data_3D67 # _model_server_result.job_id FYld4StCNxk_-Wlihsiicg _model_server_result.datetime_utc '2024-11-22 07:11:48' _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 3d67 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"I","auth_seq_id":660}' # _entry.id 3D67 # _exptl.entry_id 3D67 _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 235.261 _entity.id 4 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description '(2-GUANIDINOETHYLMERCAPTO)SUCCINIC ACID' _entity.pdbx_number_of_molecules 3 _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 3D67 _cell.length_a 161.05 _cell.length_b 161.05 _cell.length_c 138.99 _cell.Z_PDB 18 _cell.pdbx_unique_axis ? # _symmetry.entry_id 3D67 _symmetry.cell_setting ? _symmetry.Int_Tables_number 152 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 31 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 PISA monomeric 1 author_and_software_defined_assembly 1 PISA monomeric 1 author_and_software_defined_assembly 2 PISA monomeric 1 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,D,E,F,G,H,I 1 1 B,J,K,L,M,N,O 2 1 C,P,Q,R,S,T 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 ? 4 I N N ? 4 O N N ? 4 T 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 179 A CYS 156 1_555 A SG CYS 192 A CYS 169 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.032 ? disulf ? disulf2 A SG CYS 251 A CYS 228 1_555 A SG CYS 275 A CYS 252 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.058 ? disulf ? disulf3 A SG CYS 266 A CYS 243 1_555 A SG CYS 280 A CYS 257 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.084 ? disulf ? disulf4 B SG CYS 179 B CYS 156 1_555 B SG CYS 192 B CYS 169 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.038 ? disulf ? disulf5 B SG CYS 251 B CYS 228 1_555 B SG CYS 275 B CYS 252 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.063 ? disulf ? disulf6 B SG CYS 266 B CYS 243 1_555 B SG CYS 280 B CYS 257 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.111 ? disulf ? disulf7 C SG CYS 179 C CYS 156 1_555 C SG CYS 192 C CYS 169 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.012 ? disulf ? disulf8 C SG CYS 251 C CYS 228 1_555 C SG CYS 275 C CYS 252 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.041 ? disulf ? disulf9 C SG CYS 266 C CYS 243 1_555 C SG CYS 280 C CYS 257 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.122 ? covale ? covale1 A ND2 ASN 45 A ASN 22 1_555 D C1 NAG . A NAG 601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.446 ? covale ? covale2 A ND2 ASN 74 A ASN 51 1_555 E C1 NAG . A NAG 602 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.464 ? covale ? covale3 A ND2 ASN 86 A ASN 63 1_555 F C1 NAG . A NAG 603 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.476 ? covale ? covale4 A ND2 ASN 109 A ASN 86 1_555 G C1 NAG . A NAG 604 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.461 ? covale ? covale5 B ND2 ASN 45 B ASN 22 1_555 J C1 NAG . B NAG 601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.448 ? covale ? covale6 B ND2 ASN 74 B ASN 51 1_555 K C1 NAG . B NAG 602 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.459 ? covale ? covale7 B ND2 ASN 86 B ASN 63 1_555 L C1 NAG . B NAG 603 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.461 ? covale ? covale8 B ND2 ASN 109 B ASN 86 1_555 M C1 NAG . B NAG 604 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.458 ? covale ? covale9 C ND2 ASN 45 C ASN 22 1_555 P C1 NAG . C NAG 601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.461 ? covale ? covale10 C ND2 ASN 74 C ASN 51 1_555 Q C1 NAG . C NAG 602 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.449 ? covale ? covale11 C ND2 ASN 109 C ASN 86 1_555 R C1 NAG . C NAG 604 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.45 ? metalc ? metalc1 A ND1 HIS 182 A HIS 159 1_555 H ZN ZN . A ZN 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.085 ? metalc ? metalc2 A OE1 GLU 185 A GLU 162 1_555 H ZN ZN . A ZN 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.013 ? metalc ? metalc3 A OE2 GLU 185 A GLU 162 1_555 H ZN ZN . A ZN 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.026 ? metalc ? metalc4 A ND1 HIS 311 A HIS 288 1_555 H ZN ZN . A ZN 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.068 ? metalc ? metalc5 H ZN ZN . A ZN 501 1_555 I O13 GEM . A GEM 660 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.667 ? metalc ? metalc6 B ND1 HIS 182 B HIS 159 1_555 N ZN ZN . B ZN 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.053 ? metalc ? metalc7 B OE1 GLU 185 B GLU 162 1_555 N ZN ZN . B ZN 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.011 ? metalc ? metalc8 B OE2 GLU 185 B GLU 162 1_555 N ZN ZN . B ZN 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.021 ? metalc ? metalc9 B ND1 HIS 311 B HIS 288 1_555 N ZN ZN . B ZN 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.093 ? metalc ? metalc10 N ZN ZN . B ZN 501 1_555 O O13 GEM . B GEM 660 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.052 ? metalc ? metalc11 C ND1 HIS 182 C HIS 159 1_555 S ZN ZN . C ZN 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.073 ? metalc ? metalc12 C OE1 GLU 185 C GLU 162 1_555 S ZN ZN . C ZN 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.029 ? metalc ? metalc13 C OE2 GLU 185 C GLU 162 1_555 S ZN ZN . C ZN 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.997 ? metalc ? metalc14 C ND1 HIS 311 C HIS 288 1_555 S ZN ZN . C ZN 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.075 ? metalc ? metalc15 S ZN ZN . C ZN 501 1_555 T O13 GEM . C GEM 660 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.143 ? # _chem_comp.formula 'C7 H13 N3 O4 S' _chem_comp.formula_weight 235.261 _chem_comp.id GEM _chem_comp.mon_nstd_flag . _chem_comp.name '(2-GUANIDINOETHYLMERCAPTO)SUCCINIC ACID' _chem_comp.type non-polymer _chem_comp.pdbx_synonyms '2-GUANIDINOETHYLTHIO)SUCCINIC ACID;GUANIDINOETHYL MERCAPTOSUCCINIC ACID;GEMSA' # 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 C8 S7 GEM sing 83 n n C8 C9 GEM sing 84 n n C8 C10 GEM sing 85 n n C8 HC8 GEM sing 86 n n S7 C6 GEM sing 87 n n C6 C5 GEM sing 88 n n C6 HC61 GEM sing 89 n n C6 HC62 GEM sing 90 n n C5 N3 GEM sing 91 n n C5 HC51 GEM sing 92 n n C5 HC52 GEM sing 93 n n N3 C1 GEM sing 94 n n N3 HN3 GEM sing 95 n n C1 N4 GEM sing 96 n n C1 N2 GEM doub 97 n n N4 HN41 GEM sing 98 n n N4 HN42 GEM sing 99 n n N2 HN21 GEM sing 100 n n C9 O14 GEM sing 101 n n C9 O15 GEM doub 102 n n O14 HO41 GEM sing 103 n n C10 C11 GEM sing 104 n n C10 H101 GEM sing 105 n n C10 H102 GEM sing 106 n n C11 O12 GEM doub 107 n n C11 O13 GEM sing 108 n n O13 HO31 GEM sing 109 n n # _atom_sites.entry_id 3D67 _atom_sites.fract_transf_matrix[1][1] 0.006209 _atom_sites.fract_transf_matrix[1][2] 0.003585 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.00717 _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] 0.007195 _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 D 2 NAG A 1 601 601 NAG NAG . E 2 NAG A 1 602 602 NAG NAG . F 2 NAG A 1 603 603 NAG NAG . G 2 NAG A 1 604 604 NAG NAG . H 3 ZN A 1 501 501 ZN ZN . I 4 GEM A 1 660 660 GEM GEM . J 2 NAG B 1 601 601 NAG NAG . K 2 NAG B 1 602 602 NAG NAG . L 2 NAG B 1 603 603 NAG NAG . M 2 NAG B 1 604 604 NAG NAG . N 3 ZN B 1 501 501 ZN ZN . O 4 GEM B 1 660 660 GEM GEM . P 2 NAG C 1 601 601 NAG NAG . Q 2 NAG C 1 602 602 NAG NAG . R 2 NAG C 1 604 604 NAG NAG . S 3 ZN C 1 501 501 ZN ZN . T 4 GEM C 1 660 660 GEM GEM . # 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 C8 GEM . . . I 4 43.009 39.105 42.479 1 108.7 ? C8 GEM 660 A 1 HETATM 2 S S7 GEM . . . I 4 42.089 38.232 41.178 1 111.89 ? S7 GEM 660 A 1 HETATM 3 C C6 GEM . . . I 4 42.832 36.582 41.074 1 111.89 ? C6 GEM 660 A 1 HETATM 4 C C5 GEM . . . I 4 44.354 36.506 41.222 1 112.45 ? C5 GEM 660 A 1 HETATM 5 N N3 GEM . . . I 4 44.831 35.152 41.498 1 112.57 ? N3 GEM 660 A 1 HETATM 6 C C1 GEM . . . I 4 44.172 34.044 41.175 1 111.8 ? C1 GEM 660 A 1 HETATM 7 N N4 GEM . . . I 4 44.232 33.589 39.93 1 111.68 ? N4 GEM 660 A 1 HETATM 8 N N2 GEM . . . I 4 43.442 33.413 42.088 1 110.36 ? N2 GEM 660 A 1 HETATM 9 C C9 GEM . . . I 4 42.836 38.485 43.841 1 107.92 ? C9 GEM 660 A 1 HETATM 10 O O14 GEM . . . I 4 41.867 37.729 44.06 1 106.44 ? O14 GEM 660 A 1 HETATM 11 O O15 GEM . . . I 4 43.68 38.771 44.711 1 107.03 ? O15 GEM 660 A 1 HETATM 12 C C10 GEM . . . I 4 42.541 40.561 42.537 1 107.19 ? C10 GEM 660 A 1 HETATM 13 C C11 GEM . . . I 4 41.094 40.674 42.157 1 104.55 ? C11 GEM 660 A 1 HETATM 14 O O12 GEM . . . I 4 40.791 41.28 41.125 1 103.13 ? O12 GEM 660 A 1 HETATM 15 O O13 GEM . . . I 4 40.256 40.15 42.894 1 102.93 ? O13 GEM 660 A 1 # _model_server_stats.io_time_ms 40 _model_server_stats.parse_time_ms 100 _model_server_stats.create_model_time_ms 121 _model_server_stats.query_time_ms 256 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 15 #