data_3IK9 # _model_server_result.job_id e2c37OAUwT42ldQWXu-3bQ _model_server_result.datetime_utc '2024-11-27 04:01:57' _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 3ik9 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"N","auth_seq_id":506}' # _entry.id 3IK9 # _exptl.entry_id 3IK9 _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 465.562 _entity.id 2 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description '(S)-2-amino-5-((R)-1-(carboxymethylamino)-3-((3S,4R)-1,4-dihydroxynonan-3-ylthio)-1-oxopropan-2-ylamino)-5-oxopentanoic acid' _entity.pdbx_number_of_molecules 8 _entity.pdbx_parent_entity_id . _entity.pdbx_mutation ? _entity.pdbx_fragment ? _entity.pdbx_ec ? # _cell.angle_alpha 90 _cell.angle_beta 117.76 _cell.angle_gamma 90 _cell.entry_id 3IK9 _cell.length_a 95.889 _cell.length_b 114.658 _cell.length_c 96.239 _cell.Z_PDB 16 _cell.pdbx_unique_axis ? # _symmetry.entry_id 3IK9 _symmetry.cell_setting ? _symmetry.Int_Tables_number 4 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 1 21 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 PISA dimeric 2 author_and_software_defined_assembly 4 # loop_ _pdbx_struct_assembly_gen.asym_id_list _pdbx_struct_assembly_gen.assembly_id _pdbx_struct_assembly_gen.oper_expression A,B,I,J,Q,R 1 1 C,D,K,L,S,T 2 1 E,F,M,N,U,V 3 1 G,H,O,P,W,X 4 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 I N N ? 2 J N N ? 2 K N N ? 2 L N N ? 2 M N N ? 2 N N N ? 2 O N N ? 2 P N N # _chem_comp.formula 'C19 H35 N3 O8 S' _chem_comp.formula_weight 465.562 _chem_comp.id BOB _chem_comp.mon_nstd_flag . _chem_comp.name '(S)-2-amino-5-((R)-1-(carboxymethylamino)-3-((3S,4R)-1,4-dihydroxynonan-3-ylthio)-1-oxopropan-2-ylamino)-5-oxopentanoic acid' _chem_comp.type non-polymer _chem_comp.pdbx_synonyms L-gamma-glutamyl-S-[(1S,2R)-2-hydroxy-1-(2-hydroxyethyl)heptyl]-L-cysteinylglycine # 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 O11 C1 BOB doub 70 n n CA1 C1 BOB sing 71 n n C1 O12 BOB sing 72 n n N1 CA1 BOB sing 73 n n N1 HN1 BOB sing 74 n n N1 HN1A BOB sing 75 n n CA2 C2 BOB sing 76 n n C2 N3 BOB sing 77 n n C2 O2 BOB doub 78 n n CD1 N2 BOB sing 79 n n N2 CA2 BOB sing 80 n n N2 HN2 BOB sing 81 n n O32 C3 BOB doub 82 n n C3 CA3 BOB sing 83 n n C3 O31 BOB sing 84 n n N3 CA3 BOB sing 85 n n N3 HN3 BOB sing 86 n n O12 HO12 BOB sing 87 n n O31 HO31 BOB sing 88 n n C42 C40 BOB sing 89 n n C40 SG2 BOB sing 90 n n C40 C54 BOB sing 91 n n C40 H40 BOB sing 92 n n C42 O60 BOB sing 93 n n C42 C43 BOB sing 94 n n C42 H42 BOB sing 95 n n C43 C44 BOB sing 96 n n C43 H43 BOB sing 97 n n C43 H43A BOB sing 98 n n C44 C45 BOB sing 99 n n C44 H44 BOB sing 100 n n C44 H44A BOB sing 101 n n C45 C46 BOB sing 102 n n C45 H45 BOB sing 103 n n C45 H45A BOB sing 104 n n C47 C46 BOB sing 105 n n C46 H46 BOB sing 106 n n C46 H46A BOB sing 107 n n C47 H47 BOB sing 108 n n C47 H47A BOB sing 109 n n C47 H47B BOB sing 110 n n C55 C54 BOB sing 111 n n C54 H54 BOB sing 112 n n C54 H54A BOB sing 113 n n C55 O56 BOB sing 114 n n C55 H55 BOB sing 115 n n C55 H55A BOB sing 116 n n O56 HO56 BOB sing 117 n n O60 HO60 BOB sing 118 n n CA1 CB1 BOB sing 119 n n CA1 HA1 BOB sing 120 n n CA2 CB2 BOB sing 121 n n CA2 HA2 BOB sing 122 n n CA3 HA3 BOB sing 123 n n CA3 HA3A BOB sing 124 n n CB1 CG1 BOB sing 125 n n CB1 HB1 BOB sing 126 n n CB1 HB1A BOB sing 127 n n SG2 CB2 BOB sing 128 n n CB2 HB2 BOB sing 129 n n CB2 HB2A BOB sing 130 n n OE1 CD1 BOB doub 131 n n CG1 CD1 BOB sing 132 n n CG1 HG1 BOB sing 133 n n CG1 HG1A BOB sing 134 n n # _atom_sites.entry_id 3IK9 _atom_sites.fract_transf_matrix[1][1] 0.010429 _atom_sites.fract_transf_matrix[1][2] 0 _atom_sites.fract_transf_matrix[1][3] 0.00549 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.008722 _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] 0.011742 _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 I 2 BOB A 1 501 501 BOB BOB . J 2 BOB B 1 502 502 BOB BOB . K 2 BOB C 1 503 503 BOB BOB . L 2 BOB D 1 504 504 BOB BOB . M 2 BOB E 1 505 505 BOB BOB . N 2 BOB F 1 506 506 BOB BOB . O 2 BOB G 1 507 507 BOB BOB . P 2 BOB H 1 508 508 BOB BOB . Q 3 HOH A 1 6001 6001 HOH HOH . Q 3 HOH A 2 6005 6005 HOH HOH . Q 3 HOH A 3 6013 6013 HOH HOH . Q 3 HOH A 4 6017 6017 HOH HOH . Q 3 HOH A 5 6039 6039 HOH HOH . Q 3 HOH A 6 6059 6059 HOH HOH . R 3 HOH B 1 6003 6003 HOH HOH . R 3 HOH B 2 6004 6004 HOH HOH . R 3 HOH B 3 6009 6009 HOH HOH . R 3 HOH B 4 6010 6010 HOH HOH . R 3 HOH B 5 6015 6015 HOH HOH . R 3 HOH B 6 6016 6016 HOH HOH . R 3 HOH B 7 6021 6021 HOH HOH . R 3 HOH B 8 6025 6025 HOH HOH . R 3 HOH B 9 6028 6028 HOH HOH . R 3 HOH B 10 6040 6040 HOH HOH . R 3 HOH B 11 6055 6055 HOH HOH . R 3 HOH B 12 6056 6056 HOH HOH . R 3 HOH B 13 6057 6057 HOH HOH . R 3 HOH B 14 6058 6058 HOH HOH . S 3 HOH C 1 6007 6007 HOH HOH . S 3 HOH C 2 6008 6008 HOH HOH . S 3 HOH C 3 6019 6019 HOH HOH . S 3 HOH C 4 6020 6020 HOH HOH . S 3 HOH C 5 6027 6027 HOH HOH . S 3 HOH C 6 6032 6032 HOH HOH . S 3 HOH C 7 6037 6037 HOH HOH . S 3 HOH C 8 6038 6038 HOH HOH . S 3 HOH C 9 6052 6052 HOH HOH . S 3 HOH C 10 6053 6053 HOH HOH . S 3 HOH C 11 6054 6054 HOH HOH . T 3 HOH D 1 6006 6006 HOH HOH . T 3 HOH D 2 6012 6012 HOH HOH . T 3 HOH D 3 6014 6014 HOH HOH . T 3 HOH D 4 6018 6018 HOH HOH . T 3 HOH D 5 6022 6022 HOH HOH . T 3 HOH D 6 6033 6033 HOH HOH . T 3 HOH D 7 6034 6034 HOH HOH . T 3 HOH D 8 6035 6035 HOH HOH . T 3 HOH D 9 6036 6036 HOH HOH . T 3 HOH D 10 6049 6049 HOH HOH . T 3 HOH D 11 6050 6050 HOH HOH . T 3 HOH D 12 6051 6051 HOH HOH . U 3 HOH E 1 6002 6002 HOH HOH . U 3 HOH E 2 6011 6011 HOH HOH . U 3 HOH E 3 6023 6023 HOH HOH . U 3 HOH E 4 6044 6044 HOH HOH . V 3 HOH F 1 6026 6026 HOH HOH . V 3 HOH F 2 6029 6029 HOH HOH . V 3 HOH F 3 6030 6030 HOH HOH . V 3 HOH F 4 6045 6045 HOH HOH . V 3 HOH F 5 6046 6046 HOH HOH . W 3 HOH G 1 6031 6031 HOH HOH . W 3 HOH G 2 6041 6041 HOH HOH . W 3 HOH G 3 6042 6042 HOH HOH . W 3 HOH G 4 6043 6043 HOH HOH . X 3 HOH H 1 6024 6024 HOH HOH . X 3 HOH H 2 6047 6047 HOH HOH . X 3 HOH H 3 6048 6048 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 BOB . . . N 2 18.591 -19.394 45.134 1 46.8 ? C1 BOB 506 F 1 HETATM 2 N N1 BOB . . . N 2 19.847 -21.232 46.186 1 45.86 ? N1 BOB 506 F 1 HETATM 3 C C2 BOB . . . N 2 15.795 -17.162 51.952 1 53.19 ? C2 BOB 506 F 1 HETATM 4 N N2 BOB . . . N 2 17.063 -17.285 49.953 1 50.48 ? N2 BOB 506 F 1 HETATM 5 O O2 BOB . . . N 2 14.644 -16.891 51.344 1 52.08 ? O2 BOB 506 F 1 HETATM 6 C C3 BOB . . . N 2 14.849 -19.846 53.935 1 60.85 ? C3 BOB 506 F 1 HETATM 7 N N3 BOB . . . N 2 15.868 -17.812 53.106 1 55.48 ? N3 BOB 506 F 1 HETATM 8 O O11 BOB . . . N 2 19.58 -19.149 44.398 1 42.78 ? O11 BOB 506 F 1 HETATM 9 O O12 BOB . . . N 2 17.457 -18.923 44.901 1 48.52 ? O12 BOB 506 F 1 HETATM 10 O O31 BOB . . . N 2 14.23 -20.466 54.841 1 60.76 ? O31 BOB 506 F 1 HETATM 11 O O32 BOB . . . N 2 15.528 -20.431 53.049 1 62.36 ? O32 BOB 506 F 1 HETATM 12 C C40 BOB . . . N 2 20.036 -14.092 51.423 1 59.09 ? C40 BOB 506 F 1 HETATM 13 C C42 BOB . . . N 2 20.521 -15.104 52.468 1 58.55 ? C42 BOB 506 F 1 HETATM 14 C C43 BOB . . . N 2 19.676 -15.176 53.746 1 58.84 ? C43 BOB 506 F 1 HETATM 15 C C44 BOB . . . N 2 20.461 -14.787 55.002 0.5 57.71 ? C44 BOB 506 F 1 HETATM 16 C C45 BOB . . . N 2 19.519 -14.389 56.14 0.5 56.95 ? C45 BOB 506 F 1 HETATM 17 C C46 BOB . . . N 2 20.002 -14.914 57.488 0.5 57.02 ? C46 BOB 506 F 1 HETATM 18 C C47 BOB . . . N 2 21.509 -15.06 57.531 0.5 56.13 ? C47 BOB 506 F 1 HETATM 19 C C54 BOB . . . N 2 19.834 -12.694 52.037 1 61.41 ? C54 BOB 506 F 1 HETATM 20 C C55 BOB . . . N 2 20.792 -11.628 51.484 1 63.2 ? C55 BOB 506 F 1 HETATM 21 O O56 BOB . . . N 2 20.189 -10.889 50.406 1 64.16 ? O56 BOB 506 F 1 HETATM 22 O O60 BOB . . . N 2 20.541 -16.399 51.853 1 58.28 ? O60 BOB 506 F 1 HETATM 23 C CA1 BOB . . . N 2 18.753 -20.274 46.346 1 47.35 ? CA1 BOB 506 F 1 HETATM 24 C CA2 BOB . . . N 2 17.083 -16.752 51.319 1 53.69 ? CA2 BOB 506 F 1 HETATM 25 C CA3 BOB . . . N 2 14.774 -18.331 53.912 1 58.2 ? CA3 BOB 506 F 1 HETATM 26 C CB1 BOB . . . N 2 19.036 -19.395 47.556 1 46.13 ? CB1 BOB 506 F 1 HETATM 27 C CB2 BOB . . . N 2 17.156 -15.226 51.343 1 54.97 ? CB2 BOB 506 F 1 HETATM 28 C CD1 BOB . . . N 2 17.945 -18.186 49.489 1 48.52 ? CD1 BOB 506 F 1 HETATM 29 O OE1 BOB . . . N 2 18.944 -18.61 50.258 1 49.62 ? OE1 BOB 506 F 1 HETATM 30 C CG1 BOB . . . N 2 17.781 -18.682 48.058 1 46.99 ? CG1 BOB 506 F 1 HETATM 31 S SG2 BOB . . . N 2 18.587 -14.643 50.51 1 56.08 ? SG2 BOB 506 F 1 # _model_server_stats.io_time_ms 22 _model_server_stats.parse_time_ms 7 _model_server_stats.create_model_time_ms 22 _model_server_stats.query_time_ms 266 _model_server_stats.encode_time_ms 5 _model_server_stats.element_count 31 #