data_358D
#
_model_server_result.job_id            OR9jM8F_hxhjwGsBIV65NA 
_model_server_result.datetime_utc      '2025-01-11 06:53:49' 
_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          358d 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"D","auth_seq_id":22}' 
#
_entry.id    358D 
#
_exptl.entry_id    358D 
_exptl.method      'X-RAY DIFFRACTION' 
#
_entity.details                     ? 
_entity.formula_weight              430.464 
_entity.id                          2 
_entity.src_method                  syn 
_entity.type                        non-polymer 
_entity.pdbx_description            NETROPSIN 
_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 
_cell.angle_gamma         120 
_cell.entry_id            358D 
_cell.length_a            32.13 
_cell.length_b            32.13 
_cell.length_c            143.92 
_cell.Z_PDB               12 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 358D 
_symmetry.cell_setting             ? 
_symmetry.Int_Tables_number        169 
_symmetry.space_group_name_Hall    . 
_symmetry.space_group_name_H-M     'P 61' 
#
_pdbx_struct_assembly.method_details        ? 
_pdbx_struct_assembly.oligomeric_details    dimeric 
_pdbx_struct_assembly.oligomeric_count      2 
_pdbx_struct_assembly.details               author_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 
#
_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 ? covale1 A O3' DC 1 A DC 1 1_555 A P CBR 2 A CBR 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.612 ? 
covale ? covale2 A O3' CBR 2 A CBR 2 1_555 A P DC 3 A DC 3 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.611 ? 
covale ? covale3 B O3' DC 1 B DC 11 1_555 B P CBR 2 B CBR 12 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.608 ? 
covale ? covale4 B O3' CBR 2 B CBR 12 1_555 B P DC 3 B DC 13 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.609 ? 
#
_chem_comp.formula           'C18 H26 N10 O3' 
_chem_comp.formula_weight    430.464 
_chem_comp.id                NT 
_chem_comp.mon_nstd_flag     . 
_chem_comp.name              NETROPSIN 
_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 N1 NT doub 110 n n 
C1 N2 NT sing 111 n n 
C1 N3 NT sing 112 n n 
N1 HN1 NT sing 113 n n 
N2 HN21 NT sing 114 n n 
N2 HN22 NT sing 115 n n 
N3 C2 NT sing 116 n n 
N3 HN3 NT sing 117 n n 
C2 C3 NT sing 118 n n 
C2 H21 NT sing 119 n n 
C2 H22 NT sing 120 n n 
C3 O1 NT doub 121 n n 
C3 N4 NT sing 122 n n 
N4 C4 NT sing 123 n n 
N4 HN4 NT sing 124 n n 
C4 C5 NT sing 125 n y 
C4 C7 NT doub 126 n y 
C5 C6 NT doub 127 n y 
C5 H5 NT sing 128 n n 
C6 N5 NT sing 129 n y 
C6 C9 NT sing 130 n n 
N5 C8 NT sing 131 n n 
N5 C7 NT sing 132 n y 
C8 H81 NT sing 133 n n 
C8 H82 NT sing 134 n n 
C8 H83 NT sing 135 n n 
C7 H7 NT sing 136 n n 
C9 O2 NT doub 137 n n 
C9 N6 NT sing 138 n n 
N6 C10 NT sing 139 n n 
N6 HN6 NT sing 140 n n 
C10 C11 NT sing 141 n y 
C10 C13 NT doub 142 n y 
C11 C12 NT doub 143 n y 
C11 H11 NT sing 144 n n 
C12 N7 NT sing 145 n y 
C12 C15 NT sing 146 n n 
N7 C14 NT sing 147 n n 
N7 C13 NT sing 148 n y 
C14 H141 NT sing 149 n n 
C14 H142 NT sing 150 n n 
C14 H143 NT sing 151 n n 
C13 H13 NT sing 152 n n 
C15 O3 NT doub 153 n n 
C15 N8 NT sing 154 n n 
N8 C16 NT sing 155 n n 
N8 HN8 NT sing 156 n n 
C16 C17 NT sing 157 n n 
C16 H161 NT sing 158 n n 
C16 H162 NT sing 159 n n 
C17 C18 NT sing 160 n n 
C17 H171 NT sing 161 n n 
C17 H172 NT sing 162 n n 
C18 N9 NT doub 163 n n 
C18 N10 NT sing 164 n n 
N9 HN9 NT sing 165 n n 
N10 HN01 NT sing 166 n n 
N10 HN02 NT sing 167 n n 
#
_atom_sites.entry_id                     358D 
_atom_sites.fract_transf_matrix[1][1]    0.031124 
_atom_sites.fract_transf_matrix[1][2]    0.017969 
_atom_sites.fract_transf_matrix[1][3]    0 
_atom_sites.fract_transf_matrix[2][1]    0 
_atom_sites.fract_transf_matrix[2][2]    0.035938 
_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]    0.006948 
_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 NT A 1 21 21 NT NT . 
D 2 NT A 1 22 22 NT NT . 
E 3 HOH A 1 23 23 HOH HOH . 
E 3 HOH A 2 24 24 HOH HOH . 
E 3 HOH A 3 25 25 HOH HOH . 
E 3 HOH A 4 26 26 HOH HOH . 
E 3 HOH A 5 30 30 HOH HOH . 
E 3 HOH A 6 32 32 HOH HOH . 
E 3 HOH A 7 33 33 HOH HOH . 
E 3 HOH A 8 34 34 HOH HOH . 
E 3 HOH A 9 37 37 HOH HOH . 
E 3 HOH A 10 38 38 HOH HOH . 
E 3 HOH A 11 39 39 HOH HOH . 
E 3 HOH A 12 40 40 HOH HOH . 
E 3 HOH A 13 41 41 HOH HOH . 
E 3 HOH A 14 43 43 HOH HOH . 
E 3 HOH A 15 45 45 HOH HOH . 
E 3 HOH A 16 49 49 HOH HOH . 
E 3 HOH A 17 51 51 HOH HOH . 
E 3 HOH A 18 52 52 HOH HOH . 
E 3 HOH A 19 53 53 HOH HOH . 
E 3 HOH A 20 54 54 HOH HOH . 
E 3 HOH A 21 55 55 HOH HOH . 
E 3 HOH A 22 56 56 HOH HOH . 
E 3 HOH A 23 57 57 HOH HOH . 
E 3 HOH A 24 60 60 HOH HOH . 
F 3 HOH B 1 27 27 HOH HOH . 
F 3 HOH B 2 28 28 HOH HOH . 
F 3 HOH B 3 29 29 HOH HOH . 
F 3 HOH B 4 31 31 HOH HOH . 
F 3 HOH B 5 35 35 HOH HOH . 
F 3 HOH B 6 36 36 HOH HOH . 
F 3 HOH B 7 42 42 HOH HOH . 
F 3 HOH B 8 44 44 HOH HOH . 
F 3 HOH B 9 46 46 HOH HOH . 
F 3 HOH B 10 47 47 HOH HOH . 
F 3 HOH B 11 48 48 HOH HOH . 
F 3 HOH B 12 50 50 HOH HOH . 
F 3 HOH B 13 58 58 HOH HOH . 
F 3 HOH B 14 59 59 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 NT . . . D 2 1.786 21.657 6.591 1 9.37 ? C1 NT 22 A 1 
HETATM 2 N N1 NT . . . D 2 1.883 21.505 7.91 1 10.44 ? N1 NT 22 A 1 
HETATM 3 N N2 NT . . . D 2 1.812 20.59 5.784 1 2.41 ? N2 NT 22 A 1 
HETATM 4 N N3 NT . . . D 2 1.682 22.889 6.095 1 9.23 ? N3 NT 22 A 1 
HETATM 5 C C2 NT . . . D 2 2.794 23.358 5.302 1 6.36 ? C2 NT 22 A 1 
HETATM 6 C C3 NT . . . D 2 3.215 24.756 5.705 1 5.91 ? C3 NT 22 A 1 
HETATM 7 O O1 NT . . . D 2 2.892 25.097 6.841 1 10.93 ? O1 NT 22 A 1 
HETATM 8 N N4 NT . . . D 2 3.9 25.526 4.838 1 7.2 ? N4 NT 22 A 1 
HETATM 9 C C4 NT . . . D 2 4.372 26.796 5.168 1 14.59 ? C4 NT 22 A 1 
HETATM 10 C C5 NT . . . D 2 4.644 27.844 4.298 1 14.5 ? C5 NT 22 A 1 
HETATM 11 C C6 NT . . . D 2 5.137 28.932 4.999 1 14.73 ? C6 NT 22 A 1 
HETATM 12 N N5 NT . . . D 2 5.152 28.516 6.371 1 15.98 ? N5 NT 22 A 1 
HETATM 13 C C8 NT . . . D 2 5.577 29.219 7.655 1 17.18 ? C8 NT 22 A 1 
HETATM 14 C C7 NT . . . D 2 4.706 27.263 6.477 1 10.5 ? C7 NT 22 A 1 
HETATM 15 C C9 NT . . . D 2 5.61 30.223 4.465 1 13.83 ? C9 NT 22 A 1 
HETATM 16 O O2 NT . . . D 2 6.577 30.784 4.986 1 7.61 ? O2 NT 22 A 1 
HETATM 17 N N6 NT . . . D 2 4.915 30.692 3.392 1 10.43 ? N6 NT 22 A 1 
HETATM 18 C C10 NT . . . D 2 5.073 31.854 2.604 1 11.84 ? C10 NT 22 A 1 
HETATM 19 C C11 NT . . . D 2 4.196 32.244 1.598 1 13.56 ? C11 NT 22 A 1 
HETATM 20 C C12 NT . . . D 2 4.633 33.406 0.982 1 13.89 ? C12 NT 22 A 1 
HETATM 21 N N7 NT . . . D 2 5.822 33.761 1.618 1 8.83 ? N7 NT 22 A 1 
HETATM 22 C C14 NT . . . D 2 6.769 34.936 1.368 1 5.37 ? C14 NT 22 A 1 
HETATM 23 C C13 NT . . . D 2 6.093 32.863 2.576 1 8.5 ? C13 NT 22 A 1 
HETATM 24 C C15 NT . . . D 2 4.022 34.167 -0.134 1 13.33 ? C15 NT 22 A 1 
HETATM 25 O O3 NT . . . D 2 4.292 35.343 -0.398 1 11.25 ? O3 NT 22 A 1 
HETATM 26 N N8 NT . . . D 2 3.104 33.509 -0.904 1 10.99 ? N8 NT 22 A 1 
HETATM 27 C C16 NT . . . D 2 2.439 34.107 -2.075 1 11.29 ? C16 NT 22 A 1 
HETATM 28 C C17 NT . . . D 2 1.735 35.426 -2.325 1 9.86 ? C17 NT 22 A 1 
HETATM 29 C C18 NT . . . D 2 1.846 35.824 -3.785 1 2.99 ? C18 NT 22 A 1 
HETATM 30 N N9 NT . . . D 2 0.934 35.451 -4.672 1 3.91 ? N9 NT 22 A 1 
HETATM 31 N N10 NT . . . D 2 2.575 36.876 -4.114 1 9.58 ? N10 NT 22 A 1 
#
_model_server_stats.io_time_ms              86 
_model_server_stats.parse_time_ms           6 
_model_server_stats.create_model_time_ms    1 
_model_server_stats.query_time_ms           273 
_model_server_stats.encode_time_ms          4 
_model_server_stats.element_count           31 
#