data_7EFM # _model_server_result.job_id yW-MWcrYR6nRRvP-jdo7RQ _model_server_result.datetime_utc '2024-11-15 15:18:25' _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 7efm # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"F","auth_seq_id":1104}' # _entry.id 7EFM # _exptl.entry_id 7EFM _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 309.362 _entity.id 5 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description (7R,8R,9S)-2,3-dimethyl-9-phenyl-7,8,9,10-tetrahydroimidazo[1,2-h][1,7]naphthyridine-7,8-diol _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 120 _cell.entry_id 7EFM _cell.length_a 104.69 _cell.length_b 104.69 _cell.length_c 368.02 _cell.Z_PDB 6 _cell.pdbx_unique_axis ? # _symmetry.entry_id 7EFM _symmetry.cell_setting ? _symmetry.Int_Tables_number 152 _symmetry.space_group_name_Hall 'P 31 2"' _symmetry.space_group_name_H-M 'P 31 2 1' # _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,G,H,I,J _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 5 _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 B SG CYS 102 B CYS 131 1_555 B SG CYS 123 B CYS 152 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.035 ? disulf ? disulf2 B SG CYS 172 B CYS 201 1_555 B SG CYS 233 B CYS 262 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.043 ? covale ? covale1 A C SER 338 A SER 384 1_555 A N BFD 339 A BFD 385 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.333 ? covale ? covale2 A C BFD 339 A BFD 385 1_555 A N LYS 340 A LYS 386 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.338 ? covale ? covale3 B ND2 ASN 70 B ASN 99 1_555 H C1 NAG . B NAG 301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.448 ? covale ? covale4 B ND2 ASN 101 B ASN 130 1_555 I C1 NAG . B NAG 302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.464 ? covale ? covale5 B ND2 ASN 132 B ASN 161 1_555 J C1 NAG . B NAG 303 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.45 ? metalc ? metalc1 A O ASP 137 A ASP 183 1_555 E RB RB . A RB 1103 6_655 ? ? ? ? ? ? ? ? ? ? ? ? 3.067 ? metalc ? metalc2 A OD1 ASP 139 A ASP 185 1_555 E RB RB . A RB 1103 6_655 ? ? ? ? ? ? ? ? ? ? ? ? 2.877 ? metalc ? metalc3 A O VAL 295 A VAL 341 1_555 G RB RB . A RB 1105 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 3.097 ? metalc ? metalc4 A OE1 GLU 297 A GLU 343 1_555 G RB RB . A RB 1105 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 3.036 ? metalc ? metalc5 A OD2 BFD 339 A BFD 385 1_555 C MG MG . A MG 1101 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.193 ? metalc ? metalc6 A O THR 341 A THR 387 1_555 C MG MG . A MG 1101 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.35 ? metalc ? metalc7 A O SER 362 A SER 408 1_555 E RB RB . A RB 1103 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.737 ? metalc ? metalc8 A O GLN 372 A GLN 418 1_555 E RB RB . A RB 1103 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.936 ? metalc ? metalc9 A OD1 ASP 680 A ASP 726 1_555 C MG MG . A MG 1101 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.221 ? metalc ? metalc10 A O LEU 688 A LEU 734 1_555 D RB RB . A RB 1102 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 3.137 ? metalc ? metalc11 A O LYS 689 A LYS 735 1_555 D RB RB . A RB 1102 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.828 ? metalc ? metalc12 A O ALA 691 A ALA 737 1_555 D RB RB . A RB 1102 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.819 ? metalc ? metalc13 A OD2 ASP 710 A ASP 756 1_555 D RB RB . A RB 1102 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.885 ? metalc ? metalc14 A OD1 ASN 746 A ASN 792 1_555 G RB RB . A RB 1105 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.895 ? metalc ? metalc15 A OE1 GLU 749 A GLU 795 1_555 G RB RB . A RB 1105 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 3.122 ? metalc ? metalc16 A OD2 ASP 774 A ASP 820 1_555 G RB RB . A RB 1105 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.936 ? # _chem_comp.formula 'C18 H19 N3 O2' _chem_comp.formula_weight 309.362 _chem_comp.id J3C _chem_comp.mon_nstd_flag . _chem_comp.name (7R,8R,9S)-2,3-dimethyl-9-phenyl-7,8,9,10-tetrahydroimidazo[1,2-h][1,7]naphthyridine-7,8-diol _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 O1 C6 J3C sing 189 n n O2 C11 J3C sing 190 n n C6 C3 J3C sing 191 n n C6 C11 J3C sing 192 n n C2 C3 J3C sing 193 n y C2 C1 J3C doub 194 n y C3 C4 J3C doub 195 n y C11 C12 J3C sing 196 n n C1 N1 J3C sing 197 n y C4 N3 J3C sing 198 n n C4 C5 J3C sing 199 n y N1 C5 J3C sing 200 n y N1 C8 J3C sing 201 n y C18 C17 J3C doub 202 n y C18 C13 J3C sing 203 n y C12 N3 J3C sing 204 n n C12 C13 J3C sing 205 n n C5 N2 J3C doub 206 n y C17 C16 J3C sing 207 n y C13 C14 J3C doub 208 n y C10 C8 J3C sing 209 n n C8 C7 J3C doub 210 n y N2 C7 J3C sing 211 n y C7 C9 J3C sing 212 n n C16 C15 J3C doub 213 n y C14 C15 J3C sing 214 n y C10 H1 J3C sing 215 n n C10 H2 J3C sing 216 n n C10 H3 J3C sing 217 n n C11 H4 J3C sing 218 n n C12 H5 J3C sing 219 n n C14 H6 J3C sing 220 n n C15 H7 J3C sing 221 n n C16 H8 J3C sing 222 n n C17 H9 J3C sing 223 n n C18 H10 J3C sing 224 n n C1 H11 J3C sing 225 n n C2 H12 J3C sing 226 n n C6 H13 J3C sing 227 n n C9 H14 J3C sing 228 n n C9 H15 J3C sing 229 n n C9 H16 J3C sing 230 n n N3 H17 J3C sing 231 n n O1 H18 J3C sing 232 n n O2 H19 J3C sing 233 n n # _atom_sites.entry_id 7EFM _atom_sites.fract_transf_matrix[1][1] 0.009552 _atom_sites.fract_transf_matrix[1][2] 0.005515 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.01103 _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] 0.002717 _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 3 MG A 1 1101 1102 MG MG . D 4 RB A 1 1102 1105 RB RB . E 4 RB A 1 1103 1106 RB RB . F 5 J3C A 1 1104 1 J3C BYK . G 4 RB A 1 1105 1 RB RB . H 6 NAG B 1 301 301 NAG NAG . I 6 NAG B 1 302 302 NAG NAG . J 6 NAG B 1 303 303 NAG NAG . # 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 C10 J3C . . . F 5 50.578 -11.741 -6.536 1 90.86 ? C10 J3C 1104 A 1 HETATM 2 C C11 J3C . . . F 5 48.574 -18.591 -9.115 1 81.02 ? C11 J3C 1104 A 1 HETATM 3 C C12 J3C . . . F 5 48.572 -18.54 -7.576 1 75.6 ? C12 J3C 1104 A 1 HETATM 4 C C13 J3C . . . F 5 47.647 -19.44 -6.82 1 73.99 ? C13 J3C 1104 A 1 HETATM 5 C C14 J3C . . . F 5 48.046 -19.893 -5.559 1 71.29 ? C14 J3C 1104 A 1 HETATM 6 C C15 J3C . . . F 5 47.222 -20.708 -4.786 1 68.24 ? C15 J3C 1104 A 1 HETATM 7 C C16 J3C . . . F 5 45.974 -21.09 -5.262 1 68.55 ? C16 J3C 1104 A 1 HETATM 8 C C17 J3C . . . F 5 45.573 -20.654 -6.521 1 71.04 ? C17 J3C 1104 A 1 HETATM 9 C C18 J3C . . . F 5 46.395 -19.827 -7.291 1 73.16 ? C18 J3C 1104 A 1 HETATM 10 C C1 J3C . . . F 5 50.592 -14.135 -8.56 1 79.48 ? C1 J3C 1104 A 1 HETATM 11 C C2 J3C . . . F 5 50.478 -15.284 -9.345 1 78.09 ? C2 J3C 1104 A 1 HETATM 12 C C3 J3C . . . F 5 49.703 -16.356 -8.899 1 81.49 ? C3 J3C 1104 A 1 HETATM 13 C C4 J3C . . . F 5 49.073 -16.22 -7.667 1 80.09 ? C4 J3C 1104 A 1 HETATM 14 C C5 J3C . . . F 5 49.226 -15.061 -6.93 1 82.29 ? C5 J3C 1104 A 1 HETATM 15 C C6 J3C . . . F 5 49.58 -17.609 -9.711 1 82.6 ? C6 J3C 1104 A 1 HETATM 16 C C7 J3C . . . F 5 49.112 -13.503 -5.404 1 81.52 ? C7 J3C 1104 A 1 HETATM 17 C C8 J3C . . . F 5 49.906 -13.073 -6.459 1 84.13 ? C8 J3C 1104 A 1 HETATM 18 C C9 J3C . . . F 5 48.759 -12.759 -4.135 1 74.39 ? C9 J3C 1104 A 1 HETATM 19 N N1 J3C . . . F 5 49.969 -14.042 -7.378 1 81.85 ? N1 J3C 1104 A 1 HETATM 20 N N2 J3C . . . F 5 48.703 -14.742 -5.729 1 84.11 ? N2 J3C 1104 A 1 HETATM 21 N N3 J3C . . . F 5 48.312 -17.192 -7.136 1 76.1 ? N3 J3C 1104 A 1 HETATM 22 O O1 J3C . . . F 5 50.832 -18.3 -9.819 1 81.25 ? O1 J3C 1104 A 1 HETATM 23 O O2 J3C . . . F 5 47.328 -18.215 -9.697 1 88.25 ? O2 J3C 1104 A 1 # _model_server_stats.io_time_ms 133 _model_server_stats.parse_time_ms 31 _model_server_stats.create_model_time_ms 20 _model_server_stats.query_time_ms 284 _model_server_stats.encode_time_ms 5 _model_server_stats.element_count 23 #