data_8YNA
#
_model_server_result.job_id            Z7PDQdizevTkd8LOKrImbw 
_model_server_result.datetime_utc      '2024-12-22 07:26:43' 
_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          8yna 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"F","auth_seq_id":701}' 
#
_entry.id    8YNA 
#
_exptl.entry_id    8YNA 
_exptl.method      'ELECTRON MICROSCOPY' 
#
_entity.details                     ? 
_entity.formula_weight              165.235 
_entity.id                          6 
_entity.src_method                  syn 
_entity.type                        non-polymer 
_entity.pdbx_description            4-(1H-imidazol-5-ylmethyl)piperidine 
_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            8YNA 
_cell.length_a            1 
_cell.length_b            1 
_cell.length_c            1 
_cell.Z_PDB               ? 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 8YNA 
_symmetry.cell_setting             ? 
_symmetry.Int_Tables_number        1 
_symmetry.space_group_name_Hall    ? 
_symmetry.space_group_name_H-M     'P 1' 
#
_pdbx_struct_assembly.method_details        ? 
_pdbx_struct_assembly.oligomeric_details    pentameric 
_pdbx_struct_assembly.oligomeric_count      5 
_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,G,H,I,J,K,L,M 
_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                      6 
_struct_asym.id                             F 
_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
disulf ? disulf1 D SG CYS 22 E CYS 22 1_555 D SG CYS 96 E CYS 96 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.031 ? 
disulf ? disulf2 D SG CYS 159 E CYS 159 1_555 D SG CYS 229 E CYS 229 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.032 ? 
disulf ? disulf3 E SG CYS 172 R CYS 87 1_555 E SG CYS 249 R CYS 164 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.031 ? 
#
_chem_comp.formula           'C9 H15 N3' 
_chem_comp.formula_weight    165.235 
_chem_comp.id                A1LY4 
_chem_comp.mon_nstd_flag     . 
_chem_comp.name              4-(1H-imidazol-5-ylmethyl)piperidine 
_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
N03 C04 A1LY4 sing 1 n n 
N03 C02 A1LY4 sing 2 n n 
C04 C05 A1LY4 sing 3 n n 
C02 C01 A1LY4 sing 4 n n 
C05 C06 A1LY4 sing 5 n n 
C06 C01 A1LY4 sing 6 n n 
C06 C07 A1LY4 sing 7 n n 
N10 C09 A1LY4 sing 8 n y 
N10 C11 A1LY4 doub 9 n y 
C09 C08 A1LY4 doub 10 n y 
C11 N12 A1LY4 sing 11 n y 
C08 C07 A1LY4 sing 12 n n 
C08 N12 A1LY4 sing 13 n y 
N12 H1 A1LY4 sing 14 n n 
C01 H2 A1LY4 sing 15 n n 
C01 H3 A1LY4 sing 16 n n 
C02 H4 A1LY4 sing 17 n n 
C02 H5 A1LY4 sing 18 n n 
C04 H6 A1LY4 sing 19 n n 
C04 H7 A1LY4 sing 20 n n 
C05 H8 A1LY4 sing 21 n n 
C05 H9 A1LY4 sing 22 n n 
C06 H10 A1LY4 sing 23 n n 
C07 H11 A1LY4 sing 24 n n 
C07 H12 A1LY4 sing 25 n n 
C09 H13 A1LY4 sing 26 n n 
C11 H14 A1LY4 sing 27 n n 
N03 H15 A1LY4 sing 28 n n 
#
_atom_sites.entry_id                     8YNA 
_atom_sites.fract_transf_matrix[1][1]    1 
_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]    1 
_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]    1 
_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
F 6 A1LY4 R 1 701 701 A1LY4 LIG . 
G 7 CLR R 1 702 801 CLR CLR . 
H 7 CLR R 1 703 802 CLR CLR . 
I 7 CLR R 1 704 803 CLR CLR . 
J 7 CLR R 1 705 804 CLR CLR . 
K 7 CLR R 1 706 805 CLR CLR . 
L 7 CLR R 1 707 806 CLR CLR . 
M 7 CLR R 1 708 807 CLR CLR . 
#
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 N12 A1LY4 . . . F 6 92.922 121.886 123.05 1 68 ? N12 A1LY4 701 R 1 
HETATM 2 C C01 A1LY4 . . . F 6 95.458 125.748 122.163 1 68.05 ? C01 A1LY4 701 R 1 
HETATM 3 C C02 A1LY4 . . . F 6 95.77 126.583 120.923 1 67.06 ? C02 A1LY4 701 R 1 
HETATM 4 C C04 A1LY4 . . . F 6 97.341 124.736 120.577 1 65.33 ? C04 A1LY4 701 R 1 
HETATM 5 C C05 A1LY4 . . . F 6 96.427 123.694 121.214 1 64.49 ? C05 A1LY4 701 R 1 
HETATM 6 C C06 A1LY4 . . . F 6 95.22 124.332 121.794 1 66.03 ? C06 A1LY4 701 R 1 
HETATM 7 C C07 A1LY4 . . . F 6 94.809 123.564 123.045 1 63.91 ? C07 A1LY4 701 R 1 
HETATM 8 C C08 A1LY4 . . . F 6 93.371 123.097 122.86 1 64.46 ? C08 A1LY4 701 R 1 
HETATM 9 C C09 A1LY4 . . . F 6 92.331 123.873 122.458 1 66.04 ? C09 A1LY4 701 R 1 
HETATM 10 C C11 A1LY4 . . . F 6 91.616 121.873 122.781 1 66.12 ? C11 A1LY4 701 R 1 
HETATM 11 N N03 A1LY4 . . . F 6 96.532 125.792 119.929 1 66.31 ? N03 A1LY4 701 R 1 
HETATM 12 N N10 A1LY4 . . . F 6 91.257 123.111 122.413 1 64.66 ? N10 A1LY4 701 R 1 
#
_model_server_stats.io_time_ms              17 
_model_server_stats.parse_time_ms           17 
_model_server_stats.create_model_time_ms    16 
_model_server_stats.query_time_ms           269 
_model_server_stats.encode_time_ms          3 
_model_server_stats.element_count           12 
#