data_101D
#
_model_server_result.job_id            kRefdVxxMskDJNBeC-2CPw 
_model_server_result.datetime_utc      '2024-11-12 20:38:31' 
_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          101d 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"D","auth_seq_id":25}' 
#
_entry.id    101D 
#
_exptl.entry_id    101D 
_exptl.method      'X-RAY DIFFRACTION' 
#
_entity.details                     ? 
_entity.formula_weight              430.464 
_entity.id                          3 
_entity.src_method                  syn 
_entity.type                        non-polymer 
_entity.pdbx_description            NETROPSIN 
_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            101D 
_cell.length_a            24.27 
_cell.length_b            39.62 
_cell.length_c            63.57 
_cell.Z_PDB               8 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 101D 
_symmetry.cell_setting             ? 
_symmetry.Int_Tables_number        19 
_symmetry.space_group_name_Hall    . 
_symmetry.space_group_name_H-M     'P 21 21 21' 
#
_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 
#
_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
covale ? covale1 A O3' DT 8 A DT 8 1_555 A P CBR 9 A CBR 9 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.624 ? 
covale ? covale2 A O3' CBR 9 A CBR 9 1_555 A P DG 10 A DG 10 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.551 ? 
covale ? covale3 B O3' DT 8 B DT 20 1_555 B P CBR 9 B CBR 21 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.578 ? 
covale ? covale4 B O3' CBR 9 B CBR 21 1_555 B P DG 10 B DG 22 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.595 ? 
metalc ? metalc1 C MG MG . A MG 26 1_555 E O HOH . A HOH 61 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.164 ? 
metalc ? metalc2 C MG MG . A MG 26 1_555 F O HOH . B HOH 60 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.101 ? 
metalc ? metalc3 C MG MG . A MG 26 1_555 F O HOH . B HOH 62 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.11 ? 
hydrog WATSON-CRICK hydrog1 A N3 DC 1 A DC 1 1_555 B N1 DG 12 B DG 24 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? 
hydrog WATSON-CRICK hydrog2 A N4 DC 1 A DC 1 1_555 B O6 DG 12 B DG 24 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? 
hydrog WATSON-CRICK hydrog3 A O2 DC 1 A DC 1 1_555 B N2 DG 12 B DG 24 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? 
hydrog WATSON-CRICK hydrog4 A N1 DG 2 A DG 2 1_555 B N3 DC 11 B DC 23 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? 
hydrog WATSON-CRICK hydrog5 A N2 DG 2 A DG 2 1_555 B O2 DC 11 B DC 23 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? 
hydrog WATSON-CRICK hydrog6 A O6 DG 2 A DG 2 1_555 B N4 DC 11 B DC 23 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? 
hydrog WATSON-CRICK hydrog7 A N3 DC 3 A DC 3 1_555 B N1 DG 10 B DG 22 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? 
hydrog WATSON-CRICK hydrog8 A N4 DC 3 A DC 3 1_555 B O6 DG 10 B DG 22 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? 
hydrog WATSON-CRICK hydrog9 A O2 DC 3 A DC 3 1_555 B N2 DG 10 B DG 22 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? 
hydrog WATSON-CRICK hydrog10 A N1 DG 4 A DG 4 1_555 B N3 CBR 9 B CBR 21 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? 
hydrog WATSON-CRICK hydrog11 A N2 DG 4 A DG 4 1_555 B O2 CBR 9 B CBR 21 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? 
hydrog WATSON-CRICK hydrog12 A O6 DG 4 A DG 4 1_555 B N4 CBR 9 B CBR 21 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? 
hydrog WATSON-CRICK hydrog13 A N1 DA 5 A DA 5 1_555 B N3 DT 8 B DT 20 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? 
hydrog WATSON-CRICK hydrog14 A N6 DA 5 A DA 5 1_555 B O4 DT 8 B DT 20 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? 
hydrog WATSON-CRICK hydrog15 A N1 DA 6 A DA 6 1_555 B N3 DT 7 B DT 19 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? 
hydrog WATSON-CRICK hydrog16 A N6 DA 6 A DA 6 1_555 B O4 DT 7 B DT 19 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? 
hydrog WATSON-CRICK hydrog17 A N3 DT 7 A DT 7 1_555 B N1 DA 6 B DA 18 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? 
hydrog WATSON-CRICK hydrog18 A O4 DT 7 A DT 7 1_555 B N6 DA 6 B DA 18 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? 
hydrog WATSON-CRICK hydrog19 A N3 DT 8 A DT 8 1_555 B N1 DA 5 B DA 17 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? 
hydrog WATSON-CRICK hydrog20 A O4 DT 8 A DT 8 1_555 B N6 DA 5 B DA 17 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? 
hydrog WATSON-CRICK hydrog21 A N3 CBR 9 A CBR 9 1_555 B N1 DG 4 B DG 16 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? 
hydrog WATSON-CRICK hydrog22 A N4 CBR 9 A CBR 9 1_555 B O6 DG 4 B DG 16 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? 
hydrog WATSON-CRICK hydrog23 A O2 CBR 9 A CBR 9 1_555 B N2 DG 4 B DG 16 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? 
hydrog WATSON-CRICK hydrog24 A N1 DG 10 A DG 10 1_555 B N3 DC 3 B DC 15 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? 
hydrog WATSON-CRICK hydrog25 A N2 DG 10 A DG 10 1_555 B O2 DC 3 B DC 15 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? 
hydrog WATSON-CRICK hydrog26 A O6 DG 10 A DG 10 1_555 B N4 DC 3 B DC 15 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? 
hydrog WATSON-CRICK hydrog27 A N3 DC 11 A DC 11 1_555 B N1 DG 2 B DG 14 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? 
hydrog WATSON-CRICK hydrog28 A N4 DC 11 A DC 11 1_555 B O6 DG 2 B DG 14 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? 
hydrog WATSON-CRICK hydrog29 A O2 DC 11 A DC 11 1_555 B N2 DG 2 B DG 14 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? 
hydrog WATSON-CRICK hydrog30 A N1 DG 12 A DG 12 1_555 B N3 DC 1 B DC 13 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? 
hydrog WATSON-CRICK hydrog31 A N2 DG 12 A DG 12 1_555 B O2 DC 1 B DC 13 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? 
hydrog WATSON-CRICK hydrog32 A O6 DG 12 A DG 12 1_555 B N4 DC 1 B DC 13 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? 
#
_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 187 n n 
C1 N2 NT sing 188 n n 
C1 N3 NT sing 189 n n 
N1 HN1 NT sing 190 n n 
N2 HN21 NT sing 191 n n 
N2 HN22 NT sing 192 n n 
N3 C2 NT sing 193 n n 
N3 HN3 NT sing 194 n n 
C2 C3 NT sing 195 n n 
C2 H21 NT sing 196 n n 
C2 H22 NT sing 197 n n 
C3 O1 NT doub 198 n n 
C3 N4 NT sing 199 n n 
N4 C4 NT sing 200 n n 
N4 HN4 NT sing 201 n n 
C4 C5 NT sing 202 n y 
C4 C7 NT doub 203 n y 
C5 C6 NT doub 204 n y 
C5 H5 NT sing 205 n n 
C6 N5 NT sing 206 n y 
C6 C9 NT sing 207 n n 
N5 C8 NT sing 208 n n 
N5 C7 NT sing 209 n y 
C8 H81 NT sing 210 n n 
C8 H82 NT sing 211 n n 
C8 H83 NT sing 212 n n 
C7 H7 NT sing 213 n n 
C9 O2 NT doub 214 n n 
C9 N6 NT sing 215 n n 
N6 C10 NT sing 216 n n 
N6 HN6 NT sing 217 n n 
C10 C11 NT sing 218 n y 
C10 C13 NT doub 219 n y 
C11 C12 NT doub 220 n y 
C11 H11 NT sing 221 n n 
C12 N7 NT sing 222 n y 
C12 C15 NT sing 223 n n 
N7 C14 NT sing 224 n n 
N7 C13 NT sing 225 n y 
C14 H141 NT sing 226 n n 
C14 H142 NT sing 227 n n 
C14 H143 NT sing 228 n n 
C13 H13 NT sing 229 n n 
C15 O3 NT doub 230 n n 
C15 N8 NT sing 231 n n 
N8 C16 NT sing 232 n n 
N8 HN8 NT sing 233 n n 
C16 C17 NT sing 234 n n 
C16 H161 NT sing 235 n n 
C16 H162 NT sing 236 n n 
C17 C18 NT sing 237 n n 
C17 H171 NT sing 238 n n 
C17 H172 NT sing 239 n n 
C18 N9 NT doub 240 n n 
C18 N10 NT sing 241 n n 
N9 HN9 NT sing 242 n n 
N10 HN01 NT sing 243 n n 
N10 HN02 NT sing 244 n n 
#
_atom_sites.entry_id                     101D 
_atom_sites.fract_transf_matrix[1][1]    0.041203 
_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]    0.02524 
_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]    0.015731 
_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 MG A 1 26 26 MG MO3 . 
D 3 NT B 1 25 25 NT NT . 
E 4 HOH A 1 27 27 HOH HOH . 
E 4 HOH A 2 28 28 HOH HOH . 
E 4 HOH A 3 33 33 HOH HOH . 
E 4 HOH A 4 34 34 HOH HOH . 
E 4 HOH A 5 35 35 HOH HOH . 
E 4 HOH A 6 39 39 HOH HOH . 
E 4 HOH A 7 44 44 HOH HOH . 
E 4 HOH A 8 46 46 HOH HOH . 
E 4 HOH A 9 48 48 HOH HOH . 
E 4 HOH A 10 52 52 HOH HOH . 
E 4 HOH A 11 53 53 HOH HOH . 
E 4 HOH A 12 54 54 HOH HOH . 
E 4 HOH A 13 59 59 HOH HOH . 
E 4 HOH A 14 61 26 HOH MO3 . 
F 4 HOH B 1 29 29 HOH HOH . 
F 4 HOH B 2 30 30 HOH HOH . 
F 4 HOH B 3 31 31 HOH HOH . 
F 4 HOH B 4 32 32 HOH HOH . 
F 4 HOH B 5 36 36 HOH HOH . 
F 4 HOH B 6 37 37 HOH HOH . 
F 4 HOH B 7 38 38 HOH HOH . 
F 4 HOH B 8 40 40 HOH HOH . 
F 4 HOH B 9 41 41 HOH HOH . 
F 4 HOH B 10 42 42 HOH HOH . 
F 4 HOH B 11 43 43 HOH HOH . 
F 4 HOH B 12 45 45 HOH HOH . 
F 4 HOH B 13 47 47 HOH HOH . 
F 4 HOH B 14 49 49 HOH HOH . 
F 4 HOH B 15 50 50 HOH HOH . 
F 4 HOH B 16 51 51 HOH HOH . 
F 4 HOH B 17 55 55 HOH HOH . 
F 4 HOH B 18 56 56 HOH HOH . 
F 4 HOH B 19 57 57 HOH HOH . 
F 4 HOH B 20 58 58 HOH HOH . 
F 4 HOH B 21 60 26 HOH MO3 . 
F 4 HOH B 22 62 26 HOH MO3 . 
#
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 3 10.388 19.251 16.217 1 28.86 ? C1 NT 25 B 1 
HETATM 2 N N1 NT . . . D 3 11.57 18.812 16.07 1 26.98 ? N1 NT 25 B 1 
HETATM 3 N N2 NT . . . D 3 9.754 19.105 17.316 1 29.03 ? N2 NT 25 B 1 
HETATM 4 N N3 NT . . . D 3 9.861 19.846 15.231 1 31.99 ? N3 NT 25 B 1 
HETATM 5 C C2 NT . . . D 3 10.371 20.123 13.915 1 29.06 ? C2 NT 25 B 1 
HETATM 6 C C3 NT . . . D 3 9.147 20.484 13.038 1 27.54 ? C3 NT 25 B 1 
HETATM 7 O O1 NT . . . D 3 8.024 19.996 13.248 1 18.33 ? O1 NT 25 B 1 
HETATM 8 N N4 NT . . . D 3 9.465 21.339 12.11 1 27.55 ? N4 NT 25 B 1 
HETATM 9 C C4 NT . . . D 3 8.485 21.787 11.22 1 29.42 ? C4 NT 25 B 1 
HETATM 10 C C5 NT . . . D 3 8.917 22.465 10.114 1 31.2 ? C5 NT 25 B 1 
HETATM 11 C C6 NT . . . D 3 7.82 22.805 9.383 1 32.91 ? C6 NT 25 B 1 
HETATM 12 N N5 NT . . . D 3 6.732 22.369 10.025 1 31.39 ? N5 NT 25 B 1 
HETATM 13 C C8 NT . . . D 3 5.313 22.512 9.624 1 31.13 ? C8 NT 25 B 1 
HETATM 14 C C7 NT . . . D 3 7.143 21.728 11.176 1 28.87 ? C7 NT 25 B 1 
HETATM 15 C C9 NT . . . D 3 7.701 23.59 8.124 1 33.53 ? C9 NT 25 B 1 
HETATM 16 O O2 NT . . . D 3 6.822 24.469 8.042 1 40.41 ? O2 NT 25 B 1 
HETATM 17 N N6 NT . . . D 3 8.519 23.388 7.158 1 34.19 ? N6 NT 25 B 1 
HETATM 18 C C10 NT . . . D 3 8.436 24.144 5.918 1 35.1 ? C10 NT 25 B 1 
HETATM 19 C C11 NT . . . D 3 9.344 23.911 4.876 1 36.86 ? C11 NT 25 B 1 
HETATM 20 C C12 NT . . . D 3 8.98 24.79 3.865 1 34.66 ? C12 NT 25 B 1 
HETATM 21 N N7 NT . . . D 3 7.888 25.539 4.278 1 32.61 ? N7 NT 25 B 1 
HETATM 22 C C14 NT . . . D 3 7.198 26.573 3.547 1 32.87 ? C14 NT 25 B 1 
HETATM 23 C C13 NT . . . D 3 7.589 25.131 5.518 1 31.93 ? C13 NT 25 B 1 
HETATM 24 C C15 NT . . . D 3 9.623 25.004 2.587 1 32.56 ? C15 NT 25 B 1 
HETATM 25 O O3 NT . . . D 3 9.259 25.9 1.863 1 36.71 ? O3 NT 25 B 1 
HETATM 26 N N8 NT . . . D 3 10.667 24.212 2.403 1 35.36 ? N8 NT 25 B 1 
HETATM 27 C C16 NT . . . D 3 11.582 24.172 1.246 1 38.28 ? C16 NT 25 B 1 
HETATM 28 C C17 NT . . . D 3 11.951 25.511 0.737 1 39.05 ? C17 NT 25 B 1 
HETATM 29 C C18 NT . . . D 3 12.754 25.408 -0.572 1 45.66 ? C18 NT 25 B 1 
HETATM 30 N N9 NT . . . D 3 12.407 26.121 -1.627 1 42.63 ? N9 NT 25 B 1 
HETATM 31 N N10 NT . . . D 3 13.773 24.596 -0.566 1 43.85 ? N10 NT 25 B 1 
#
_model_server_stats.io_time_ms              10 
_model_server_stats.parse_time_ms           5 
_model_server_stats.create_model_time_ms    1 
_model_server_stats.query_time_ms           246 
_model_server_stats.encode_time_ms          1 
_model_server_stats.element_count           31 
#