data_2F3M # _model_server_result.job_id MTeMRljao4olttaBnGd0xA _model_server_result.datetime_utc '2024-11-24 19:48:03' _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 2f3m # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"G","auth_seq_id":1218}' # _entry.id 2F3M # _exptl.entry_id 2F3M _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 520.428 _entity.id 2 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description 1-(S-GLUTATHIONYL)-2,4,6-TRINITROCYCLOHEXA-2,5-DIENE _entity.pdbx_number_of_molecules 6 _entity.pdbx_parent_entity_id . _entity.pdbx_mutation ? _entity.pdbx_fragment ? _entity.pdbx_ec ? # _cell.angle_alpha 120.53 _cell.angle_beta 106.19 _cell.angle_gamma 89.97 _cell.entry_id 2F3M _cell.length_a 51.965 _cell.length_b 93.096 _cell.length_c 92.998 _cell.Z_PDB 6 _cell.pdbx_unique_axis ? # _symmetry.entry_id 2F3M _symmetry.cell_setting ? _symmetry.Int_Tables_number 1 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 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 PISA dimeric 2 author_and_software_defined_assembly 1 PISA dimeric 2 author_and_software_defined_assembly 2 PISA dimeric 2 author_and_software_defined_assembly 3 # loop_ _pdbx_struct_assembly_gen.asym_id_list _pdbx_struct_assembly_gen.assembly_id _pdbx_struct_assembly_gen.oper_expression A,B,G,H,M,N 1 1 C,D,I,J,O,P 2 1 E,F,K,L,Q,R 3 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 G N N ? 2 H N N ? 2 I N N ? 2 J N N ? 2 K N N ? 2 L 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 78 A CYS 77 1_555 A SG CYS 87 A CYS 86 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.879 ? disulf ? disulf2 B SG CYS 78 B CYS 77 1_555 B SG CYS 87 B CYS 86 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.943 ? disulf ? disulf3 C SG CYS 78 C CYS 77 1_555 C SG CYS 87 C CYS 86 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.199 ? disulf ? disulf4 D SG CYS 78 D CYS 77 1_555 D SG CYS 87 D CYS 86 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.074 ? disulf ? disulf5 E SG CYS 78 E CYS 77 1_555 E SG CYS 87 E CYS 86 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.955 ? disulf ? disulf6 F SG CYS 78 F CYS 77 1_555 F SG CYS 87 F CYS 86 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.826 ? # _chem_comp.formula 'C16 H20 N6 O12 S' _chem_comp.formula_weight 520.428 _chem_comp.id GTD _chem_comp.mon_nstd_flag . _chem_comp.name 1-(S-GLUTATHIONYL)-2,4,6-TRINITROCYCLOHEXA-2,5-DIENE _chem_comp.type non-polymer _chem_comp.pdbx_synonyms '(S)-2-AMINO-5-((R)-1-(CARBOXYMETHYLAMINO)-1-OXO-3-(2,4,6-TRINITROCYCLOHEXA-2,5-DIENYLTHIO)PROPAN-2-YLAMINO)-5-OXOPENTANOIC ACID' # 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 N1 CA1 GTD sing 129 n n N1 HN11 GTD sing 130 n n N1 HN12 GTD sing 131 n n CA1 C1 GTD sing 132 n n CA1 CB1 GTD sing 133 n n CA1 HA1 GTD sing 134 n n C1 O11 GTD doub 135 n n C1 O12 GTD sing 136 n n O12 HO1 GTD sing 137 n n CB1 CG1 GTD sing 138 n n CB1 HB11 GTD sing 139 n n CB1 HB12 GTD sing 140 n n CG1 CD1 GTD sing 141 n n CG1 HG11 GTD sing 142 n n CG1 HG12 GTD sing 143 n n CD1 OE1 GTD doub 144 n n CD1 N2 GTD sing 145 n n N2 CA2 GTD sing 146 n n N2 HN2 GTD sing 147 n n CA2 C2 GTD sing 148 n n CA2 CB2 GTD sing 149 n n CA2 HA2 GTD sing 150 n n C2 O2 GTD doub 151 n n C2 N3 GTD sing 152 n n CB2 SG2 GTD sing 153 n n CB2 HB21 GTD sing 154 n n CB2 HB22 GTD sing 155 n n SG2 C1' GTD sing 156 n n N3 CA3 GTD sing 157 n n N3 HN3 GTD sing 158 n n CA3 C3 GTD sing 159 n n CA3 HA31 GTD sing 160 n n CA3 HA32 GTD sing 161 n n C3 O31 GTD doub 162 n n C3 O32 GTD sing 163 n n O32 HO3 GTD sing 164 n n C1' C2' GTD sing 165 n n C1' C6' GTD sing 166 n n C1' H1' GTD sing 167 n n C2' N2' GTD sing 168 n n C2' C3' GTD doub 169 n n N2' O21 GTD doub 170 n n N2' O22 GTD sing 171 n n C3' C4' GTD sing 172 n n C3' H3' GTD sing 173 n n C4' N4' GTD sing 174 n n C4' C5' GTD sing 175 n n C4' H4' GTD sing 176 n n N4' O41 GTD doub 177 n n N4' O42 GTD sing 178 n n C5' C6' GTD doub 179 n n C5' H5' GTD sing 180 n n C6' N6' GTD sing 181 n n N6' O61 GTD doub 182 n n N6' O62 GTD sing 183 n n # _atom_sites.entry_id 2F3M _atom_sites.fract_transf_matrix[1][1] 0.019244 _atom_sites.fract_transf_matrix[1][2] -0.000009 _atom_sites.fract_transf_matrix[1][3] 0.006579 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.010742 _atom_sites.fract_transf_matrix[2][3] 0.006693 _atom_sites.fract_transf_matrix[3][1] 0 _atom_sites.fract_transf_matrix[3][2] 0 _atom_sites.fract_transf_matrix[3][3] 0.013193 _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 G 2 GTD A 1 1218 218 GTD GTD . H 2 GTD B 1 2218 218 GTD GTD . I 2 GTD C 1 3218 218 GTD GTD . J 2 GTD D 1 4218 218 GTD GTD . K 2 GTD E 1 5218 218 GTD GTD . L 2 GTD F 1 6218 218 GTD GTD . M 3 HOH A 1 1219 4 HOH HOH . M 3 HOH A 2 1220 5 HOH HOH . M 3 HOH A 3 1221 6 HOH HOH . M 3 HOH A 4 1222 7 HOH HOH . M 3 HOH A 5 1223 16 HOH HOH . M 3 HOH A 6 1224 17 HOH HOH . M 3 HOH A 7 1225 21 HOH HOH . M 3 HOH A 8 1226 22 HOH HOH . M 3 HOH A 9 1227 23 HOH HOH . M 3 HOH A 10 1228 28 HOH HOH . M 3 HOH A 11 1229 37 HOH HOH . M 3 HOH A 12 1230 38 HOH HOH . M 3 HOH A 13 1231 50 HOH HOH . N 3 HOH B 1 2219 8 HOH HOH . N 3 HOH B 2 2220 9 HOH HOH . N 3 HOH B 3 2221 10 HOH HOH . N 3 HOH B 4 2222 15 HOH HOH . N 3 HOH B 5 2223 19 HOH HOH . N 3 HOH B 6 2224 20 HOH HOH . N 3 HOH B 7 2225 44 HOH HOH . N 3 HOH B 8 2226 51 HOH HOH . O 3 HOH C 1 3219 11 HOH HOH . O 3 HOH C 2 3220 12 HOH HOH . O 3 HOH C 3 3221 29 HOH HOH . O 3 HOH C 4 3222 42 HOH HOH . O 3 HOH C 5 3223 45 HOH HOH . O 3 HOH C 6 3224 52 HOH HOH . O 3 HOH C 7 3225 53 HOH HOH . O 3 HOH C 8 3226 54 HOH HOH . P 3 HOH D 1 4219 13 HOH HOH . P 3 HOH D 2 4220 14 HOH HOH . P 3 HOH D 3 4221 30 HOH HOH . P 3 HOH D 4 4222 31 HOH HOH . P 3 HOH D 5 4223 32 HOH HOH . P 3 HOH D 6 4224 33 HOH HOH . P 3 HOH D 7 4225 34 HOH HOH . P 3 HOH D 8 4226 35 HOH HOH . P 3 HOH D 9 4227 36 HOH HOH . P 3 HOH D 10 4228 55 HOH HOH . Q 3 HOH E 1 5219 3 HOH HOH . Q 3 HOH E 2 5220 26 HOH HOH . Q 3 HOH E 3 5221 41 HOH HOH . Q 3 HOH E 4 5222 46 HOH HOH . Q 3 HOH E 5 5223 47 HOH HOH . Q 3 HOH E 6 5224 49 HOH HOH . R 3 HOH F 1 6219 2 HOH HOH . R 3 HOH F 2 6220 24 HOH HOH . R 3 HOH F 3 6221 25 HOH HOH . R 3 HOH F 4 6222 27 HOH HOH . R 3 HOH F 5 6223 39 HOH HOH . R 3 HOH F 6 6224 40 HOH HOH . R 3 HOH F 7 6225 43 HOH HOH . R 3 HOH F 8 6226 48 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 N1 GTD . . . G 2 -5.605 -2.789 -0.159 1 52.21 ? N1 GTD 1218 A 1 HETATM 2 C CA1 GTD . . . G 2 -6.633 -3.682 0.306 1 52.26 ? CA1 GTD 1218 A 1 HETATM 3 C C1 GTD . . . G 2 -6.097 -4.408 1.481 1 52.22 ? C1 GTD 1218 A 1 HETATM 4 O O11 GTD . . . G 2 -6.906 -4.88 2.287 1 52.11 ? O11 GTD 1218 A 1 HETATM 5 O O12 GTD . . . G 2 -4.871 -4.51 1.604 1 51.86 ? O12 GTD 1218 A 1 HETATM 6 C CB1 GTD . . . G 2 -6.924 -4.679 -0.794 1 52.52 ? CB1 GTD 1218 A 1 HETATM 7 C CG1 GTD . . . G 2 -8.326 -5.233 -0.67 1 53.14 ? CG1 GTD 1218 A 1 HETATM 8 C CD1 GTD . . . G 2 -8.649 -6.055 -1.883 1 53.4 ? CD1 GTD 1218 A 1 HETATM 9 O OE1 GTD . . . G 2 -8.202 -5.768 -2.972 1 53.47 ? OE1 GTD 1218 A 1 HETATM 10 N N2 GTD . . . G 2 -9.444 -7.083 -1.672 1 53.84 ? N2 GTD 1218 A 1 HETATM 11 C CA2 GTD . . . G 2 -9.967 -7.876 -2.752 1 54.38 ? CA2 GTD 1218 A 1 HETATM 12 C C2 GTD . . . G 2 -11.459 -7.959 -2.677 1 54.16 ? C2 GTD 1218 A 1 HETATM 13 O O2 GTD . . . G 2 -12.033 -9.009 -2.8 1 54.14 ? O2 GTD 1218 A 1 HETATM 14 C CB2 GTD . . . G 2 -9.339 -9.255 -2.669 1 54.82 ? CB2 GTD 1218 A 1 HETATM 15 S SG2 GTD . . . G 2 -7.591 -9.149 -2.742 1 56.19 ? SG2 GTD 1218 A 1 HETATM 16 N N3 GTD . . . G 2 -12.117 -6.841 -2.463 1 54.01 ? N3 GTD 1218 A 1 HETATM 17 C CA3 GTD . . . G 2 -13.514 -6.884 -2.119 1 53.96 ? CA3 GTD 1218 A 1 HETATM 18 C C3 GTD . . . G 2 -14.267 -5.751 -2.753 1 53.99 ? C3 GTD 1218 A 1 HETATM 19 O O31 GTD . . . G 2 -13.615 -4.795 -3.2 1 54.06 ? O31 GTD 1218 A 1 HETATM 20 O O32 GTD . . . G 2 -15.508 -5.8 -2.8 1 54.12 ? O32 GTD 1218 A 1 HETATM 21 C C1' GTD . . . G 2 -7.21 -9.963 -4.253 0.7 56.52 ? C1' GTD 1218 A 1 HETATM 22 C C2' GTD . . . G 2 -5.86 -10.608 -4.147 0.7 56.9 ? C2' GTD 1218 A 1 HETATM 23 N N2' GTD . . . G 2 -5.727 -11.895 -3.508 0.7 56.97 ? N2' GTD 1218 A 1 HETATM 24 O O21 GTD . . . G 2 -6.714 -12.534 -3.415 0.7 56.94 ? O21 GTD 1218 A 1 HETATM 25 O O22 GTD . . . G 2 -4.695 -12.209 -2.955 0.7 57.14 ? O22 GTD 1218 A 1 HETATM 26 C C3' GTD . . . G 2 -4.761 -10.041 -4.654 0.7 56.88 ? C3' GTD 1218 A 1 HETATM 27 C C4' GTD . . . G 2 -4.891 -9.357 -5.987 0.7 57.12 ? C4' GTD 1218 A 1 HETATM 28 N N4' GTD . . . G 2 -3.776 -8.743 -6.371 0.7 57.12 ? N4' GTD 1218 A 1 HETATM 29 O O41 GTD . . . G 2 -2.854 -8.602 -5.587 0.7 57.31 ? O41 GTD 1218 A 1 HETATM 30 O O42 GTD . . . G 2 -3.668 -8.333 -7.512 0.7 57.27 ? O42 GTD 1218 A 1 HETATM 31 C C5' GTD . . . G 2 -6.109 -8.474 -5.886 0.7 56.85 ? C5' GTD 1218 A 1 HETATM 32 C C6' GTD . . . G 2 -7.234 -9.055 -5.453 0.7 56.92 ? C6' GTD 1218 A 1 HETATM 33 N N6' GTD . . . G 2 -8.461 -8.86 -6.213 0.7 56.93 ? N6' GTD 1218 A 1 HETATM 34 O O61 GTD . . . G 2 -8.915 -9.783 -6.864 0.7 57.07 ? O61 GTD 1218 A 1 HETATM 35 O O62 GTD . . . G 2 -9.034 -7.786 -6.229 0.7 57.13 ? O62 GTD 1218 A 1 # _model_server_stats.io_time_ms 31 _model_server_stats.parse_time_ms 16 _model_server_stats.create_model_time_ms 19 _model_server_stats.query_time_ms 689 _model_server_stats.encode_time_ms 7 _model_server_stats.element_count 35 #