data_4IU5
#
_model_server_result.job_id            LhDR9a-AiGLfQEps-BHPqA 
_model_server_result.datetime_utc      '2024-11-08 03:12:07' 
_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          4iu5 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"D","auth_seq_id":403}' 
#
_entry.id    4IU5 
#
_exptl.entry_id    4IU5 
_exptl.method      'X-RAY DIFFRACTION' 
#
_entity.details                     ? 
_entity.formula_weight              132.161 
_entity.id                          3 
_entity.src_method                  syn 
_entity.type                        non-polymer 
_entity.pdbx_description            L-ornithine 
_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         120 
_cell.entry_id            4IU5 
_cell.length_a            89.617 
_cell.length_b            89.617 
_cell.length_c            114.359 
_cell.Z_PDB               9 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 4IU5 
_symmetry.cell_setting             ? 
_symmetry.Int_Tables_number        146 
_symmetry.space_group_name_Hall    ? 
_symmetry.space_group_name_H-M     'H 3' 
#
_pdbx_struct_assembly.method_details        PISA 
_pdbx_struct_assembly.oligomeric_details    trimeric 
_pdbx_struct_assembly.oligomeric_count      3 
_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,F 
_pdbx_struct_assembly_gen.assembly_id        1 
_pdbx_struct_assembly_gen.oper_expression    1,2,3 
#
loop_
_pdbx_struct_oper_list.id
_pdbx_struct_oper_list.type
_pdbx_struct_oper_list.name
_pdbx_struct_oper_list.symmetry_operation
_pdbx_struct_oper_list.matrix[1][1]
_pdbx_struct_oper_list.matrix[1][2]
_pdbx_struct_oper_list.matrix[1][3]
_pdbx_struct_oper_list.matrix[2][1]
_pdbx_struct_oper_list.matrix[2][2]
_pdbx_struct_oper_list.matrix[2][3]
_pdbx_struct_oper_list.matrix[3][1]
_pdbx_struct_oper_list.matrix[3][2]
_pdbx_struct_oper_list.matrix[3][3]
_pdbx_struct_oper_list.vector[1]
_pdbx_struct_oper_list.vector[2]
_pdbx_struct_oper_list.vector[3]
1 'identity operation' 1_555 x,y,z 1 0 0 0 1 0 0 0 1 0 0 0 
2 'crystal symmetry operation' 2_555 -y,x-y,z -0.5 -0.866025 0 0.866025 -0.5 0 0 0 1 0 0 0 
3 'crystal symmetry operation' 3_555 -x+y,-x,z -0.5 0.866025 0 -0.866025 -0.5 0 0 0 1 0 0 0 
#
_struct_asym.details                        ? 
_struct_asym.entity_id                      3 
_struct_asym.id                             D 
_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
metalc ? metalc1 A ND1 HIS 115 A HIS 114 1_555 B MN MN . A MN 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.366 ? 
metalc ? metalc2 A OD2 ASP 138 A ASP 137 1_555 B MN MN . A MN 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.044 ? 
metalc ? metalc3 A OD1 ASP 138 A ASP 137 1_555 C MN MN . A MN 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.221 ? 
metalc ? metalc4 A ND1 HIS 140 A HIS 139 1_555 C MN MN . A MN 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.428 ? 
metalc ? metalc5 A OD2 ASP 142 A ASP 141 1_555 B MN MN . A MN 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.193 ? 
metalc ? metalc6 A OD2 ASP 244 A ASP 243 1_555 B MN MN . A MN 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.265 ? 
metalc ? metalc7 A OD2 ASP 244 A ASP 243 1_555 C MN MN . A MN 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.56 ? 
metalc ? metalc8 A OD1 ASP 246 A ASP 245 1_555 C MN MN . A MN 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.233 ? 
metalc ? metalc9 B MN MN . A MN 401 1_555 C MN MN . A MN 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.88 ? 
metalc ? metalc10 B MN MN . A MN 401 1_555 F O HOH . A HOH 566 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.502 ? 
#
_chem_comp.formula           'C5 H12 N2 O2' 
_chem_comp.formula_weight    132.161 
_chem_comp.id                ORN 
_chem_comp.mon_nstd_flag     n 
_chem_comp.name              L-ornithine 
_chem_comp.type              'l-peptide linking' 
_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
N CA ORN sing 250 n n 
N H ORN sing 251 n n 
N H2 ORN sing 252 n n 
CA CB ORN sing 253 n n 
CA C ORN sing 254 n n 
CA HA ORN sing 255 n n 
CB CG ORN sing 256 n n 
CB HB2 ORN sing 257 n n 
CB HB3 ORN sing 258 n n 
CG CD ORN sing 259 n n 
CG HG2 ORN sing 260 n n 
CG HG3 ORN sing 261 n n 
CD NE ORN sing 262 n n 
CD HD2 ORN sing 263 n n 
CD HD3 ORN sing 264 n n 
NE HE1 ORN sing 265 n n 
NE HE2 ORN sing 266 n n 
C O ORN doub 267 n n 
C OXT ORN sing 268 n n 
OXT HXT ORN sing 269 n n 
#
_atom_sites.entry_id                     4IU5 
_atom_sites.fract_transf_matrix[1][1]    0.011159 
_atom_sites.fract_transf_matrix[1][2]    0.006442 
_atom_sites.fract_transf_matrix[1][3]    0 
_atom_sites.fract_transf_matrix[2][1]    0 
_atom_sites.fract_transf_matrix[2][2]    0.012885 
_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]    0.008744 
_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
B 2 MN A 1 401 400 MN MN . 
C 2 MN A 1 402 401 MN MN . 
D 3 ORN A 1 403 500 ORN ORN . 
E 4 GOL A 1 404 501 GOL GOL . 
F 5 HOH A 1 501 1 HOH HOH . 
F 5 HOH A 2 502 2 HOH HOH . 
F 5 HOH A 3 503 3 HOH HOH . 
F 5 HOH A 4 504 4 HOH HOH . 
F 5 HOH A 5 505 5 HOH HOH . 
F 5 HOH A 6 506 6 HOH HOH . 
F 5 HOH A 7 507 7 HOH HOH . 
F 5 HOH A 8 508 8 HOH HOH . 
F 5 HOH A 9 509 9 HOH HOH . 
F 5 HOH A 10 510 10 HOH HOH . 
F 5 HOH A 11 511 11 HOH HOH . 
F 5 HOH A 12 512 12 HOH HOH . 
F 5 HOH A 13 513 13 HOH HOH . 
F 5 HOH A 14 514 14 HOH HOH . 
F 5 HOH A 15 515 15 HOH HOH . 
F 5 HOH A 16 516 16 HOH HOH . 
F 5 HOH A 17 517 17 HOH HOH . 
F 5 HOH A 18 518 18 HOH HOH . 
F 5 HOH A 19 519 19 HOH HOH . 
F 5 HOH A 20 520 20 HOH HOH . 
F 5 HOH A 21 521 21 HOH HOH . 
F 5 HOH A 22 522 22 HOH HOH . 
F 5 HOH A 23 523 23 HOH HOH . 
F 5 HOH A 24 524 24 HOH HOH . 
F 5 HOH A 25 525 25 HOH HOH . 
F 5 HOH A 26 526 26 HOH HOH . 
F 5 HOH A 27 527 27 HOH HOH . 
F 5 HOH A 28 528 28 HOH HOH . 
F 5 HOH A 29 529 29 HOH HOH . 
F 5 HOH A 30 530 30 HOH HOH . 
F 5 HOH A 31 531 31 HOH HOH . 
F 5 HOH A 32 532 32 HOH HOH . 
F 5 HOH A 33 533 33 HOH HOH . 
F 5 HOH A 34 534 34 HOH HOH . 
F 5 HOH A 35 535 35 HOH HOH . 
F 5 HOH A 36 536 36 HOH HOH . 
F 5 HOH A 37 537 37 HOH HOH . 
F 5 HOH A 38 538 38 HOH HOH . 
F 5 HOH A 39 539 39 HOH HOH . 
F 5 HOH A 40 540 40 HOH HOH . 
F 5 HOH A 41 541 41 HOH HOH . 
F 5 HOH A 42 542 42 HOH HOH . 
F 5 HOH A 43 543 43 HOH HOH . 
F 5 HOH A 44 544 44 HOH HOH . 
F 5 HOH A 45 545 45 HOH HOH . 
F 5 HOH A 46 546 46 HOH HOH . 
F 5 HOH A 47 547 47 HOH HOH . 
F 5 HOH A 48 548 48 HOH HOH . 
F 5 HOH A 49 549 49 HOH HOH . 
F 5 HOH A 50 550 50 HOH HOH . 
F 5 HOH A 51 551 51 HOH HOH . 
F 5 HOH A 52 552 52 HOH HOH . 
F 5 HOH A 53 553 53 HOH HOH . 
F 5 HOH A 54 554 54 HOH HOH . 
F 5 HOH A 55 555 55 HOH HOH . 
F 5 HOH A 56 556 56 HOH HOH . 
F 5 HOH A 57 557 57 HOH HOH . 
F 5 HOH A 58 558 58 HOH HOH . 
F 5 HOH A 59 559 59 HOH HOH . 
F 5 HOH A 60 560 60 HOH HOH . 
F 5 HOH A 61 561 61 HOH HOH . 
F 5 HOH A 62 562 62 HOH HOH . 
F 5 HOH A 63 563 63 HOH HOH . 
F 5 HOH A 64 564 64 HOH HOH . 
F 5 HOH A 65 565 65 HOH HOH . 
F 5 HOH A 66 566 66 HOH HOH . 
F 5 HOH A 67 567 67 HOH HOH . 
F 5 HOH A 68 568 68 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 N N ORN . . . D 3 12.461 -22.158 -6.607 1 48.7 ? N ORN 403 A 1 
HETATM 2 C CA ORN . . . D 3 12.681 -21.985 -8.057 1 48.75 ? CA ORN 403 A 1 
HETATM 3 C CB ORN . . . D 3 13.039 -20.514 -8.394 1 47.68 ? CB ORN 403 A 1 
HETATM 4 C CG ORN . . . D 3 14.128 -19.947 -7.461 1 46.45 ? CG ORN 403 A 1 
HETATM 5 C CD ORN . . . D 3 14.563 -18.571 -7.982 1 45.43 ? CD ORN 403 A 1 
HETATM 6 N NE ORN . . . D 3 15.946 -18.298 -7.572 1 44.48 ? NE ORN 403 A 1 
HETATM 7 C C ORN . . . D 3 13.785 -22.935 -8.537 1 49.12 ? C ORN 403 A 1 
HETATM 8 O O ORN . . . D 3 14.173 -22.882 -9.682 1 48.46 ? O ORN 403 A 1 
HETATM 9 O OXT ORN . . . D 3 14.326 -23.84 -7.693 1 49.45 ? OXT ORN 403 A 1 
#
_model_server_stats.io_time_ms              8 
_model_server_stats.parse_time_ms           22 
_model_server_stats.create_model_time_ms    6 
_model_server_stats.query_time_ms           275 
_model_server_stats.encode_time_ms          2 
_model_server_stats.element_count           9 
#