data_1DIB # _model_server_result.job_id EC2t37StHgLbDPd2rNDi2A _model_server_result.datetime_utc '2024-11-23 11:21:43' _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 1dib # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"D","auth_seq_id":3001}' # _entry.id 1DIB # _exptl.entry_id 1DIB _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 471.423 _entity.id 3 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description '4-(7-AMINO-9-HYDROXY-1-OXO-3,3A,4,5-TETRAHYDRO-2,5,6,8,9B-PENTAAZA-CYCLOPENTA[A]NAPHTHALEN-2-YL)-PHENYLCARBONYL-GLUTAMI C ACID' _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 1DIB _cell.length_a 67.49 _cell.length_b 136.37 _cell.length_c 61.38 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 1DIB _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 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 _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 # _chem_comp.formula 'C20 H21 N7 O7' _chem_comp.formula_weight 471.423 _chem_comp.id L34 _chem_comp.mon_nstd_flag . _chem_comp.name '4-(7-AMINO-9-HYDROXY-1-OXO-3,3A,4,5-TETRAHYDRO-2,5,6,8,9B-PENTAAZA-CYCLOPENTA[A]NAPHTHALEN-2-YL)-PHENYLCARBONYL-GLUTAMI C ACID' _chem_comp.type non-polymer _chem_comp.pdbx_synonyms LY345899 # 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 N2A C2 L34 sing 173 n n N2A HN21 L34 sing 174 n n N2A HN22 L34 sing 175 n n N1 C2 L34 doub 176 n y N1 C8A L34 sing 177 n y C2 N3 L34 sing 178 n y N3 C4 L34 doub 179 n y C4 O4A L34 sing 180 n n C4 C4A L34 sing 181 n y O4A HO4 L34 sing 182 n n C4A N5 L34 sing 183 n n C4A C8A L34 doub 184 n y N5 C6 L34 sing 185 n n N5 CX L34 sing 186 n n C6 C7 L34 sing 187 n n C6 C9 L34 sing 188 n n C6 H6 L34 sing 189 n n C7 N8 L34 sing 190 n n C7 H71 L34 sing 191 n n C7 H72 L34 sing 192 n n N8 C8A L34 sing 193 n n N8 HN8 L34 sing 194 n n CX OX L34 doub 195 n n CX N10 L34 sing 196 n n C9 N10 L34 sing 197 n n C9 H91 L34 sing 198 n n C9 H92 L34 sing 199 n n N10 C1B L34 sing 200 n n C1B C2B L34 doub 201 n y C1B C6B L34 sing 202 n y C2B C3B L34 sing 203 n y C2B H2B L34 sing 204 n n C3B C4B L34 doub 205 n y C3B H3B L34 sing 206 n n C4B C5B L34 sing 207 n y C4B C7B L34 sing 208 n n C5B C6B L34 doub 209 n y C5B H5B L34 sing 210 n n C6B H6B L34 sing 211 n n C7B O7B L34 doub 212 n n C7B N L34 sing 213 n n N CA L34 sing 214 n n N HN L34 sing 215 n n CA CB L34 sing 216 n n CA C L34 sing 217 n n CA HA L34 sing 218 n n CB CG L34 sing 219 n n CB HB1 L34 sing 220 n n CB HB2 L34 sing 221 n n CG CD L34 sing 222 n n CG HG1 L34 sing 223 n n CG HG2 L34 sing 224 n n CD OE1 L34 doub 225 n n CD OE2 L34 sing 226 n n OE2 HE2 L34 sing 227 n n C O L34 doub 228 n n C OXT L34 sing 229 n n OXT HXT L34 sing 230 n n # _atom_sites.entry_id 1DIB _atom_sites.fract_transf_matrix[1][1] 0.014817 _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] 0.007333 _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] 0.016292 _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 NAP A 1 2001 2001 NAP NAP . D 3 L34 A 1 3001 3001 L34 L34 . E 2 NAP B 1 2002 2002 NAP NAP . F 4 HOH A 1 4001 4001 HOH HOH . F 4 HOH A 2 4002 4002 HOH HOH . F 4 HOH A 3 4003 4003 HOH HOH . F 4 HOH A 4 4004 4004 HOH HOH . F 4 HOH A 5 4005 4005 HOH HOH . F 4 HOH A 6 4006 4006 HOH HOH . F 4 HOH A 7 4007 4007 HOH HOH . F 4 HOH A 8 4008 4008 HOH HOH . F 4 HOH A 9 4018 4018 HOH HOH . F 4 HOH A 10 4019 4019 HOH HOH . F 4 HOH A 11 4020 4020 HOH HOH . F 4 HOH A 12 4021 4021 HOH HOH . F 4 HOH A 13 4023 4023 HOH HOH . F 4 HOH A 14 4026 4026 HOH HOH . F 4 HOH A 15 4027 4027 HOH HOH . F 4 HOH A 16 4028 4028 HOH HOH . F 4 HOH A 17 4031 4031 HOH HOH . F 4 HOH A 18 4033 4033 HOH HOH . F 4 HOH A 19 4035 4035 HOH HOH . F 4 HOH A 20 4036 4036 HOH HOH . F 4 HOH A 21 4037 4037 HOH HOH . F 4 HOH A 22 4038 4038 HOH HOH . F 4 HOH A 23 4039 4039 HOH HOH . F 4 HOH A 24 4040 4040 HOH HOH . F 4 HOH A 25 4041 4041 HOH HOH . F 4 HOH A 26 4049 4049 HOH HOH . F 4 HOH A 27 4050 4050 HOH HOH . F 4 HOH A 28 4051 4051 HOH HOH . F 4 HOH A 29 4052 4052 HOH HOH . F 4 HOH A 30 4053 4053 HOH HOH . F 4 HOH A 31 4056 4056 HOH HOH . F 4 HOH A 32 4058 4058 HOH HOH . F 4 HOH A 33 4059 4059 HOH HOH . F 4 HOH A 34 4073 4073 HOH HOH . F 4 HOH A 35 4074 4074 HOH HOH . F 4 HOH A 36 4075 4075 HOH HOH . F 4 HOH A 37 4076 4076 HOH HOH . F 4 HOH A 38 4077 4077 HOH HOH . F 4 HOH A 39 4078 4078 HOH HOH . F 4 HOH A 40 4079 4079 HOH HOH . F 4 HOH A 41 4080 4080 HOH HOH . F 4 HOH A 42 4081 4081 HOH HOH . F 4 HOH A 43 4082 4082 HOH HOH . F 4 HOH A 44 4083 4083 HOH HOH . F 4 HOH A 45 4086 4086 HOH HOH . F 4 HOH A 46 4088 4088 HOH HOH . F 4 HOH A 47 4090 4090 HOH HOH . F 4 HOH A 48 4099 4099 HOH HOH . F 4 HOH A 49 4100 4100 HOH HOH . F 4 HOH A 50 4101 4101 HOH HOH . F 4 HOH A 51 4103 4103 HOH HOH . F 4 HOH A 52 4107 4107 HOH HOH . G 4 HOH B 1 4009 4009 HOH HOH . G 4 HOH B 2 4010 4010 HOH HOH . G 4 HOH B 3 4011 4011 HOH HOH . G 4 HOH B 4 4012 4012 HOH HOH . G 4 HOH B 5 4013 4013 HOH HOH . G 4 HOH B 6 4014 4014 HOH HOH . G 4 HOH B 7 4015 4015 HOH HOH . G 4 HOH B 8 4016 4016 HOH HOH . G 4 HOH B 9 4017 4017 HOH HOH . G 4 HOH B 10 4022 4022 HOH HOH . G 4 HOH B 11 4024 4024 HOH HOH . G 4 HOH B 12 4025 4025 HOH HOH . G 4 HOH B 13 4029 4029 HOH HOH . G 4 HOH B 14 4030 4030 HOH HOH . G 4 HOH B 15 4032 4032 HOH HOH . G 4 HOH B 16 4034 4034 HOH HOH . G 4 HOH B 17 4042 4042 HOH HOH . G 4 HOH B 18 4043 4043 HOH HOH . G 4 HOH B 19 4044 4044 HOH HOH . G 4 HOH B 20 4045 4045 HOH HOH . G 4 HOH B 21 4046 4046 HOH HOH . G 4 HOH B 22 4047 4047 HOH HOH . G 4 HOH B 23 4048 4048 HOH HOH . G 4 HOH B 24 4054 4054 HOH HOH . G 4 HOH B 25 4055 4055 HOH HOH . G 4 HOH B 26 4057 4057 HOH HOH . G 4 HOH B 27 4060 4060 HOH HOH . G 4 HOH B 28 4061 4061 HOH HOH . G 4 HOH B 29 4062 4062 HOH HOH . G 4 HOH B 30 4063 4063 HOH HOH . G 4 HOH B 31 4064 4064 HOH HOH . G 4 HOH B 32 4065 4065 HOH HOH . G 4 HOH B 33 4066 4066 HOH HOH . G 4 HOH B 34 4067 4067 HOH HOH . G 4 HOH B 35 4068 4068 HOH HOH . G 4 HOH B 36 4069 4069 HOH HOH . G 4 HOH B 37 4070 4070 HOH HOH . G 4 HOH B 38 4071 4071 HOH HOH . G 4 HOH B 39 4072 4072 HOH HOH . G 4 HOH B 40 4084 4084 HOH HOH . G 4 HOH B 41 4085 4085 HOH HOH . G 4 HOH B 42 4087 4087 HOH HOH . G 4 HOH B 43 4089 4089 HOH HOH . G 4 HOH B 44 4091 4091 HOH HOH . G 4 HOH B 45 4092 4092 HOH HOH . G 4 HOH B 46 4093 4093 HOH HOH . G 4 HOH B 47 4094 4094 HOH HOH . G 4 HOH B 48 4095 4095 HOH HOH . G 4 HOH B 49 4096 4096 HOH HOH . G 4 HOH B 50 4097 4097 HOH HOH . G 4 HOH B 51 4098 4098 HOH HOH . G 4 HOH B 52 4102 4102 HOH HOH . G 4 HOH B 53 4104 4104 HOH HOH . G 4 HOH B 54 4105 4105 HOH HOH . G 4 HOH B 55 4106 4106 HOH HOH . G 4 HOH B 56 4108 4108 HOH HOH . G 4 HOH B 57 4109 4109 HOH HOH . G 4 HOH B 58 4110 4110 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 N N2A L34 . . . D 3 1.311 49.658 13.575 0.4 16.7 ? N2A L34 3001 A 1 HETATM 2 N N1 L34 . . . D 3 0.129 50.607 15.33 0.4 16.12 ? N1 L34 3001 A 1 HETATM 3 C C2 L34 . . . D 3 1.278 50.375 14.708 0.4 16.86 ? C2 L34 3001 A 1 HETATM 4 N N3 L34 . . . D 3 2.458 50.958 15.227 0.4 17.48 ? N3 L34 3001 A 1 HETATM 5 C C4 L34 . . . D 3 2.374 51.796 16.31 0.4 17.14 ? C4 L34 3001 A 1 HETATM 6 O O4A L34 . . . D 3 3.535 52.296 16.88 0.4 16.8 ? O4A L34 3001 A 1 HETATM 7 C C4A L34 . . . D 3 1.16 52.057 16.908 0.4 16.52 ? C4A L34 3001 A 1 HETATM 8 N N5 L34 . . . D 3 1.03 53.187 17.844 0.4 16.31 ? N5 L34 3001 A 1 HETATM 9 C C6 L34 . . . D 3 -0.258 53.376 18.595 0.4 16 ? C6 L34 3001 A 1 HETATM 10 C C7 L34 . . . D 3 -1.385 52.906 17.659 0.4 16.07 ? C7 L34 3001 A 1 HETATM 11 N N8 L34 . . . D 3 -1.125 51.755 16.98 0.4 16.51 ? N8 L34 3001 A 1 HETATM 12 C C8A L34 . . . D 3 0.079 51.465 16.43 0.4 16.51 ? C8A L34 3001 A 1 HETATM 13 C CX L34 . . . D 3 1.687 54.342 17.871 0.4 16.32 ? CX L34 3001 A 1 HETATM 14 O OX L34 . . . D 3 2.573 54.627 17.095 0.4 17.9 ? OX L34 3001 A 1 HETATM 15 C C9 L34 . . . D 3 -0.3 54.925 18.767 0.4 15.5 ? C9 L34 3001 A 1 HETATM 16 N N10 L34 . . . D 3 1.125 55.234 18.691 0.4 15.53 ? N10 L34 3001 A 1 HETATM 17 C C1B L34 . . . D 3 1.45 56.65 18.93 0.5 14.91 ? C1B L34 3001 A 1 HETATM 18 C C2B L34 . . . D 3 2.398 57.321 18.106 0.5 14.37 ? C2B L34 3001 A 1 HETATM 19 C C3B L34 . . . D 3 2.853 58.592 18.455 0.5 14.52 ? C3B L34 3001 A 1 HETATM 20 C C4B L34 . . . D 3 2.339 59.217 19.587 0.5 14.42 ? C4B L34 3001 A 1 HETATM 21 C C5B L34 . . . D 3 1.406 58.562 20.378 0.5 14.87 ? C5B L34 3001 A 1 HETATM 22 C C6B L34 . . . D 3 0.944 57.3 20.04 0.5 14.61 ? C6B L34 3001 A 1 HETATM 23 C C7B L34 . . . D 3 2.828 60.587 20.022 0.5 14.27 ? C7B L34 3001 A 1 HETATM 24 O O7B L34 . . . D 3 3.715 61.17 19.392 0.5 13.57 ? O7B L34 3001 A 1 HETATM 25 N N L34 . . . D 3 2.416 60.948 21.24 0.5 14.95 ? N L34 3001 A 1 HETATM 26 C CA L34 . . . D 3 2.856 62.161 21.926 0.4 15.49 ? CA L34 3001 A 1 HETATM 27 C CB L34 . . . D 3 1.685 63.104 22.158 0.1 15.27 ? CB L34 3001 A 1 HETATM 28 C CG L34 . . . D 3 0.908 63.488 20.939 0.1 15.06 ? CG L34 3001 A 1 HETATM 29 C CD L34 . . . D 3 -0.163 64.496 21.271 0.1 15.02 ? CD L34 3001 A 1 HETATM 30 O OE1 L34 . . . D 3 -1.294 64.082 21.601 0.1 14.81 ? OE1 L34 3001 A 1 HETATM 31 O OE2 L34 . . . D 3 0.128 65.708 21.217 0.1 14.99 ? OE2 L34 3001 A 1 HETATM 32 C C L34 . . . D 3 3.426 61.837 23.298 0.4 15.89 ? C L34 3001 A 1 HETATM 33 O O L34 . . . D 3 3.006 60.825 23.898 0.4 16.69 ? O L34 3001 A 1 HETATM 34 O OXT L34 . . . D 3 4.214 62.662 23.796 0.4 15.87 ? OXT L34 3001 A 1 # _model_server_stats.io_time_ms 43 _model_server_stats.parse_time_ms 5 _model_server_stats.create_model_time_ms 10 _model_server_stats.query_time_ms 218 _model_server_stats.encode_time_ms 3 _model_server_stats.element_count 34 #