data_5GIB # _model_server_result.job_id dpHKUtxOKin68gh4Zkg_Xw _model_server_result.datetime_utc '2024-11-08 05:39:52' _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 5gib # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"C","auth_seq_id":301}' # _entry.id 5GIB # _exptl.entry_id 5GIB _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 118.088 _entity.id 2 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description 'SUCCINIC 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 5GIB _cell.length_a 53.29 _cell.length_b 58.26 _cell.length_c 136.47 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 5GIB _symmetry.cell_setting ? _symmetry.Int_Tables_number 19 _symmetry.space_group_name_Hall . _symmetry.space_group_name_H-M 'P 21 21 21' # 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 monomeric 1 author_and_software_defined_assembly 1 PISA monomeric 1 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,D,F 1 1 B,E,G 2 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 2 _struct_asym.id C _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 A SG CYS 7 A CYS 7 1_555 A SG CYS 137 A CYS 137 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.029 ? disulf ? disulf2 A SG CYS 25 A CYS 25 1_555 A SG CYS 41 A CYS 41 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.032 ? disulf ? disulf3 A SG CYS 109 A CYS 109 1_555 A SG CYS 210 A CYS 210 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.03 ? disulf ? disulf4 A SG CYS 116 A CYS 116 1_555 A SG CYS 183 A CYS 183 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.029 ? disulf ? disulf5 A SG CYS 148 A CYS 148 1_555 A SG CYS 162 A CYS 162 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.029 ? disulf ? disulf6 A SG CYS 173 A CYS 173 1_555 A SG CYS 197 A CYS 197 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.03 ? disulf ? disulf7 B SG CYS 7 B CYS 7 1_555 B SG CYS 137 B CYS 137 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.029 ? disulf ? disulf8 B SG CYS 25 B CYS 25 1_555 B SG CYS 41 B CYS 41 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.033 ? disulf ? disulf9 B SG CYS 109 B CYS 109 1_555 B SG CYS 210 B CYS 210 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.031 ? disulf ? disulf10 B SG CYS 116 B CYS 116 1_555 B SG CYS 183 B CYS 183 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.029 ? disulf ? disulf11 B SG CYS 148 B CYS 148 1_555 B SG CYS 162 B CYS 162 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.031 ? disulf ? disulf12 B SG CYS 173 B CYS 173 1_555 B SG CYS 197 B CYS 197 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.03 ? metalc ? metalc1 A OE2 GLU 52 A GLU 52 1_555 D CA CA . A CA 302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.474 ? metalc ? metalc2 A O ASN 54 A ASN 54 1_555 D CA CA . A CA 302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.464 ? metalc ? metalc3 A O VAL 57 A VAL 57 1_555 D CA CA . A CA 302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.493 ? metalc ? metalc4 A OE2 GLU 62 A GLU 62 1_555 D CA CA . A CA 302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.459 ? metalc ? metalc5 B OE2 GLU 52 B GLU 52 1_555 E CA CA . B CA 301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.942 ? metalc ? metalc6 B O ASN 54 B ASN 54 1_555 E CA CA . B CA 301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.414 ? metalc ? metalc7 B O VAL 57 B VAL 57 1_555 E CA CA . B CA 301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.563 ? metalc ? metalc8 B OE2 GLU 59 B GLU 59 1_555 E CA CA . B CA 301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.924 ? metalc ? metalc9 B OE2 GLU 62 B GLU 62 1_555 E CA CA . B CA 301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.433 ? # _chem_comp.formula 'C4 H6 O4' _chem_comp.formula_weight 118.088 _chem_comp.id SIN _chem_comp.mon_nstd_flag . _chem_comp.name 'SUCCINIC ACID' _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 C1 O1 SIN doub 290 n n C1 O2 SIN sing 291 n n C1 C2 SIN sing 292 n n O2 HO2 SIN sing 293 n n C2 C3 SIN sing 294 n n C2 H21 SIN sing 295 n n C2 H22 SIN sing 296 n n C3 C4 SIN sing 297 n n C3 H31 SIN sing 298 n n C3 H32 SIN sing 299 n n C4 O3 SIN doub 300 n n C4 O4 SIN sing 301 n n O4 HO4 SIN sing 302 n n # _atom_sites.entry_id 5GIB _atom_sites.fract_transf_matrix[1][1] 0.018765 _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] 0.017164 _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] 0.007328 _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 SIN A 1 301 1 SIN SIN . D 3 CA A 1 302 1 CA CA . E 3 CA B 1 301 1 CA CA . F 4 HOH A 1 401 38 HOH HOH . F 4 HOH A 2 402 54 HOH HOH . F 4 HOH A 3 403 46 HOH HOH . F 4 HOH A 4 404 12 HOH HOH . F 4 HOH A 5 405 36 HOH HOH . F 4 HOH A 6 406 3 HOH HOH . F 4 HOH A 7 407 37 HOH HOH . F 4 HOH A 8 408 23 HOH HOH . F 4 HOH A 9 409 51 HOH HOH . F 4 HOH A 10 410 32 HOH HOH . F 4 HOH A 11 411 48 HOH HOH . F 4 HOH A 12 412 17 HOH HOH . F 4 HOH A 13 413 42 HOH HOH . F 4 HOH A 14 414 19 HOH HOH . F 4 HOH A 15 415 15 HOH HOH . F 4 HOH A 16 416 57 HOH HOH . F 4 HOH A 17 417 26 HOH HOH . F 4 HOH A 18 418 25 HOH HOH . F 4 HOH A 19 419 5 HOH HOH . F 4 HOH A 20 420 10 HOH HOH . F 4 HOH A 21 421 9 HOH HOH . F 4 HOH A 22 422 39 HOH HOH . F 4 HOH A 23 423 29 HOH HOH . F 4 HOH A 24 424 24 HOH HOH . F 4 HOH A 25 425 21 HOH HOH . F 4 HOH A 26 426 11 HOH HOH . F 4 HOH A 27 427 40 HOH HOH . F 4 HOH A 28 428 16 HOH HOH . F 4 HOH A 29 429 28 HOH HOH . G 4 HOH B 1 401 34 HOH HOH . G 4 HOH B 2 402 45 HOH HOH . G 4 HOH B 3 403 18 HOH HOH . G 4 HOH B 4 404 44 HOH HOH . G 4 HOH B 5 405 2 HOH HOH . G 4 HOH B 6 406 8 HOH HOH . G 4 HOH B 7 407 55 HOH HOH . G 4 HOH B 8 408 1 HOH HOH . G 4 HOH B 9 409 35 HOH HOH . G 4 HOH B 10 410 20 HOH HOH . G 4 HOH B 11 411 49 HOH HOH . G 4 HOH B 12 412 60 HOH HOH . G 4 HOH B 13 413 4 HOH HOH . G 4 HOH B 14 414 22 HOH HOH . G 4 HOH B 15 415 59 HOH HOH . G 4 HOH B 16 416 56 HOH HOH . G 4 HOH B 17 417 6 HOH HOH . G 4 HOH B 18 418 13 HOH HOH . G 4 HOH B 19 419 30 HOH HOH . G 4 HOH B 20 420 41 HOH HOH . G 4 HOH B 21 421 53 HOH HOH . G 4 HOH B 22 422 43 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 C1 SIN . . . C 2 13.161 -18.946 6.175 1 7.48 ? C1 SIN 301 A 1 HETATM 2 O O1 SIN . . . C 2 13.462 -19.845 5.36 1 13.27 ? O1 SIN 301 A 1 HETATM 3 O O2 SIN . . . C 2 13.688 -18.952 7.308 1 8.14 ? O2 SIN 301 A 1 HETATM 4 C C2 SIN . . . C 2 12.175 -17.867 5.796 1 6.49 ? C2 SIN 301 A 1 HETATM 5 C C3 SIN . . . C 2 11.475 -18.247 4.498 1 7.79 ? C3 SIN 301 A 1 HETATM 6 C C4 SIN . . . C 2 10.353 -17.271 4.234 1 16.36 ? C4 SIN 301 A 1 HETATM 7 O O3 SIN . . . C 2 9.713 -17.319 3.161 1 21.67 ? O3 SIN 301 A 1 HETATM 8 O O4 SIN . . . C 2 10.058 -16.4 5.081 1 12.51 ? O4 SIN 301 A 1 # _model_server_stats.io_time_ms 61 _model_server_stats.parse_time_ms 13 _model_server_stats.create_model_time_ms 7 _model_server_stats.query_time_ms 333 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 8 #