data_3GK2
#
_model_server_result.job_id            WuvkX9gj6qKRLVkvps5IVw 
_model_server_result.datetime_utc      '2024-11-26 22:40:36' 
_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          3gk2 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"D","auth_seq_id":94}' 
#
_entry.id    3GK2 
#
_exptl.entry_id    3GK2 
_exptl.method      'X-RAY DIFFRACTION' 
#
_entity.details                     ? 
_entity.formula_weight              277.388 
_entity.id                          3 
_entity.src_method                  syn 
_entity.type                        non-polymer 
_entity.pdbx_description            (Z)-2-[2-(4-methylpiperazin-1-yl)benzyl]diazenecarbothioamide 
_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            3GK2 
_cell.length_a            34.224 
_cell.length_b            91.158 
_cell.length_c            58.649 
_cell.Z_PDB               8 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 3GK2 
_symmetry.cell_setting             ? 
_symmetry.Int_Tables_number        20 
_symmetry.space_group_name_Hall    ? 
_symmetry.space_group_name_H-M     'C 2 2 21' 
#
_pdbx_struct_assembly.method_details        PISA 
_pdbx_struct_assembly.oligomeric_details    dimeric 
_pdbx_struct_assembly.oligomeric_count      2 
_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 
#
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 
#
_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 O SER 19 A SER 18 1_555 B CA CA . A CA 92 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.405 ? 
metalc ? metalc2 A O GLU 22 A GLU 21 1_555 B CA CA . A CA 92 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.386 ? 
metalc ? metalc3 A O ASP 24 A ASP 23 1_555 B CA CA . A CA 92 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.346 ? 
metalc ? metalc4 A O LYS 27 A LYS 26 1_555 B CA CA . A CA 92 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.465 ? 
metalc ? metalc5 A OE1 GLU 32 A GLU 31 1_555 B CA CA . A CA 92 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.555 ? 
metalc ? metalc6 A OE2 GLU 32 A GLU 31 1_555 B CA CA . A CA 92 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.989 ? 
metalc ? metalc7 A OD1 ASP 62 A ASP 61 1_555 C CA CA . A CA 93 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.363 ? 
metalc ? metalc8 A OD1 ASP 64 A ASP 63 1_555 C CA CA . A CA 93 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.483 ? 
metalc ? metalc9 A OD1 ASP 66 A ASP 65 1_555 C CA CA . A CA 93 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.248 ? 
metalc ? metalc10 A O GLU 68 A GLU 67 1_555 C CA CA . A CA 93 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.311 ? 
metalc ? metalc11 A OE1 GLU 73 A GLU 72 1_555 C CA CA . A CA 93 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.554 ? 
metalc ? metalc12 A OE2 GLU 73 A GLU 72 1_555 C CA CA . A CA 93 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.766 ? 
metalc ? metalc13 B CA CA . A CA 92 1_555 F O HOH . A HOH 121 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.331 ? 
#
_chem_comp.formula           'C13 H19 N5 S' 
_chem_comp.formula_weight    277.388 
_chem_comp.id                27A 
_chem_comp.mon_nstd_flag     . 
_chem_comp.name              (Z)-2-[2-(4-methylpiperazin-1-yl)benzyl]diazenecarbothioamide 
_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
C1 C2 27A doub 1 n y 
C1 C6 27A sing 2 n y 
C2 C3 27A sing 3 n y 
C3 C4 27A doub 4 n y 
C3 N1 27A sing 5 n n 
C4 C5 27A sing 6 n y 
C4 C12 27A sing 7 n n 
C5 C6 27A doub 8 n y 
C7 C8 27A sing 9 n n 
C7 N1 27A sing 10 n n 
C8 N2 27A sing 11 n n 
C9 C10 27A sing 12 n n 
C9 N2 27A sing 13 n n 
C10 N1 27A sing 14 n n 
C11 N2 27A sing 15 n n 
C12 N3 27A sing 16 n n 
C13 N5 27A sing 17 n n 
C13 S1 27A doub 18 n n 
C13 N4 27A sing 19 n n 
N4 N3 27A doub 20 n n 
C1 H1 27A sing 21 n n 
C2 H2 27A sing 22 n n 
C5 H5 27A sing 23 n n 
C6 H6 27A sing 24 n n 
C7 H7 27A sing 25 n n 
C7 H7A 27A sing 26 n n 
C8 H8 27A sing 27 n n 
C8 H8A 27A sing 28 n n 
C9 H9 27A sing 29 n n 
C9 H9A 27A sing 30 n n 
C10 H10 27A sing 31 n n 
C10 H10A 27A sing 32 n n 
C11 H11 27A sing 33 n n 
C11 H11A 27A sing 34 n n 
C11 H11B 27A sing 35 n n 
C12 H12 27A sing 36 n n 
C12 H12A 27A sing 37 n n 
N5 HN5 27A sing 38 n n 
N5 HN5A 27A sing 39 n n 
#
_atom_sites.entry_id                     3GK2 
_atom_sites.fract_transf_matrix[1][1]    0.029219 
_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]    0.01097 
_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]    0.017051 
_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 CA A 1 92 90 CA CA . 
C 2 CA A 1 93 91 CA CA . 
D 3 27A A 1 94 1 27A 27A . 
E 4 CAC A 1 95 1 CAC CAC . 
F 5 HOH A 1 96 1 HOH HOH . 
F 5 HOH A 2 97 2 HOH HOH . 
F 5 HOH A 3 98 3 HOH HOH . 
F 5 HOH A 4 99 4 HOH HOH . 
F 5 HOH A 5 100 5 HOH HOH . 
F 5 HOH A 6 101 6 HOH HOH . 
F 5 HOH A 7 102 7 HOH HOH . 
F 5 HOH A 8 103 8 HOH HOH . 
F 5 HOH A 9 104 9 HOH HOH . 
F 5 HOH A 10 105 10 HOH HOH . 
F 5 HOH A 11 106 11 HOH HOH . 
F 5 HOH A 12 107 12 HOH HOH . 
F 5 HOH A 13 108 13 HOH HOH . 
F 5 HOH A 14 109 14 HOH HOH . 
F 5 HOH A 15 110 15 HOH HOH . 
F 5 HOH A 16 111 16 HOH HOH . 
F 5 HOH A 17 112 17 HOH HOH . 
F 5 HOH A 18 113 18 HOH HOH . 
F 5 HOH A 19 114 19 HOH HOH . 
F 5 HOH A 20 115 20 HOH HOH . 
F 5 HOH A 21 116 21 HOH HOH . 
F 5 HOH A 22 117 22 HOH HOH . 
F 5 HOH A 23 118 23 HOH HOH . 
F 5 HOH A 24 119 24 HOH HOH . 
F 5 HOH A 25 120 25 HOH HOH . 
F 5 HOH A 26 121 26 HOH HOH . 
F 5 HOH A 27 122 27 HOH HOH . 
F 5 HOH A 28 123 28 HOH HOH . 
F 5 HOH A 29 124 29 HOH HOH . 
F 5 HOH A 30 125 30 HOH HOH . 
F 5 HOH A 31 126 31 HOH HOH . 
F 5 HOH A 32 127 32 HOH HOH . 
F 5 HOH A 33 128 33 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 C1 27A . . . D 3 -0.755 6.806 14.246 0.5 52.54 ? C1 27A 94 A 1 
HETATM 2 C C2 27A . . . D 3 -0.04 7.999 14.332 0.5 52.58 ? C2 27A 94 A 1 
HETATM 3 C C3 27A . . . D 3 1.328 8.047 14.644 0.5 52.46 ? C3 27A 94 A 1 
HETATM 4 C C4 27A . . . D 3 2.028 6.723 14.859 0.5 52.51 ? C4 27A 94 A 1 
HETATM 5 C C5 27A . . . D 3 1.242 5.565 14.796 0.5 52.57 ? C5 27A 94 A 1 
HETATM 6 C C6 27A . . . D 3 -0.121 5.592 14.485 0.5 52.62 ? C6 27A 94 A 1 
HETATM 7 C C7 27A . . . D 3 1.288 10.411 13.917 0.5 52.21 ? C7 27A 94 A 1 
HETATM 8 C C8 27A . . . D 3 1.188 11.655 14.789 0.5 52.15 ? C8 27A 94 A 1 
HETATM 9 C C9 27A . . . D 3 3.642 11.012 14.962 0.5 52.09 ? C9 27A 94 A 1 
HETATM 10 C C10 27A . . . D 3 3.11 9.661 15.461 0.5 52.16 ? C10 27A 94 A 1 
HETATM 11 C C11 27A . . . D 3 2.9 13.379 15.421 0.5 52 ? C11 27A 94 A 1 
HETATM 12 C C12 27A . . . D 3 3.45 6.484 15.267 0.5 52.6 ? C12 27A 94 A 1 
HETATM 13 C C13 27A . . . D 3 5.154 7.226 12.637 0.5 52.67 ? C13 27A 94 A 1 
HETATM 14 N N5 27A . . . D 3 3.926 7.469 12.211 0.5 52.92 ? N5 27A 94 A 1 
HETATM 15 S S1 27A . . . D 3 6.484 7.465 11.618 0.5 52.65 ? S1 27A 94 A 1 
HETATM 16 N N4 27A . . . D 3 5.387 6.788 13.867 0.5 52.64 ? N4 27A 94 A 1 
HETATM 17 N N3 27A . . . D 3 4.665 6.504 14.855 0.5 52.7 ? N3 27A 94 A 1 
HETATM 18 N N1 27A . . . D 3 1.917 9.339 14.683 0.5 52.3 ? N1 27A 94 A 1 
HETATM 19 N N2 27A . . . D 3 2.574 12.009 15.058 0.5 52.09 ? N2 27A 94 A 1 
#
_model_server_stats.io_time_ms              6 
_model_server_stats.parse_time_ms           12 
_model_server_stats.create_model_time_ms    3 
_model_server_stats.query_time_ms           273 
_model_server_stats.encode_time_ms          4 
_model_server_stats.element_count           19 
#