data_4E36 # _model_server_result.job_id EN7EbGou05mRE9-o0u-_4A _model_server_result.datetime_utc '2024-11-15 10:33:00' _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 4e36 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"M","auth_seq_id":1005}' # _entry.id 4E36 # _exptl.entry_id 4E36 _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 147.195 _entity.id 4 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description LYSINE _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 90.85 _cell.angle_gamma 90 _cell.entry_id 4E36 _cell.length_a 74.34 _cell.length_b 134.45 _cell.length_c 127.37 _cell.Z_PDB 4 _cell.pdbx_unique_axis ? # _symmetry.entry_id 4E36 _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 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,G,H,I,J,K,L,Q 1 1 B,E,F,M,N,O,P,R 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 # loop_ _struct_asym.details _struct_asym.entity_id _struct_asym.id _struct_asym.pdbx_modified _struct_asym.pdbx_blank_PDB_chainid_flag ? 4 G N N ? 4 M N N # loop_ _pdbx_entity_branch.entity_id _pdbx_entity_branch.type 2 oligosaccharide 3 oligosaccharide # loop_ _pdbx_entity_branch_link.link_id _pdbx_entity_branch_link.details _pdbx_entity_branch_link.entity_id _pdbx_entity_branch_link.entity_branch_list_num_1 _pdbx_entity_branch_link.entity_branch_list_num_2 _pdbx_entity_branch_link.comp_id_1 _pdbx_entity_branch_link.comp_id_2 _pdbx_entity_branch_link.atom_id_1 _pdbx_entity_branch_link.leaving_atom_id_1 _pdbx_entity_branch_link.atom_stereo_config_1 _pdbx_entity_branch_link.atom_id_2 _pdbx_entity_branch_link.leaving_atom_id_2 _pdbx_entity_branch_link.atom_stereo_config_2 _pdbx_entity_branch_link.value_order 1 ? 2 2 1 NAG NAG C1 O1 . O4 HO4 . sing 2 ? 3 2 1 NAG NAG C1 O1 . O4 HO4 . sing 3 ? 3 3 2 MAN NAG C1 O1 . O4 HO4 . sing 4 ? 3 4 3 MAN MAN C1 O1 . O4 HO4 . sing # loop_ _pdbx_branch_scheme.entity_id _pdbx_branch_scheme.hetero _pdbx_branch_scheme.asym_id _pdbx_branch_scheme.mon_id _pdbx_branch_scheme.num _pdbx_branch_scheme.pdb_asym_id _pdbx_branch_scheme.pdb_seq_num _pdbx_branch_scheme.pdb_mon_id _pdbx_branch_scheme.auth_asym_id _pdbx_branch_scheme.auth_seq_num _pdbx_branch_scheme.auth_mon_id 2 n C NAG 1 C 1 NAG A 1002 NAG 2 n C NAG 2 C 2 NAG A 1003 NAG 2 n D NAG 1 D 1 NAG A 1004 NAG 2 n D NAG 2 D 2 NAG A 1005 NAG 3 n E NAG 1 E 1 NAG B 1003 NAG 3 n E NAG 2 E 2 NAG B 1004 NAG 3 n E MAN 3 E 3 MAN B 1001 MAN 3 n E MAN 4 E 4 MAN B 1002 MAN 2 n F NAG 1 F 1 NAG B 1007 NAG 2 n F NAG 2 F 2 NAG B 1008 NAG # 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 421 A CYS 421 1_555 A SG CYS 460 A CYS 460 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.052 ? disulf ? disulf2 A SG CYS 759 A CYS 759 1_555 A SG CYS 766 A CYS 766 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.044 ? disulf ? disulf3 B SG CYS 421 B CYS 421 1_555 B SG CYS 460 B CYS 460 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.056 ? disulf ? disulf4 B SG CYS 759 B CYS 759 1_555 B SG CYS 766 B CYS 766 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.045 ? covale ? covale1 A ND2 ASN 85 A ASN 85 1_555 C C1 NAG . C NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.43 ? covale ? covale2 A ND2 ASN 103 A ASN 103 1_555 J C1 NAG . A NAG 1008 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.439 ? covale ? covale3 A ND2 ASN 219 A ASN 219 1_555 D C1 NAG . D NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.452 ? covale ? covale4 A ND2 ASN 405 A ASN 405 1_555 H C1 NAG . A NAG 1006 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.443 ? covale ? covale5 A ND2 ASN 650 A ASN 650 1_555 I C1 NAG . A NAG 1007 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.456 ? covale ? covale6 B ND2 ASN 85 B ASN 85 1_555 E C1 NAG . E NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.455 ? covale ? covale7 B ND2 ASN 219 B ASN 219 1_555 F C1 NAG . F NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.442 ? covale ? covale8 B ND2 ASN 431 B ASN 431 1_555 O C1 NAG . B NAG 1009 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.449 ? covale ? covale9 C O4 NAG . C NAG 1 1_555 C C1 NAG . C NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.411 ? covale ? covale10 D O4 NAG . D NAG 1 1_555 D C1 NAG . D NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.449 ? covale ? covale11 E O4 NAG . E NAG 1 1_555 E C1 NAG . E NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.456 ? covale ? covale12 E O4 NAG . E NAG 2 1_555 E C1 MAN . E MAN 3 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.453 ? covale ? covale13 E O4 MAN . E MAN 3 1_555 E C1 MAN . E MAN 4 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.422 ? covale ? covale14 F O4 NAG . F NAG 1 1_555 F C1 NAG . F NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.463 ? metalc ? metalc1 A NE2 HIS 370 A HIS 370 1_555 L ZN ZN . A ZN 1010 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.096 ? metalc ? metalc2 A NE2 HIS 374 A HIS 374 1_555 L ZN ZN . A ZN 1010 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.114 ? metalc ? metalc3 A OE1 GLU 393 A GLU 393 1_555 L ZN ZN . A ZN 1010 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.053 ? metalc ? metalc4 A OE2 GLU 393 A GLU 393 1_555 L ZN ZN . A ZN 1010 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.679 ? metalc ? metalc5 G OXT LYS . A LYS 1001 1_555 L ZN ZN . A ZN 1010 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.072 ? metalc ? metalc6 B NE2 HIS 370 B HIS 370 1_555 N ZN ZN . B ZN 1006 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.07 ? metalc ? metalc7 B NE2 HIS 374 B HIS 374 1_555 N ZN ZN . B ZN 1006 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.015 ? metalc ? metalc8 B OE1 GLU 393 B GLU 393 1_555 N ZN ZN . B ZN 1006 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.039 ? metalc ? metalc9 B OE2 GLU 393 B GLU 393 1_555 N ZN ZN . B ZN 1006 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.663 ? metalc ? metalc10 M OXT LYS . B LYS 1005 1_555 N ZN ZN . B ZN 1006 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.122 ? # _chem_comp.formula 'C6 H15 N2 O2 1' _chem_comp.formula_weight 147.195 _chem_comp.id LYS _chem_comp.mon_nstd_flag y _chem_comp.name LYSINE _chem_comp.type 'l-peptide linking' _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 N CA LYS sing 194 n n N H LYS sing 195 n n N H2 LYS sing 196 n n CA C LYS sing 197 n n CA CB LYS sing 198 n n CA HA LYS sing 199 n n C O LYS doub 200 n n C OXT LYS sing 201 n n CB CG LYS sing 202 n n CB HB2 LYS sing 203 n n CB HB3 LYS sing 204 n n CG CD LYS sing 205 n n CG HG2 LYS sing 206 n n CG HG3 LYS sing 207 n n CD CE LYS sing 208 n n CD HD2 LYS sing 209 n n CD HD3 LYS sing 210 n n CE NZ LYS sing 211 n n CE HE2 LYS sing 212 n n CE HE3 LYS sing 213 n n NZ HZ1 LYS sing 214 n n NZ HZ2 LYS sing 215 n n NZ HZ3 LYS sing 216 n n OXT HXT LYS sing 217 n n # _atom_sites.entry_id 4E36 _atom_sites.fract_transf_matrix[1][1] 0.013452 _atom_sites.fract_transf_matrix[1][2] 0 _atom_sites.fract_transf_matrix[1][3] 0.0002 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.007438 _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] 0.007852 _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 4 LYS A 1 1001 1001 LYS LYS . H 5 NAG A 1 1006 1006 NAG NAG . I 5 NAG A 1 1007 1007 NAG NAG . J 5 NAG A 1 1008 1008 NAG NAG . K 6 MES A 1 1009 1009 MES MES . L 7 ZN A 1 1010 1010 ZN ZN . M 4 LYS B 1 1005 1005 LYS LYS . N 7 ZN B 1 1006 1006 ZN ZN . O 5 NAG B 1 1009 1009 NAG NAG . P 6 MES B 1 1010 1010 MES MES . Q 8 HOH A 1 1101 1 HOH HOH . Q 8 HOH A 2 1102 2 HOH HOH . Q 8 HOH A 3 1103 3 HOH HOH . Q 8 HOH A 4 1104 4 HOH HOH . Q 8 HOH A 5 1105 5 HOH HOH . Q 8 HOH A 6 1106 6 HOH HOH . Q 8 HOH A 7 1107 7 HOH HOH . Q 8 HOH A 8 1108 8 HOH HOH . Q 8 HOH A 9 1109 9 HOH HOH . Q 8 HOH A 10 1110 10 HOH HOH . Q 8 HOH A 11 1111 11 HOH HOH . Q 8 HOH A 12 1112 12 HOH HOH . Q 8 HOH A 13 1113 13 HOH HOH . Q 8 HOH A 14 1114 14 HOH HOH . Q 8 HOH A 15 1115 15 HOH HOH . Q 8 HOH A 16 1116 16 HOH HOH . Q 8 HOH A 17 1117 17 HOH HOH . Q 8 HOH A 18 1118 18 HOH HOH . Q 8 HOH A 19 1119 19 HOH HOH . Q 8 HOH A 20 1120 20 HOH HOH . Q 8 HOH A 21 1121 21 HOH HOH . Q 8 HOH A 22 1122 22 HOH HOH . Q 8 HOH A 23 1123 23 HOH HOH . Q 8 HOH A 24 1124 24 HOH HOH . Q 8 HOH A 25 1125 25 HOH HOH . Q 8 HOH A 26 1126 26 HOH HOH . Q 8 HOH A 27 1127 27 HOH HOH . Q 8 HOH A 28 1128 28 HOH HOH . Q 8 HOH A 29 1129 29 HOH HOH . Q 8 HOH A 30 1130 30 HOH HOH . Q 8 HOH A 31 1131 31 HOH HOH . Q 8 HOH A 32 1132 32 HOH HOH . Q 8 HOH A 33 1133 33 HOH HOH . Q 8 HOH A 34 1134 34 HOH HOH . Q 8 HOH A 35 1135 35 HOH HOH . Q 8 HOH A 36 1136 36 HOH HOH . Q 8 HOH A 37 1137 37 HOH HOH . Q 8 HOH A 38 1138 38 HOH HOH . Q 8 HOH A 39 1139 39 HOH HOH . Q 8 HOH A 40 1140 40 HOH HOH . Q 8 HOH A 41 1141 41 HOH HOH . Q 8 HOH A 42 1142 42 HOH HOH . Q 8 HOH A 43 1143 43 HOH HOH . Q 8 HOH A 44 1144 44 HOH HOH . Q 8 HOH A 45 1145 45 HOH HOH . Q 8 HOH A 46 1146 46 HOH HOH . Q 8 HOH A 47 1147 47 HOH HOH . Q 8 HOH A 48 1148 48 HOH HOH . Q 8 HOH A 49 1149 49 HOH HOH . Q 8 HOH A 50 1150 50 HOH HOH . Q 8 HOH A 51 1151 51 HOH HOH . Q 8 HOH A 52 1152 52 HOH HOH . Q 8 HOH A 53 1153 53 HOH HOH . Q 8 HOH A 54 1154 54 HOH HOH . Q 8 HOH A 55 1155 55 HOH HOH . Q 8 HOH A 56 1156 56 HOH HOH . Q 8 HOH A 57 1157 90 HOH HOH . Q 8 HOH A 58 1158 92 HOH HOH . Q 8 HOH A 59 1159 93 HOH HOH . Q 8 HOH A 60 1160 94 HOH HOH . Q 8 HOH A 61 1161 96 HOH HOH . Q 8 HOH A 62 1162 99 HOH HOH . Q 8 HOH A 63 1163 100 HOH HOH . Q 8 HOH A 64 1164 102 HOH HOH . Q 8 HOH A 65 1165 104 HOH HOH . Q 8 HOH A 66 1166 105 HOH HOH . R 8 HOH B 1 1101 57 HOH HOH . R 8 HOH B 2 1102 58 HOH HOH . R 8 HOH B 3 1103 59 HOH HOH . R 8 HOH B 4 1104 60 HOH HOH . R 8 HOH B 5 1105 61 HOH HOH . R 8 HOH B 6 1106 62 HOH HOH . R 8 HOH B 7 1107 63 HOH HOH . R 8 HOH B 8 1108 64 HOH HOH . R 8 HOH B 9 1109 65 HOH HOH . R 8 HOH B 10 1110 66 HOH HOH . R 8 HOH B 11 1111 67 HOH HOH . R 8 HOH B 12 1112 68 HOH HOH . R 8 HOH B 13 1113 69 HOH HOH . R 8 HOH B 14 1114 70 HOH HOH . R 8 HOH B 15 1115 71 HOH HOH . R 8 HOH B 16 1116 72 HOH HOH . R 8 HOH B 17 1117 73 HOH HOH . R 8 HOH B 18 1118 74 HOH HOH . R 8 HOH B 19 1119 75 HOH HOH . R 8 HOH B 20 1120 76 HOH HOH . R 8 HOH B 21 1121 77 HOH HOH . R 8 HOH B 22 1122 78 HOH HOH . R 8 HOH B 23 1123 79 HOH HOH . R 8 HOH B 24 1124 80 HOH HOH . R 8 HOH B 25 1125 81 HOH HOH . R 8 HOH B 26 1126 82 HOH HOH . R 8 HOH B 27 1127 83 HOH HOH . R 8 HOH B 28 1128 84 HOH HOH . R 8 HOH B 29 1129 85 HOH HOH . R 8 HOH B 30 1130 86 HOH HOH . R 8 HOH B 31 1131 87 HOH HOH . R 8 HOH B 32 1132 88 HOH HOH . R 8 HOH B 33 1133 89 HOH HOH . R 8 HOH B 34 1134 91 HOH HOH . R 8 HOH B 35 1135 95 HOH HOH . R 8 HOH B 36 1136 97 HOH HOH . R 8 HOH B 37 1137 98 HOH HOH . R 8 HOH B 38 1138 101 HOH HOH . R 8 HOH B 39 1139 103 HOH HOH . R 8 HOH B 40 1140 106 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 N LYS . . . M 4 17.919 13.343 61.07 1 59.53 ? N LYS 1005 B 1 HETATM 2 C CA LYS . . . M 4 17.073 12.577 60.138 1 69.98 ? CA LYS 1005 B 1 HETATM 3 C C LYS . . . M 4 15.652 12.434 60.645 1 50.71 ? C LYS 1005 B 1 HETATM 4 O O LYS . . . M 4 15.195 11.34 60.934 1 46.98 ? O LYS 1005 B 1 HETATM 5 C CB LYS . . . M 4 17.669 11.189 59.826 1 65.92 ? CB LYS 1005 B 1 HETATM 6 C CG LYS . . . M 4 18.547 11.154 58.562 1 63.2 ? CG LYS 1005 B 1 HETATM 7 C CD LYS . . . M 4 19.464 9.943 58.516 1 57.37 ? CD LYS 1005 B 1 HETATM 8 C CE LYS . . . M 4 20.374 9.992 57.292 1 62.65 ? CE LYS 1005 B 1 HETATM 9 N NZ LYS . . . M 4 21.226 11.216 57.266 1 62.9 ? NZ LYS 1005 B 1 HETATM 10 O OXT LYS . . . M 4 14.951 13.424 60.792 1 55.99 ? OXT LYS 1005 B 1 # _model_server_stats.io_time_ms 11 _model_server_stats.parse_time_ms 14 _model_server_stats.create_model_time_ms 17 _model_server_stats.query_time_ms 255 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 10 #