data_1VDD
#
_model_server_result.job_id            d2gOcNuV7tkXkQwMjcVMtg 
_model_server_result.datetime_utc      '2024-12-27 03:11:06' 
_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          1vdd 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"H","auth_seq_id":2025}' 
#
_entry.id    1VDD 
#
_exptl.entry_id    1VDD 
_exptl.method      'X-RAY DIFFRACTION' 
#
_entity.details                     ? 
_entity.formula_weight              69.085 
_entity.id                          3 
_entity.src_method                  syn 
_entity.type                        non-polymer 
_entity.pdbx_description            IMIDAZOLE 
_entity.pdbx_number_of_molecules    5 
_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            1VDD 
_cell.length_a            106.218 
_cell.length_b            121.386 
_cell.length_c            154.993 
_cell.Z_PDB               32 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 1VDD 
_symmetry.cell_setting             ? 
_symmetry.Int_Tables_number        20 
_symmetry.space_group_name_Hall    . 
_symmetry.space_group_name_H-M     'C 2 2 21' 
#
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 tetrameric 4 author_and_software_defined_assembly 1 
PISA octameric 8 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,B,C,D,E,F,G,H,I,J,K,L,M,N,O,P,Q 1 1 
A,B,C,D,E,F,G,H,I,J,K,L,M,N,O,P,Q 2 1,2 
#
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' 4_555 x,-y,-z 1 0 0 0 -1 0 0 0 -1 0 0 0 
#
loop_
_struct_asym.details
_struct_asym.entity_id
_struct_asym.id
_struct_asym.pdbx_modified
_struct_asym.pdbx_blank_PDB_chainid_flag
? 3 F N N 
? 3 H N N 
? 3 J N N 
? 3 L N N 
? 3 M 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
disulf ? disulf1 C SG CYS 69 C CYS 69 1_555 C SG CYS 72 C CYS 72 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.984 ? 
metalc ? metalc1 A SG CYS 57 A CYS 57 1_555 E ZN ZN . A ZN 230 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.491 ? 
metalc ? metalc2 A SG CYS 60 A CYS 60 1_555 E ZN ZN . A ZN 230 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.913 ? 
metalc ? metalc3 A SG CYS 69 A CYS 69 1_555 E ZN ZN . A ZN 230 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.03 ? 
metalc ? metalc4 A SG CYS 72 A CYS 72 1_555 E ZN ZN . A ZN 230 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.16 ? 
metalc ? metalc5 B SG CYS 57 B CYS 57 1_555 G ZN ZN . B ZN 231 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.395 ? 
metalc ? metalc6 B SG CYS 60 B CYS 60 1_555 G ZN ZN . B ZN 231 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.015 ? 
metalc ? metalc7 B SG CYS 69 B CYS 69 1_555 G ZN ZN . B ZN 231 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.069 ? 
metalc ? metalc8 B SG CYS 72 B CYS 72 1_555 G ZN ZN . B ZN 231 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.243 ? 
metalc ? metalc9 C SG CYS 57 C CYS 57 1_555 I ZN ZN . C ZN 232 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.317 ? 
metalc ? metalc10 C SG CYS 60 C CYS 60 1_555 I ZN ZN . C ZN 232 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 4.239 ? 
metalc ? metalc11 C SG CYS 69 C CYS 69 1_555 I ZN ZN . C ZN 232 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.07 ? 
metalc ? metalc12 C SG CYS 72 C CYS 72 1_555 I ZN ZN . C ZN 232 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.325 ? 
metalc ? metalc13 D SG CYS 57 D CYS 57 1_555 K ZN ZN . D ZN 233 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.318 ? 
metalc ? metalc14 D SG CYS 60 D CYS 60 1_555 K ZN ZN . D ZN 233 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.303 ? 
metalc ? metalc15 D SG CYS 69 D CYS 69 1_555 K ZN ZN . D ZN 233 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.33 ? 
metalc ? metalc16 D SG CYS 72 D CYS 72 1_555 K ZN ZN . D ZN 233 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.211 ? 
#
_chem_comp.formula           'C3 H5 N2 1' 
_chem_comp.formula_weight    69.085 
_chem_comp.id                IMD 
_chem_comp.mon_nstd_flag     . 
_chem_comp.name              IMIDAZOLE 
_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
N1 C2 IMD sing 173 n y 
N1 C5 IMD sing 174 n y 
N1 HN1 IMD sing 175 n n 
C2 N3 IMD doub 176 n y 
C2 H2 IMD sing 177 n n 
N3 C4 IMD sing 178 n y 
N3 HN3 IMD sing 179 n n 
C4 C5 IMD doub 180 n y 
C4 H4 IMD sing 181 n n 
C5 H5 IMD sing 182 n n 
#
_atom_sites.entry_id                     1VDD 
_atom_sites.fract_transf_matrix[1][1]    0.009415 
_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]    0.008238 
_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]    0.006452 
_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
E 2 ZN A 1 230 230 ZN ZN . 
F 3 IMD A 1 2027 2027 IMD IMD . 
G 2 ZN B 1 231 231 ZN ZN . 
H 3 IMD B 1 2025 2025 IMD IMD . 
I 2 ZN C 1 232 232 ZN ZN . 
J 3 IMD C 1 2024 2024 IMD IMD . 
K 2 ZN D 1 233 233 ZN ZN . 
L 3 IMD D 1 2023 2023 IMD IMD . 
M 3 IMD D 1 2026 2026 IMD IMD . 
N 4 HOH A 1 2028 6 HOH TIP . 
N 4 HOH A 2 2029 8 HOH TIP . 
N 4 HOH A 3 2030 22 HOH TIP . 
N 4 HOH A 4 2031 23 HOH TIP . 
N 4 HOH A 5 2032 25 HOH TIP . 
N 4 HOH A 6 2033 27 HOH TIP . 
N 4 HOH A 7 2034 31 HOH TIP . 
N 4 HOH A 8 2035 34 HOH TIP . 
N 4 HOH A 9 2036 48 HOH TIP . 
N 4 HOH A 10 2037 53 HOH TIP . 
N 4 HOH A 11 2038 63 HOH TIP . 
N 4 HOH A 12 2039 64 HOH TIP . 
O 4 HOH B 1 2026 14 HOH TIP . 
O 4 HOH B 2 2027 15 HOH TIP . 
O 4 HOH B 3 2028 20 HOH TIP . 
O 4 HOH B 4 2029 30 HOH TIP . 
O 4 HOH B 5 2030 32 HOH TIP . 
O 4 HOH B 6 2031 33 HOH TIP . 
O 4 HOH B 7 2032 36 HOH TIP . 
O 4 HOH B 8 2033 40 HOH TIP . 
O 4 HOH B 9 2034 42 HOH TIP . 
O 4 HOH B 10 2035 44 HOH TIP . 
O 4 HOH B 11 2036 46 HOH TIP . 
O 4 HOH B 12 2037 52 HOH TIP . 
O 4 HOH B 13 2038 56 HOH TIP . 
O 4 HOH B 14 2039 57 HOH TIP . 
P 4 HOH C 1 2025 3 HOH TIP . 
P 4 HOH C 2 2026 5 HOH TIP . 
P 4 HOH C 3 2027 11 HOH TIP . 
P 4 HOH C 4 2028 12 HOH TIP . 
P 4 HOH C 5 2029 16 HOH TIP . 
P 4 HOH C 6 2030 18 HOH TIP . 
P 4 HOH C 7 2031 19 HOH TIP . 
P 4 HOH C 8 2032 21 HOH TIP . 
P 4 HOH C 9 2033 26 HOH TIP . 
P 4 HOH C 10 2034 37 HOH TIP . 
P 4 HOH C 11 2035 38 HOH TIP . 
P 4 HOH C 12 2036 39 HOH TIP . 
P 4 HOH C 13 2037 41 HOH TIP . 
P 4 HOH C 14 2038 43 HOH TIP . 
P 4 HOH C 15 2039 45 HOH TIP . 
P 4 HOH C 16 2040 47 HOH TIP . 
P 4 HOH C 17 2041 51 HOH TIP . 
P 4 HOH C 18 2042 55 HOH TIP . 
P 4 HOH C 19 2043 58 HOH TIP . 
P 4 HOH C 20 2044 59 HOH TIP . 
P 4 HOH C 21 2045 62 HOH TIP . 
P 4 HOH C 22 2046 65 HOH TIP . 
Q 4 HOH D 1 2027 1 HOH TIP . 
Q 4 HOH D 2 2028 2 HOH TIP . 
Q 4 HOH D 3 2029 4 HOH TIP . 
Q 4 HOH D 4 2030 7 HOH TIP . 
Q 4 HOH D 5 2031 9 HOH TIP . 
Q 4 HOH D 6 2032 10 HOH TIP . 
Q 4 HOH D 7 2033 13 HOH TIP . 
Q 4 HOH D 8 2034 17 HOH TIP . 
Q 4 HOH D 9 2035 24 HOH TIP . 
Q 4 HOH D 10 2036 28 HOH TIP . 
Q 4 HOH D 11 2037 29 HOH TIP . 
Q 4 HOH D 12 2038 35 HOH TIP . 
Q 4 HOH D 13 2039 49 HOH TIP . 
Q 4 HOH D 14 2040 50 HOH TIP . 
Q 4 HOH D 15 2041 54 HOH TIP . 
Q 4 HOH D 16 2042 60 HOH TIP . 
Q 4 HOH D 17 2043 61 HOH TIP . 
#
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 N1 IMD . . . H 3 23.265 -20.478 -31.135 1 54.82 ? N1 IMD 2025 B 1 
HETATM 2 C C2 IMD . . . H 3 23.371 -19.331 -30.485 1 57.67 ? C2 IMD 2025 B 1 
HETATM 3 N N3 IMD . . . H 3 23.379 -19.565 -29.141 1 56.25 ? N3 IMD 2025 B 1 
HETATM 4 C C4 IMD . . . H 3 23.274 -20.917 -28.956 1 55.37 ? C4 IMD 2025 B 1 
HETATM 5 C C5 IMD . . . H 3 23.2 -21.514 -30.171 1 56.04 ? C5 IMD 2025 B 1 
#
_model_server_stats.io_time_ms              9 
_model_server_stats.parse_time_ms           8 
_model_server_stats.create_model_time_ms    27 
_model_server_stats.query_time_ms           230 
_model_server_stats.encode_time_ms          3 
_model_server_stats.element_count           5 
#