data_1VF3 # _model_server_result.job_id VQoXmCpqO8ULIaSSwBHEyA _model_server_result.datetime_utc '2024-11-22 04:21:42' _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 1vf3 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"C","auth_seq_id":2500}' # _entry.id 1VF3 # _exptl.entry_id 1VF3 _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 473.415 _entity.id 2 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description 'GLUTATHIONE S-(2,4 DINITROBENZENE)' _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 90 _cell.entry_id 1VF3 _cell.length_a 99.258 _cell.length_b 114.182 _cell.length_c 94.634 _cell.Z_PDB 16 _cell.pdbx_unique_axis ? # _symmetry.entry_id 1VF3 _symmetry.cell_setting ? _symmetry.Int_Tables_number 20 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'C 2 2 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 # 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 E N N # _chem_comp.formula 'C16 H19 N5 O10 S' _chem_comp.formula_weight 473.415 _chem_comp.id GDN _chem_comp.mon_nstd_flag . _chem_comp.name 'GLUTATHIONE S-(2,4 DINITROBENZENE)' _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 N1 CA1 GDN sing 90 n n N1 HN1 GDN sing 91 n n N1 HN2A GDN sing 92 n n CA1 C1 GDN sing 93 n n CA1 CB1 GDN sing 94 n n CA1 HA1 GDN sing 95 n n C1 O11 GDN doub 96 n n C1 O12 GDN sing 97 n n O12 H12 GDN sing 98 n n CB1 CG1 GDN sing 99 n n CB1 HB11 GDN sing 100 n n CB1 HB12 GDN sing 101 n n CG1 CD1 GDN sing 102 n n CG1 HG11 GDN sing 103 n n CG1 HG12 GDN sing 104 n n CD1 OE1 GDN doub 105 n n CD1 N2 GDN sing 106 n n N2 CA2 GDN sing 107 n n N2 HN2 GDN sing 108 n n CA2 C2 GDN sing 109 n n CA2 CB2 GDN sing 110 n n CA2 HA2 GDN sing 111 n n C2 O2 GDN doub 112 n n C2 N3 GDN sing 113 n n CB2 SG2 GDN sing 114 n n CB2 HB21 GDN sing 115 n n CB2 HB22 GDN sing 116 n n SG2 C1' GDN sing 117 n n N3 CA3 GDN sing 118 n n N3 HN3 GDN sing 119 n n CA3 C3 GDN sing 120 n n CA3 HA31 GDN sing 121 n n CA3 HA32 GDN sing 122 n n C3 O31 GDN doub 123 n n C3 O32 GDN sing 124 n n O32 H32 GDN sing 125 n n C1' C2' GDN doub 126 n y C1' C6' GDN sing 127 n y C2' C3' GDN sing 128 n y C2' N2' GDN sing 129 n n C3' C4' GDN doub 130 n y C3' H3' GDN sing 131 n n C4' C5' GDN sing 132 n y C4' N4' GDN sing 133 n n C5' C6' GDN doub 134 n y C5' H5' GDN sing 135 n n C6' H6' GDN sing 136 n n N2' O2A GDN sing 137 n n N2' O2B GDN doub 138 n n N4' O4A GDN sing 139 n n N4' O4B GDN doub 140 n n # _atom_sites.entry_id 1VF3 _atom_sites.fract_transf_matrix[1][1] 0.010075 _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] 0.008758 _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] 0.010567 _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 GDN A 1 2500 2500 GDN GDN . D 3 ACY A 1 5001 5001 ACY ACY . E 2 GDN B 1 3600 3600 GDN GDN . F 4 HOH A 1 4001 4001 HOH TIP . F 4 HOH A 2 4005 4005 HOH TIP . F 4 HOH A 3 4007 4007 HOH TIP . F 4 HOH A 4 4008 4008 HOH TIP . F 4 HOH A 5 4011 4011 HOH TIP . F 4 HOH A 6 4015 4015 HOH TIP . F 4 HOH A 7 4020 4020 HOH TIP . F 4 HOH A 8 4023 4023 HOH TIP . F 4 HOH A 9 4024 4024 HOH TIP . F 4 HOH A 10 4026 4026 HOH TIP . F 4 HOH A 11 4028 4028 HOH TIP . F 4 HOH A 12 4030 4030 HOH TIP . F 4 HOH A 13 4031 4031 HOH TIP . F 4 HOH A 14 4032 4032 HOH TIP . F 4 HOH A 15 4033 4033 HOH TIP . F 4 HOH A 16 4034 4034 HOH TIP . F 4 HOH A 17 4035 4035 HOH TIP . F 4 HOH A 18 4036 4036 HOH TIP . F 4 HOH A 19 4039 4039 HOH TIP . F 4 HOH A 20 4040 4040 HOH TIP . F 4 HOH A 21 4041 4041 HOH TIP . F 4 HOH A 22 4043 4043 HOH TIP . F 4 HOH A 23 4045 4045 HOH TIP . F 4 HOH A 24 4048 4048 HOH TIP . F 4 HOH A 25 4052 4052 HOH TIP . F 4 HOH A 26 4054 4054 HOH TIP . F 4 HOH A 27 4056 4056 HOH TIP . F 4 HOH A 28 4057 4057 HOH TIP . F 4 HOH A 29 4058 4058 HOH TIP . F 4 HOH A 30 4059 4059 HOH TIP . F 4 HOH A 31 4061 4061 HOH TIP . F 4 HOH A 32 4062 4062 HOH TIP . F 4 HOH A 33 4067 4067 HOH TIP . F 4 HOH A 34 4070 4070 HOH TIP . F 4 HOH A 35 4071 4071 HOH TIP . F 4 HOH A 36 4072 4072 HOH TIP . F 4 HOH A 37 4074 4074 HOH TIP . F 4 HOH A 38 4075 4075 HOH TIP . F 4 HOH A 39 4077 4077 HOH TIP . F 4 HOH A 40 4078 4078 HOH TIP . F 4 HOH A 41 4082 4082 HOH TIP . F 4 HOH A 42 4084 4084 HOH TIP . F 4 HOH A 43 4089 4089 HOH TIP . F 4 HOH A 44 4091 4091 HOH TIP . F 4 HOH A 45 4092 4092 HOH TIP . F 4 HOH A 46 4094 4094 HOH TIP . F 4 HOH A 47 4096 4096 HOH TIP . F 4 HOH A 48 4098 4098 HOH TIP . F 4 HOH A 49 4101 4101 HOH TIP . F 4 HOH A 50 4103 4103 HOH TIP . F 4 HOH A 51 4104 4104 HOH TIP . F 4 HOH A 52 4105 4105 HOH TIP . F 4 HOH A 53 4107 4107 HOH TIP . F 4 HOH A 54 4108 4108 HOH TIP . F 4 HOH A 55 4109 4109 HOH TIP . F 4 HOH A 56 4112 4112 HOH TIP . F 4 HOH A 57 4114 4114 HOH TIP . F 4 HOH A 58 4117 4117 HOH TIP . F 4 HOH A 59 4118 4118 HOH TIP . F 4 HOH A 60 4119 4119 HOH TIP . F 4 HOH A 61 4120 4120 HOH TIP . F 4 HOH A 62 4121 4121 HOH TIP . F 4 HOH A 63 4122 4122 HOH TIP . F 4 HOH A 64 4123 4123 HOH TIP . F 4 HOH A 65 4125 4125 HOH TIP . F 4 HOH A 66 4127 4127 HOH TIP . F 4 HOH A 67 4128 4128 HOH TIP . F 4 HOH A 68 4135 4135 HOH TIP . F 4 HOH A 69 4136 4136 HOH TIP . F 4 HOH A 70 4137 4137 HOH TIP . F 4 HOH A 71 4142 4142 HOH TIP . F 4 HOH A 72 4145 4145 HOH TIP . F 4 HOH A 73 4150 4150 HOH TIP . F 4 HOH A 74 4151 4151 HOH TIP . F 4 HOH A 75 4155 4155 HOH TIP . F 4 HOH A 76 4157 4157 HOH TIP . F 4 HOH A 77 4158 4158 HOH TIP . F 4 HOH A 78 4162 4162 HOH TIP . F 4 HOH A 79 4165 4165 HOH TIP . F 4 HOH A 80 4166 4166 HOH TIP . F 4 HOH A 81 4168 4168 HOH TIP . F 4 HOH A 82 4172 4172 HOH TIP . F 4 HOH A 83 4175 4175 HOH TIP . F 4 HOH A 84 4180 4180 HOH TIP . F 4 HOH A 85 4184 4184 HOH TIP . F 4 HOH A 86 4187 4187 HOH TIP . F 4 HOH A 87 4191 4191 HOH TIP . F 4 HOH A 88 4192 4192 HOH TIP . F 4 HOH A 89 4193 4193 HOH TIP . F 4 HOH A 90 4194 4194 HOH TIP . F 4 HOH A 91 4199 4199 HOH TIP . F 4 HOH A 92 4201 4201 HOH TIP . F 4 HOH A 93 4202 4202 HOH TIP . F 4 HOH A 94 4204 4204 HOH TIP . F 4 HOH A 95 4205 4205 HOH TIP . F 4 HOH A 96 4207 4207 HOH TIP . F 4 HOH A 97 4208 4208 HOH TIP . F 4 HOH A 98 4209 4209 HOH TIP . F 4 HOH A 99 4211 4211 HOH TIP . G 4 HOH B 1 4002 4002 HOH TIP . G 4 HOH B 2 4003 4003 HOH TIP . G 4 HOH B 3 4004 4004 HOH TIP . G 4 HOH B 4 4006 4006 HOH TIP . G 4 HOH B 5 4009 4009 HOH TIP . G 4 HOH B 6 4010 4010 HOH TIP . G 4 HOH B 7 4012 4012 HOH TIP . G 4 HOH B 8 4013 4013 HOH TIP . G 4 HOH B 9 4014 4014 HOH TIP . G 4 HOH B 10 4016 4016 HOH TIP . G 4 HOH B 11 4017 4017 HOH TIP . G 4 HOH B 12 4018 4018 HOH TIP . G 4 HOH B 13 4019 4019 HOH TIP . G 4 HOH B 14 4021 4021 HOH TIP . G 4 HOH B 15 4022 4022 HOH TIP . G 4 HOH B 16 4025 4025 HOH TIP . G 4 HOH B 17 4027 4027 HOH TIP . G 4 HOH B 18 4029 4029 HOH TIP . G 4 HOH B 19 4037 4037 HOH TIP . G 4 HOH B 20 4038 4038 HOH TIP . G 4 HOH B 21 4042 4042 HOH TIP . G 4 HOH B 22 4044 4044 HOH TIP . G 4 HOH B 23 4046 4046 HOH TIP . G 4 HOH B 24 4047 4047 HOH TIP . G 4 HOH B 25 4049 4049 HOH TIP . G 4 HOH B 26 4050 4050 HOH TIP . G 4 HOH B 27 4051 4051 HOH TIP . G 4 HOH B 28 4053 4053 HOH TIP . G 4 HOH B 29 4055 4055 HOH TIP . G 4 HOH B 30 4060 4060 HOH TIP . G 4 HOH B 31 4063 4063 HOH TIP . G 4 HOH B 32 4064 4064 HOH TIP . G 4 HOH B 33 4065 4065 HOH TIP . G 4 HOH B 34 4066 4066 HOH TIP . G 4 HOH B 35 4068 4068 HOH TIP . G 4 HOH B 36 4069 4069 HOH TIP . G 4 HOH B 37 4073 4073 HOH TIP . G 4 HOH B 38 4076 4076 HOH TIP . G 4 HOH B 39 4079 4079 HOH TIP . G 4 HOH B 40 4080 4080 HOH TIP . G 4 HOH B 41 4081 4081 HOH TIP . G 4 HOH B 42 4083 4083 HOH TIP . G 4 HOH B 43 4085 4085 HOH TIP . G 4 HOH B 44 4086 4086 HOH TIP . G 4 HOH B 45 4087 4087 HOH TIP . G 4 HOH B 46 4088 4088 HOH TIP . G 4 HOH B 47 4090 4090 HOH TIP . G 4 HOH B 48 4093 4093 HOH TIP . G 4 HOH B 49 4095 4095 HOH TIP . G 4 HOH B 50 4097 4097 HOH TIP . G 4 HOH B 51 4099 4099 HOH TIP . G 4 HOH B 52 4100 4100 HOH TIP . G 4 HOH B 53 4102 4102 HOH TIP . G 4 HOH B 54 4106 4106 HOH TIP . G 4 HOH B 55 4110 4110 HOH TIP . G 4 HOH B 56 4111 4111 HOH TIP . G 4 HOH B 57 4113 4113 HOH TIP . G 4 HOH B 58 4115 4115 HOH TIP . G 4 HOH B 59 4116 4116 HOH TIP . G 4 HOH B 60 4124 4124 HOH TIP . G 4 HOH B 61 4126 4126 HOH TIP . G 4 HOH B 62 4129 4129 HOH TIP . G 4 HOH B 63 4130 4130 HOH TIP . G 4 HOH B 64 4131 4131 HOH TIP . G 4 HOH B 65 4132 4132 HOH TIP . G 4 HOH B 66 4133 4133 HOH TIP . G 4 HOH B 67 4134 4134 HOH TIP . G 4 HOH B 68 4138 4138 HOH TIP . G 4 HOH B 69 4139 4139 HOH TIP . G 4 HOH B 70 4140 4140 HOH TIP . G 4 HOH B 71 4141 4141 HOH TIP . G 4 HOH B 72 4143 4143 HOH TIP . G 4 HOH B 73 4144 4144 HOH TIP . G 4 HOH B 74 4146 4146 HOH TIP . G 4 HOH B 75 4147 4147 HOH TIP . G 4 HOH B 76 4148 4148 HOH TIP . G 4 HOH B 77 4149 4149 HOH TIP . G 4 HOH B 78 4152 4152 HOH TIP . G 4 HOH B 79 4153 4153 HOH TIP . G 4 HOH B 80 4154 4154 HOH TIP . G 4 HOH B 81 4156 4156 HOH TIP . G 4 HOH B 82 4159 4159 HOH TIP . G 4 HOH B 83 4160 4160 HOH TIP . G 4 HOH B 84 4161 4161 HOH TIP . G 4 HOH B 85 4163 4163 HOH TIP . G 4 HOH B 86 4164 4164 HOH TIP . G 4 HOH B 87 4167 4167 HOH TIP . G 4 HOH B 88 4169 4169 HOH TIP . G 4 HOH B 89 4170 4170 HOH TIP . G 4 HOH B 90 4171 4171 HOH TIP . G 4 HOH B 91 4173 4173 HOH TIP . G 4 HOH B 92 4174 4174 HOH TIP . G 4 HOH B 93 4176 4176 HOH TIP . G 4 HOH B 94 4177 4177 HOH TIP . G 4 HOH B 95 4178 4178 HOH TIP . G 4 HOH B 96 4179 4179 HOH TIP . G 4 HOH B 97 4181 4181 HOH TIP . G 4 HOH B 98 4182 4182 HOH TIP . G 4 HOH B 99 4183 4183 HOH TIP . G 4 HOH B 100 4185 4185 HOH TIP . G 4 HOH B 101 4186 4186 HOH TIP . G 4 HOH B 102 4188 4188 HOH TIP . G 4 HOH B 103 4189 4189 HOH TIP . G 4 HOH B 104 4190 4190 HOH TIP . G 4 HOH B 105 4195 4195 HOH TIP . G 4 HOH B 106 4196 4196 HOH TIP . G 4 HOH B 107 4197 4197 HOH TIP . G 4 HOH B 108 4198 4198 HOH TIP . G 4 HOH B 109 4200 4200 HOH TIP . G 4 HOH B 110 4203 4203 HOH TIP . G 4 HOH B 111 4206 4206 HOH TIP . G 4 HOH B 112 4210 4210 HOH TIP . # 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 GDN . . . C 2 27.001 17.405 30.009 1 33.6 ? N1 GDN 2500 A 1 HETATM 2 C CA1 GDN . . . C 2 27.585 16.419 30.863 1 32.92 ? CA1 GDN 2500 A 1 HETATM 3 C C1 GDN . . . C 2 28.055 15.324 29.898 1 31.86 ? C1 GDN 2500 A 1 HETATM 4 O O11 GDN . . . C 2 28.983 14.605 30.239 1 29.36 ? O11 GDN 2500 A 1 HETATM 5 O O12 GDN . . . C 2 27.492 15.196 28.813 1 30.24 ? O12 GDN 2500 A 1 HETATM 6 C CB1 GDN . . . C 2 26.512 15.946 31.859 1 32.85 ? CB1 GDN 2500 A 1 HETATM 7 C CG1 GDN . . . C 2 27.005 14.908 32.84 1 34.62 ? CG1 GDN 2500 A 1 HETATM 8 C CD1 GDN . . . C 2 25.972 14.431 33.839 1 36.6 ? CD1 GDN 2500 A 1 HETATM 9 O OE1 GDN . . . C 2 24.815 14.873 33.831 1 36.19 ? OE1 GDN 2500 A 1 HETATM 10 N N2 GDN . . . C 2 26.436 13.525 34.689 1 35.27 ? N2 GDN 2500 A 1 HETATM 11 C CA2 GDN . . . C 2 25.632 12.92 35.743 1 39.04 ? CA2 GDN 2500 A 1 HETATM 12 C C2 GDN . . . C 2 26.239 13.305 37.069 1 39.43 ? C2 GDN 2500 A 1 HETATM 13 O O2 GDN . . . C 2 27.432 13.033 37.275 1 36.92 ? O2 GDN 2500 A 1 HETATM 14 C CB2 GDN . . . C 2 25.601 11.41 35.654 1 38.61 ? CB2 GDN 2500 A 1 HETATM 15 S SG2 GDN . . . C 2 24.929 10.709 34.12 1 42.16 ? SG2 GDN 2500 A 1 HETATM 16 N N3 GDN . . . C 2 25.419 13.929 37.911 1 39.48 ? N3 GDN 2500 A 1 HETATM 17 C CA3 GDN . . . C 2 25.858 14.373 39.211 1 42.64 ? CA3 GDN 2500 A 1 HETATM 18 C C3 GDN . . . C 2 25.627 15.851 39.389 1 42.92 ? C3 GDN 2500 A 1 HETATM 19 O O31 GDN . . . C 2 25.791 16.352 40.493 1 46.85 ? O31 GDN 2500 A 1 HETATM 20 O O32 GDN . . . C 2 25.235 16.522 38.438 1 45.44 ? O32 GDN 2500 A 1 HETATM 21 C C1' GDN . . . C 2 23.256 10.573 34.229 1 43.76 ? C1' GDN 2500 A 1 HETATM 22 C C2' GDN . . . C 2 22.574 9.915 33.18 1 46.32 ? C2' GDN 2500 A 1 HETATM 23 C C3' GDN . . . C 2 21.162 9.805 33.282 1 46.28 ? C3' GDN 2500 A 1 HETATM 24 C C4' GDN . . . C 2 20.45 10.361 34.438 1 47.35 ? C4' GDN 2500 A 1 HETATM 25 C C5' GDN . . . C 2 21.212 11.02 35.473 1 46.1 ? C5' GDN 2500 A 1 HETATM 26 C C6' GDN . . . C 2 22.591 11.132 35.385 1 43.61 ? C6' GDN 2500 A 1 HETATM 27 N N2' GDN . . . C 2 23.146 9.318 31.97 1 47.08 ? N2' GDN 2500 A 1 HETATM 28 O O2A GDN . . . C 2 24.387 9.368 31.785 1 46 ? O2A GDN 2500 A 1 HETATM 29 O O2B GDN . . . C 2 22.373 8.77 31.141 1 51.44 ? O2B GDN 2500 A 1 HETATM 30 N N4' GDN . . . C 2 19.043 10.246 34.517 1 46.69 ? N4' GDN 2500 A 1 HETATM 31 O O4A GDN . . . C 2 18.387 9.668 33.598 1 49.61 ? O4A GDN 2500 A 1 HETATM 32 O O4B GDN . . . C 2 18.419 10.727 35.51 1 49.18 ? O4B GDN 2500 A 1 # _model_server_stats.io_time_ms 7 _model_server_stats.parse_time_ms 7 _model_server_stats.create_model_time_ms 5 _model_server_stats.query_time_ms 286 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 32 #