data_2VD5 # _model_server_result.job_id VuXOMg8cA-ZNpgLx4hahmA _model_server_result.datetime_utc '2024-10-13 02:27:22' _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 2vd5 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"D","auth_seq_id":1417}' # _entry.id 2VD5 # _exptl.entry_id 2VD5 _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 398.457 _entity.id 2 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description 3-[1-(3-AMINOPROPYL)-1H-INDOL-3-YL]-4-(1-METHYL-1H-INDOL-3-YL)-1H-PYRROLE-2,5-DIONE _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 2VD5 _cell.length_a 122.599 _cell.length_b 122.599 _cell.length_c 134.278 _cell.Z_PDB 12 _cell.pdbx_unique_axis ? # _symmetry.entry_id 2VD5 _symmetry.cell_setting ? _symmetry.Int_Tables_number 154 _symmetry.space_group_name_Hall . _symmetry.space_group_name_H-M 'P 32 2 1' # loop_ _pdbx_struct_assembly.method_details _pdbx_struct_assembly.oligomeric_details _pdbx_struct_assembly.oligomeric_count _pdbx_struct_assembly.details _pdbx_struct_assembly.id PQS dimeric 2 author_and_software_defined_assembly 1 PQS dimeric 2 author_and_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,C,E 1 1,2 B,D,F 2 1,3 # 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_645 y+1,x-1,-z -0.5 0.866025 0 0.866025 0.5 0 0 0 -1 183.8985 -106.173848 0 3 'crystal symmetry operation' 6_555 -x,-x+y,-z+2/3 -0.5 -0.866025 0 -0.866025 0.5 0 0 0 -1 0 0 89.518667 # 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 disulf ? disulf1 A SG CYS 198 A CYS 206 1_555 B SG CYS 357 B CYS 365 5_545 ? ? ? ? ? ? ? ? ? ? ? ? 2.037 ? disulf ? disulf2 A SG CYS 357 A CYS 365 1_555 B SG CYS 198 B CYS 206 5_545 ? ? ? ? ? ? ? ? ? ? ? ? 2.044 ? # _chem_comp.formula 'C24 H22 N4 O2' _chem_comp.formula_weight 398.457 _chem_comp.id BI8 _chem_comp.mon_nstd_flag . _chem_comp.name 3-[1-(3-AMINOPROPYL)-1H-INDOL-3-YL]-4-(1-METHYL-1H-INDOL-3-YL)-1H-PYRROLE-2,5-DIONE _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 CB0 NAO BI8 sing 70 n n CB0 HB01 BI8 sing 71 n n CB0 HB02 BI8 sing 72 n n CB0 HB03 BI8 sing 73 n n NBC CBB BI8 sing 74 n n NBC HBC1 BI8 sing 75 n n NBC HBC2 BI8 sing 76 n n CBB CBA BI8 sing 77 n n CBB HBB1 BI8 sing 78 n n CBB HBB2 BI8 sing 79 n n CBA CAY BI8 sing 80 n n CBA HBA1 BI8 sing 81 n n CBA HBA2 BI8 sing 82 n n CAY NAH BI8 sing 83 n n CAY HAY1 BI8 sing 84 n n CAY HAY2 BI8 sing 85 n n NAH CAW BI8 sing 86 n y NAH CAE BI8 sing 87 n y CAW CAG BI8 doub 88 n y CAW HAW BI8 sing 89 n n CAE CAF BI8 sing 90 n y CAE CAD BI8 doub 91 n y CAF CAA BI8 doub 92 n y CAF HAF BI8 sing 93 n n CAA CAB BI8 sing 94 n y CAA HAA BI8 sing 95 n n CAB CAC BI8 doub 96 n y CAB HAB BI8 sing 97 n n CAC CAD BI8 sing 98 n y CAC HAC BI8 sing 99 n n CAD CAG BI8 sing 100 n y CAG CAI BI8 sing 101 n n CAI CAT BI8 sing 102 n n CAI CAJ BI8 doub 103 n n CAT OAZ BI8 doub 104 n n CAT NAU BI8 sing 105 n n NAU CAV BI8 sing 106 n n NAU HAU BI8 sing 107 n n CAV OAX BI8 doub 108 n n CAV CAJ BI8 sing 109 n n CAJ CAK BI8 sing 110 n n CAK CAM BI8 sing 111 n y CAK CAL BI8 doub 112 n y CAM CAP BI8 doub 113 n y CAM CAN BI8 sing 114 n y CAP CAQ BI8 sing 115 n y CAP HAP BI8 sing 116 n n CAQ CAR BI8 doub 117 n y CAQ HAQ BI8 sing 118 n n CAR CAS BI8 sing 119 n y CAR HAR BI8 sing 120 n n CAS CAN BI8 doub 121 n y CAS HAS BI8 sing 122 n n CAN NAO BI8 sing 123 n y NAO CAL BI8 sing 124 n y CAL HAL BI8 sing 125 n n # _atom_sites.entry_id 2VD5 _atom_sites.fract_transf_matrix[1][1] 0.008157 _atom_sites.fract_transf_matrix[1][2] 0.004709 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.009419 _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] 0.007447 _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 BI8 A 1 1417 1417 BI8 BI8 . D 2 BI8 B 1 1417 1417 BI8 BI8 . E 3 HOH A 1 2001 2001 HOH HOH . E 3 HOH A 2 2002 2002 HOH HOH . E 3 HOH A 3 2003 2003 HOH HOH . E 3 HOH A 4 2004 2004 HOH HOH . E 3 HOH A 5 2005 2005 HOH HOH . E 3 HOH A 6 2006 2006 HOH HOH . F 3 HOH B 1 2001 2001 HOH HOH . F 3 HOH B 2 2002 2002 HOH HOH . F 3 HOH B 3 2003 2003 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 CB0 BI8 . . . D 2 25.656 -78.55 11.707 1 52.3 ? CB0 BI8 1417 B 1 HETATM 2 N NBC BI8 . . . D 2 35.432 -79.865 12.592 1 59.84 ? NBC BI8 1417 B 1 HETATM 3 C CBB BI8 . . . D 2 34.193 -79.846 11.81 1 57.11 ? CBB BI8 1417 B 1 HETATM 4 C CBA BI8 . . . D 2 33.066 -79.304 12.688 1 57.24 ? CBA BI8 1417 B 1 HETATM 5 C CAY BI8 . . . D 2 33.367 -77.859 13.04 1 55.52 ? CAY BI8 1417 B 1 HETATM 6 N NAH BI8 . . . D 2 32.565 -77.468 14.199 1 59.79 ? NAH BI8 1417 B 1 HETATM 7 C CAW BI8 . . . D 2 31.311 -77.006 14.151 1 53.08 ? CAW BI8 1417 B 1 HETATM 8 C CAE BI8 . . . D 2 33.034 -77.522 15.43 1 50.93 ? CAE BI8 1417 B 1 HETATM 9 C CAF BI8 . . . D 2 34.267 -77.923 15.939 1 44.96 ? CAF BI8 1417 B 1 HETATM 10 C CAA BI8 . . . D 2 34.487 -77.878 17.308 1 48.29 ? CAA BI8 1417 B 1 HETATM 11 C CAB BI8 . . . D 2 33.463 -77.437 18.137 1 55.68 ? CAB BI8 1417 B 1 HETATM 12 C CAC BI8 . . . D 2 32.232 -77.04 17.609 1 56.53 ? CAC BI8 1417 B 1 HETATM 13 C CAD BI8 . . . D 2 32.005 -77.075 16.239 1 48.61 ? CAD BI8 1417 B 1 HETATM 14 C CAG BI8 . . . D 2 30.917 -76.783 15.398 1 48.29 ? CAG BI8 1417 B 1 HETATM 15 C CAI BI8 . . . D 2 29.676 -76.252 15.776 1 50.49 ? CAI BI8 1417 B 1 HETATM 16 C CAT BI8 . . . D 2 29.522 -75.206 16.703 1 50.62 ? CAT BI8 1417 B 1 HETATM 17 O OAZ BI8 . . . D 2 30.414 -74.652 17.355 1 50.73 ? OAZ BI8 1417 B 1 HETATM 18 N NAU BI8 . . . D 2 28.244 -74.866 16.809 1 48.54 ? NAU BI8 1417 B 1 HETATM 19 C CAV BI8 . . . D 2 27.55 -75.642 15.979 1 54.5 ? CAV BI8 1417 B 1 HETATM 20 O OAX BI8 . . . D 2 26.33 -75.575 15.852 1 52.87 ? OAX BI8 1417 B 1 HETATM 21 C CAJ BI8 . . . D 2 28.386 -76.527 15.294 1 53.66 ? CAJ BI8 1417 B 1 HETATM 22 C CAK BI8 . . . D 2 27.907 -77.45 14.335 1 55.68 ? CAK BI8 1417 B 1 HETATM 23 C CAM BI8 . . . D 2 28.416 -78.729 14.071 1 60.63 ? CAM BI8 1417 B 1 HETATM 24 C CAP BI8 . . . D 2 29.48 -79.478 14.589 1 54.81 ? CAP BI8 1417 B 1 HETATM 25 C CAQ BI8 . . . D 2 29.735 -80.751 14.081 1 57.56 ? CAQ BI8 1417 B 1 HETATM 26 C CAR BI8 . . . D 2 28.935 -81.289 13.063 1 56.71 ? CAR BI8 1417 B 1 HETATM 27 C CAS BI8 . . . D 2 27.871 -80.547 12.548 1 53.94 ? CAS BI8 1417 B 1 HETATM 28 C CAN BI8 . . . D 2 27.621 -79.273 13.05 1 55.91 ? CAN BI8 1417 B 1 HETATM 29 N NAO BI8 . . . D 2 26.707 -78.366 12.747 1 60.3 ? NAO BI8 1417 B 1 HETATM 30 C CAL BI8 . . . D 2 26.863 -77.275 13.508 1 60.17 ? CAL BI8 1417 B 1 # _model_server_stats.io_time_ms 68 _model_server_stats.parse_time_ms 7 _model_server_stats.create_model_time_ms 5 _model_server_stats.query_time_ms 281 _model_server_stats.encode_time_ms 6 _model_server_stats.element_count 30 #