HOH B 27 312 45 HOH WAT . 
F 3 HOH B 28 313 46 HOH WAT . 
F 3 HOH B 29 314 47 HOH WAT . 
F 3 HOH B 30 315 48 HOH WAT . 
F 3 HOH B 31 316 49 HOH WAT . 
F 3 HOH B 32 317 50 HOH WAT . 
F 3 HOH B 33 318 51 HOH WAT . 
F 3 HOH B 34 319 52 HOH WAT . 
F 3 HOH B 35 320 53 HOH WAT . 
F 3 HOH B 36 321 54 HOH WAT . 
F 3 HOH B 37 322 55 HOH WAT . 
F 3 HOH B 38 323 59 HOH WAT . 
F 3 HOH B 39 324 62 HOH WAT . 
F 3 HOH B 40 325 81 HOH WAT . 
F 3 HOH B 41 326 82 HOH WAT . 
F 3 HOH B 42 327 83 HOH WAT . 
F 3 HOH B 43 328 84 HOH WAT . 
F 3 HOH B 44 329 85 HOH WAT . 
F 3 HOH B 45 330 86 HOH WAT . 
F 3 HOH B 46 331 87 HOH WAT . 
F 3 HOH B 47 332 90 HOH WAT . 
F 3 HOH B 48 333 91 HOH WAT . 
F 3 HOH B 49 334 93 HOH WAT . 
F 3 HOH B 50 335 95 HOH WAT . 
F 3 HOH B 51 336 99 HOH WAT . 
#
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 CT1 LN5 . . . C 2 2.386 -22.078 -14.35 1 24.39 ? CT1 LN5 500 A 1 
HETATM 2 C CH1 LN5 . . . C 2 1.529 -21.929 -15.597 1 27.07 ? CH1 LN5 500 A 1 
HETATM 3 C CZ LN5 . . . C 2 1.139 -20.498 -15.908 1 8.34 ? CZ LN5 500 A 1 
HETATM 4 N NH2 LN5 . . . C 2 1.442 -19.669 -14.796 1 21.47 ? NH2 LN5 500 A 1 
HETATM 5 N NE LN5 . . . C 2 2.019 -19.885 -16.899 1 25.08 ? NE LN5 500 A 1 
HETATM 6 C CD LN5 . . . C 2 2.048 -20.462 -18.257 1 25.38 ? CD LN5 500 A 1 
HETATM 7 C CG LN5 . . . C 2 2.875 -19.552 -19.19 1 26.86 ? CG LN5 500 A 1 
HETATM 8 C CB LN5 . . . C 2 2.878 -20.075 -20.656 1 26.12 ? CB LN5 500 A 1 
HETATM 9 C CA LN5 . . . C 2 3.625 -19.146 -21.626 1 25.47 ? CA LN5 500 A 1 
HETATM 10 C C LN5 . . . C 2 5.128 -19.145 -21.34 1 27.29 ? C LN5 500 A 1 
HETATM 11 O OA2 LN5 . . . C 2 5.834 -19.925 -22.018 1 28.37 ? OA2 LN5 500 A 1 
HETATM 12 O OA1 LN5 . . . C 2 5.541 -18.346 -20.471 1 28.43 ? OA1 LN5 500 A 1 
HETATM 13 N N LN5 . . . C 2 3.417 -19.588 -23.014 1 25.74 ? N LN5 500 A 1 
#
_model_server_stats.io_time_ms              154 
_model_server_stats.parse_time_ms           297 
_model_server_stats.create_model_time_ms    101 
_model_server_stats.query_time_ms           983 
_model_server_stats.encode_time_ms          7 
_model_server_stats.element_count           13 
#