data_4LKG # _model_server_result.job_id I_6VWC3Fn6CdAwi1VN6_jg _model_server_result.datetime_utc '2024-10-17 10:24:05' _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 4lkg # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"L","auth_seq_id":601}' # _entry.id 4LKG # _exptl.entry_id 4LKG _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 221.208 _entity.id 5 _entity.src_method man _entity.type non-polymer _entity.pdbx_description 2-acetamido-2-deoxy-beta-D-glucopyranose _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 4LKG _cell.length_a 110.764 _cell.length_b 110.764 _cell.length_c 133.227 _cell.Z_PDB 9 _cell.pdbx_unique_axis ? # _symmetry.entry_id 4LKG _symmetry.cell_setting ? _symmetry.Int_Tables_number 143 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 3' # 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 hexameric 6 author_and_software_defined_assembly 1 PISA hexameric 6 author_and_software_defined_assembly 2 PISA hexameric 6 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,B,G,J 1 1,2,3 C,D,H,K 2 1,4,5 E,F,I,L 3 1,6,7 # loop_ _pdbx_struct_oper_list.id _pdbx_struct_oper_list.type _pdbx_struct_oper_list.name _pdbx_struct_oper_list.symmetry_operation _pdbx_struct_oper_list.matrix[1][1] _pdbx_struct_oper_list.matrix[1][2] _pdbx_struct_oper_list.matrix[1][3] _pdbx_struct_oper_list.matrix[2][1] _pdbx_struct_oper_list.matrix[2][2] _pdbx_struct_oper_list.matrix[2][3] _pdbx_struct_oper_list.matrix[3][1] _pdbx_struct_oper_list.matrix[3][2] _pdbx_struct_oper_list.matrix[3][3] _pdbx_struct_oper_list.vector[1] _pdbx_struct_oper_list.vector[2] _pdbx_struct_oper_list.vector[3] 1 'identity operation' 1_555 x,y,z 1 0 0 0 1 0 0 0 1 0 0 0 2 'crystal symmetry operation' 2_545 -y,x-y-1,z -0.5 -0.866025 0 0.866025 -0.5 0 0 0 1 55.382 -95.924438 0 3 'crystal symmetry operation' 3_655 -x+y+1,-x,z -0.5 0.866025 0 -0.866025 -0.5 0 0 0 1 110.764 0 0 4 'crystal symmetry operation' 2_555 -y,x-y,z -0.5 -0.866025 0 0.866025 -0.5 0 0 0 1 0 0 0 5 'crystal symmetry operation' 3_555 -x+y,-x,z -0.5 0.866025 0 -0.866025 -0.5 0 0 0 1 0 0 0 6 'crystal symmetry operation' 2_655 -y+1,x-y,z -0.5 -0.866025 0 0.866025 -0.5 0 0 0 1 110.764 0 0 7 'crystal symmetry operation' 3_665 -x+y+1,-x+1,z -0.5 0.866025 0 -0.866025 -0.5 0 0 0 1 55.382 95.924438 0 # loop_ _struct_asym.details _struct_asym.entity_id _struct_asym.id _struct_asym.pdbx_modified _struct_asym.pdbx_blank_PDB_chainid_flag ? 5 J N N ? 5 K N N ? 5 L N N # loop_ _pdbx_entity_branch.entity_id _pdbx_entity_branch.type 3 oligosaccharide 4 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 ? 3 2 1 GAL NAG C1 O1 . O4 HO4 . sing 2 ? 3 3 2 SIA GAL C2 O2 . O3 HO3 . sing 3 ? 4 2 1 SIA GAL C2 O2 . O3 HO3 . 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 3 n G NAG 1 G 1 NAG A 803 NAG 3 n G GAL 2 G 2 GAL A 802 GAL 3 n G SIA 3 G 3 SIA A 801 SIA 4 n H GAL 1 H 1 GAL C 802 GAL 4 n H SIA 2 H 2 SIA C 801 SIA 4 n I GAL 1 I 1 GAL E 802 GAL 4 n I SIA 2 I 2 SIA E 801 SIA # 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 4 A CYS 4 1_555 B SG CYS 137 B CYS 458 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.035 ? disulf ? disulf2 A SG CYS 42 A CYS 42 1_555 A SG CYS 268 A CYS 268 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.028 ? disulf ? disulf3 A SG CYS 54 A CYS 54 1_555 A SG CYS 66 A CYS 66 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.028 ? disulf ? disulf4 A SG CYS 87 A CYS 87 1_555 A SG CYS 129 A CYS 129 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.029 ? disulf ? disulf5 A SG CYS 272 A CYS 272 1_555 A SG CYS 296 A CYS 296 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.026 ? disulf ? disulf6 B SG CYS 144 B CYS 465 1_555 B SG CYS 148 B CYS 469 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.032 ? disulf ? disulf7 C SG CYS 4 C CYS 4 1_555 D SG CYS 137 D CYS 458 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.039 ? disulf ? disulf8 C SG CYS 42 C CYS 42 1_555 C SG CYS 268 C CYS 268 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.029 ? disulf ? disulf9 C SG CYS 54 C CYS 54 1_555 C SG CYS 66 C CYS 66 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.024 ? disulf ? disulf10 C SG CYS 87 C CYS 87 1_555 C SG CYS 129 C CYS 129 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.032 ? disulf ? disulf11 C SG CYS 272 C CYS 272 1_555 C SG CYS 296 C CYS 296 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.03 ? disulf ? disulf12 D SG CYS 144 D CYS 465 1_555 D SG CYS 148 D CYS 469 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.034 ? disulf ? disulf13 E SG CYS 4 E CYS 4 1_555 F SG CYS 137 F CYS 458 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.025 ? disulf ? disulf14 E SG CYS 42 E CYS 42 1_555 E SG CYS 268 E CYS 268 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.031 ? disulf ? disulf15 E SG CYS 54 E CYS 54 1_555 E SG CYS 66 E CYS 66 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.022 ? disulf ? disulf16 E SG CYS 87 E CYS 87 1_555 E SG CYS 129 E CYS 129 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.031 ? disulf ? disulf17 E SG CYS 272 E CYS 272 1_555 E SG CYS 296 E CYS 296 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.028 ? disulf ? disulf18 F SG CYS 144 F CYS 465 1_555 F SG CYS 148 F CYS 469 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.035 ? covale ? covale1 B ND2 ASN 82 B ASN 403 1_555 J C1 NAG . B NAG 601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.444 ? covale ? covale2 D ND2 ASN 82 D ASN 403 1_555 K C1 NAG . D NAG 601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.44 ? covale ? covale3 F ND2 ASN 82 F ASN 403 1_555 L C1 NAG . F NAG 601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.443 ? covale ? covale4 G O4 NAG . G NAG 1 1_555 G C1 GAL . G GAL 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.448 ? covale ? covale5 G O3 GAL . G GAL 2 1_555 G C2 SIA . G SIA 3 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.452 ? covale ? covale6 H O3 GAL . H GAL 1 1_555 H C2 SIA . H SIA 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.447 ? covale ? covale7 I O3 GAL . I GAL 1 1_555 I C2 SIA . I SIA 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.437 ? # _chem_comp.formula 'C8 H15 N O6' _chem_comp.formula_weight 221.208 _chem_comp.id NAG _chem_comp.mon_nstd_flag . _chem_comp.name 2-acetamido-2-deoxy-beta-D-glucopyranose _chem_comp.type 'd-saccharide, beta linking' _chem_comp.pdbx_synonyms N-acetyl-beta-D-glucosamine;2-acetamido-2-deoxy-beta-D-glucose;2-acetamido-2-deoxy-D-glucose;2-acetamido-2-deoxy-glucose;N-ACETYL-D-GLUCOSAMINE # 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 C2 NAG sing 259 n n C1 O1 NAG sing 260 n n C1 O5 NAG sing 261 n n C1 H1 NAG sing 262 n n C2 C3 NAG sing 263 n n C2 N2 NAG sing 264 n n C2 H2 NAG sing 265 n n C3 C4 NAG sing 266 n n C3 O3 NAG sing 267 n n C3 H3 NAG sing 268 n n C4 C5 NAG sing 269 n n C4 O4 NAG sing 270 n n C4 H4 NAG sing 271 n n C5 C6 NAG sing 272 n n C5 O5 NAG sing 273 n n C5 H5 NAG sing 274 n n C6 O6 NAG sing 275 n n C6 H61 NAG sing 276 n n C6 H62 NAG sing 277 n n C7 C8 NAG sing 278 n n C7 N2 NAG sing 279 n n C7 O7 NAG doub 280 n n C8 H81 NAG sing 281 n n C8 H82 NAG sing 282 n n C8 H83 NAG sing 283 n n N2 HN2 NAG sing 284 n n O1 HO1 NAG sing 285 n n O3 HO3 NAG sing 286 n n O4 HO4 NAG sing 287 n n O6 HO6 NAG sing 288 n n # loop_ _pdbx_chem_comp_identifier.comp_id _pdbx_chem_comp_identifier.identifier _pdbx_chem_comp_identifier.type _pdbx_chem_comp_identifier.program _pdbx_chem_comp_identifier.program_version NAG DGlcpNAcb 'CONDENSED IUPAC CARBOHYDRATE SYMBOL' GMML 1 NAG N-acetyl-b-D-glucopyranosamine 'COMMON NAME' GMML 1 NAG b-D-GlcpNAc 'IUPAC CARBOHYDRATE SYMBOL' PDB-CARE 1 NAG GlcNAc 'SNFG CARBOHYDRATE SYMBOL' GMML 1 # _atom_sites.entry_id 4LKG _atom_sites.fract_transf_matrix[1][1] 0.009028 _atom_sites.fract_transf_matrix[1][2] 0.005212 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.010425 _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] 0.007506 _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 J 5 NAG B 1 601 601 NAG NAG . K 5 NAG D 1 601 601 NAG NAG . L 5 NAG F 1 601 601 NAG NAG . # 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 NAG . . . L 5 42.606 34.628 13.43 1 115.98 ? C1 NAG 601 F 1 HETATM 2 C C2 NAG . . . L 5 42.001 35.262 14.678 1 120.83 ? C2 NAG 601 F 1 HETATM 3 C C3 NAG . . . L 5 40.661 34.625 15.019 1 120.4 ? C3 NAG 601 F 1 HETATM 4 C C4 NAG . . . L 5 39.737 34.698 13.815 1 121.09 ? C4 NAG 601 F 1 HETATM 5 C C5 NAG . . . L 5 40.425 34.136 12.571 1 125.63 ? C5 NAG 601 F 1 HETATM 6 C C6 NAG . . . L 5 39.578 34.373 11.325 1 140.25 ? C6 NAG 601 F 1 HETATM 7 C C7 NAG . . . L 5 43.358 36.188 16.459 1 117.28 ? C7 NAG 601 F 1 HETATM 8 C C8 NAG . . . L 5 44.133 35.906 17.713 1 96.51 ? C8 NAG 601 F 1 HETATM 9 N N2 NAG . . . L 5 42.911 35.125 15.797 1 118.54 ? N2 NAG 601 F 1 HETATM 10 O O3 NAG . . . L 5 40.076 35.286 16.121 1 122.84 ? O3 NAG 601 F 1 HETATM 11 O O4 NAG . . . L 5 38.56 33.972 14.094 1 115.88 ? O4 NAG 601 F 1 HETATM 12 O O5 NAG . . . L 5 41.694 34.727 12.354 1 122.17 ? O5 NAG 601 F 1 HETATM 13 O O6 NAG . . . L 5 40.325 34.002 10.187 1 140.42 ? O6 NAG 601 F 1 HETATM 14 O O7 NAG . . . L 5 43.159 37.346 16.086 1 112.92 ? O7 NAG 601 F 1 # _model_server_stats.io_time_ms 32 _model_server_stats.parse_time_ms 11 _model_server_stats.create_model_time_ms 37 _model_server_stats.query_time_ms 275 _model_server_stats.encode_time_ms 12 _model_server_stats.element_count 14 #