data_3M5I # _model_server_result.job_id eS2YProGuoZvexV9WY1_aA _model_server_result.datetime_utc '2025-01-13 06:51:00' _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 3m5i # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"O","auth_seq_id":331}' # _entry.id 3M5I # _exptl.entry_id 3M5I _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 2 _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 3M5I _cell.length_a 66.597 _cell.length_b 116.528 _cell.length_c 250.727 _cell.Z_PDB 12 _cell.pdbx_unique_axis ? # _symmetry.entry_id 3M5I _symmetry.cell_setting ? _symmetry.Int_Tables_number 19 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 21 21 21' # _pdbx_struct_assembly.method_details PISA _pdbx_struct_assembly.oligomeric_details hexameric _pdbx_struct_assembly.oligomeric_count 6 _pdbx_struct_assembly.details software_defined_assembly _pdbx_struct_assembly.id 1 # _pdbx_struct_assembly_gen.asym_id_list A,B,C,D,E,F,G,H,I,J,K,L,M,N,O,P,Q,R,S,T,U _pdbx_struct_assembly_gen.assembly_id 1 _pdbx_struct_assembly_gen.oper_expression 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 ? 5 N N N ? 5 O 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 SIA GAL C2 O2 . O6 HO6 . sing 2 ? 4 2 1 NAG NAG 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 3 n G GAL 1 G 1 GAL L 2 GAL 3 n G SIA 2 G 2 SIA L 1 SIA 4 n H NAG 1 H 1 NAG P 1 NAG 4 n H NAG 2 H 2 NAG P 2 NAG 3 n I GAL 1 I 1 GAL M 2 GAL 3 n I SIA 2 I 2 SIA M 1 SIA 4 n J NAG 1 J 1 NAG Q 1 NAG 4 n J NAG 2 J 2 NAG Q 2 NAG 4 n K NAG 1 K 1 NAG R 1 NAG 4 n K NAG 2 K 2 NAG R 2 NAG 3 n L GAL 1 L 1 GAL N 2 GAL 3 n L SIA 2 L 2 SIA N 1 SIA 4 n M NAG 1 M 1 NAG T 1 NAG 4 n M NAG 2 M 2 NAG T 2 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 8 A CYS 14 1_555 B SG CYS 137 B CYS 137 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.045 ? disulf ? disulf2 A SG CYS 46 A CYS 52 1_555 A SG CYS 264 A CYS 277 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.049 ? disulf ? disulf3 A SG CYS 58 A CYS 64 1_555 A SG CYS 70 A CYS 76 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.056 ? disulf ? disulf4 A SG CYS 91 A CYS 97 1_555 A SG CYS 133 A CYS 139 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.036 ? disulf ? disulf5 A SG CYS 268 A CYS 281 1_555 A SG CYS 292 A CYS 305 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.042 ? disulf ? disulf6 B SG CYS 144 B CYS 144 1_555 B SG CYS 148 B CYS 148 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.061 ? disulf ? disulf7 C SG CYS 8 C CYS 14 1_555 D SG CYS 137 D CYS 137 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.036 ? disulf ? disulf8 C SG CYS 46 C CYS 52 1_555 C SG CYS 264 C CYS 277 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.057 ? disulf ? disulf9 C SG CYS 58 C CYS 64 1_555 C SG CYS 70 C CYS 76 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.051 ? disulf ? disulf10 C SG CYS 91 C CYS 97 1_555 C SG CYS 133 C CYS 139 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.038 ? disulf ? disulf11 C SG CYS 268 C CYS 281 1_555 C SG CYS 292 C CYS 305 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.046 ? disulf ? disulf12 D SG CYS 144 D CYS 144 1_555 D SG CYS 148 D CYS 148 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.045 ? disulf ? disulf13 E SG CYS 8 E CYS 14 1_555 F SG CYS 137 F CYS 137 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.043 ? disulf ? disulf14 E SG CYS 46 E CYS 52 1_555 E SG CYS 264 E CYS 277 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.043 ? disulf ? disulf15 E SG CYS 58 E CYS 64 1_555 E SG CYS 70 E CYS 76 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.041 ? disulf ? disulf16 E SG CYS 91 E CYS 97 1_555 E SG CYS 133 E CYS 139 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.037 ? disulf ? disulf17 E SG CYS 268 E CYS 281 1_555 E SG CYS 292 E CYS 305 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.037 ? disulf ? disulf18 F SG CYS 144 F CYS 144 1_555 F SG CYS 148 F CYS 148 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.046 ? covale ? covale1 A ND2 ASN 32 A ASN 38 1_555 N C1 NAG . A NAG 331 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.439 ? covale ? covale2 B ND2 ASN 82 B ASN 82 1_555 H C1 NAG . H NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.441 ? covale ? covale3 C ND2 ASN 32 C ASN 38 1_555 J C1 NAG . J NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.443 ? covale ? covale4 D ND2 ASN 82 D ASN 82 1_555 K C1 NAG . K NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.443 ? covale ? covale5 E ND2 ASN 32 E ASN 38 1_555 O C1 NAG . E NAG 331 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.439 ? covale ? covale6 F ND2 ASN 82 F ASN 82 1_555 M C1 NAG . M NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.447 ? covale ? covale7 G O6 GAL . G GAL 1 1_555 G C2 SIA . G SIA 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.445 ? covale ? covale8 H O4 NAG . H NAG 1 1_555 H C1 NAG . H NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.451 ? covale ? covale9 I O6 GAL . I GAL 1 1_555 I C2 SIA . I SIA 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.446 ? covale ? covale10 J O4 NAG . J NAG 1 1_555 J C1 NAG . J NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.452 ? covale ? covale11 K O4 NAG . K NAG 1 1_555 K C1 NAG . K NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.452 ? covale ? covale12 L O6 GAL . L GAL 1 1_555 L C2 SIA . L SIA 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.441 ? covale ? covale13 M O4 NAG . M NAG 1 1_555 M C1 NAG . M NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.444 ? # _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 261 n n C1 O1 NAG sing 262 n n C1 O5 NAG sing 263 n n C1 H1 NAG sing 264 n n C2 C3 NAG sing 265 n n C2 N2 NAG sing 266 n n C2 H2 NAG sing 267 n n C3 C4 NAG sing 268 n n C3 O3 NAG sing 269 n n C3 H3 NAG sing 270 n n C4 C5 NAG sing 271 n n C4 O4 NAG sing 272 n n C4 H4 NAG sing 273 n n C5 C6 NAG sing 274 n n C5 O5 NAG sing 275 n n C5 H5 NAG sing 276 n n C6 O6 NAG sing 277 n n C6 H61 NAG sing 278 n n C6 H62 NAG sing 279 n n C7 C8 NAG sing 280 n n C7 N2 NAG sing 281 n n C7 O7 NAG doub 282 n n C8 H81 NAG sing 283 n n C8 H82 NAG sing 284 n n C8 H83 NAG sing 285 n n N2 HN2 NAG sing 286 n n O1 HO1 NAG sing 287 n n O3 HO3 NAG sing 288 n n O4 HO4 NAG sing 289 n n O6 HO6 NAG sing 290 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 3M5I _atom_sites.fract_transf_matrix[1][1] 0.015016 _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] 0.008582 _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] 0.003988 _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 N 5 NAG A 1 331 1 NAG NAG . O 5 NAG E 1 331 1 NAG NAG . P 6 HOH A 1 4 4 HOH HOH . P 6 HOH A 2 332 10 HOH HOH . P 6 HOH A 3 333 17 HOH HOH . P 6 HOH A 4 334 20 HOH HOH . P 6 HOH A 5 335 23 HOH HOH . P 6 HOH A 6 336 30 HOH HOH . P 6 HOH A 7 337 38 HOH HOH . P 6 HOH A 8 338 59 HOH HOH . P 6 HOH A 9 339 64 HOH HOH . P 6 HOH A 10 340 65 HOH HOH . P 6 HOH A 11 341 85 HOH HOH . P 6 HOH A 12 342 91 HOH HOH . P 6 HOH A 13 343 92 HOH HOH . Q 6 HOH B 1 185 1 HOH HOH . Q 6 HOH B 2 186 9 HOH HOH . Q 6 HOH B 3 187 11 HOH HOH . Q 6 HOH B 4 188 25 HOH HOH . Q 6 HOH B 5 189 29 HOH HOH . Q 6 HOH B 6 190 43 HOH HOH . Q 6 HOH B 7 191 57 HOH HOH . Q 6 HOH B 8 192 68 HOH HOH . Q 6 HOH B 9 193 71 HOH HOH . Q 6 HOH B 10 194 99 HOH HOH . R 6 HOH C 1 333 18 HOH HOH . R 6 HOH C 2 334 47 HOH HOH . R 6 HOH C 3 335 66 HOH HOH . R 6 HOH C 4 336 83 HOH HOH . R 6 HOH C 5 337 86 HOH HOH . R 6 HOH C 6 338 89 HOH HOH . R 6 HOH C 7 339 103 HOH HOH . S 6 HOH D 1 185 7 HOH HOH . S 6 HOH D 2 186 46 HOH HOH . S 6 HOH D 3 187 56 HOH HOH . S 6 HOH D 4 188 69 HOH HOH . S 6 HOH D 5 189 79 HOH HOH . S 6 HOH D 6 190 80 HOH HOH . S 6 HOH D 7 191 88 HOH HOH . S 6 HOH D 8 192 95 HOH HOH . S 6 HOH D 9 193 97 HOH HOH . T 6 HOH E 1 5 5 HOH HOH . T 6 HOH E 2 6 6 HOH HOH . T 6 HOH E 3 332 2 HOH HOH . T 6 HOH E 4 333 13 HOH HOH . T 6 HOH E 5 334 21 HOH HOH . T 6 HOH E 6 335 26 HOH HOH . T 6 HOH E 7 336 27 HOH HOH . T 6 HOH E 8 337 28 HOH HOH . T 6 HOH E 9 338 32 HOH HOH . T 6 HOH E 10 339 35 HOH HOH . T 6 HOH E 11 340 49 HOH HOH . T 6 HOH E 12 341 55 HOH HOH . T 6 HOH E 13 342 58 HOH HOH . T 6 HOH E 14 343 63 HOH HOH . T 6 HOH E 15 344 67 HOH HOH . T 6 HOH E 16 345 72 HOH HOH . T 6 HOH E 17 346 76 HOH HOH . T 6 HOH E 18 347 87 HOH HOH . T 6 HOH E 19 348 94 HOH HOH . T 6 HOH E 20 349 98 HOH HOH . T 6 HOH E 21 350 100 HOH HOH . T 6 HOH E 22 351 102 HOH HOH . T 6 HOH E 23 352 104 HOH HOH . U 6 HOH F 1 185 24 HOH HOH . U 6 HOH F 2 186 31 HOH HOH . U 6 HOH F 3 187 34 HOH HOH . U 6 HOH F 4 188 39 HOH HOH . U 6 HOH F 5 189 40 HOH HOH . U 6 HOH F 6 190 44 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 NAG . . . O 5 3.721 21.76 23.731 1 76.29 ? C1 NAG 331 E 1 HETATM 2 C C2 NAG . . . O 5 2.49 22.675 23.651 1 84.53 ? C2 NAG 331 E 1 HETATM 3 C C3 NAG . . . O 5 2.66 23.919 24.532 1 86.07 ? C3 NAG 331 E 1 HETATM 4 C C4 NAG . . . O 5 3.269 23.627 25.91 1 86.88 ? C4 NAG 331 E 1 HETATM 5 C C5 NAG . . . O 5 4.37 22.555 25.867 1 84.91 ? C5 NAG 331 E 1 HETATM 6 C C6 NAG . . . O 5 4.732 22.061 27.265 1 83.04 ? C6 NAG 331 E 1 HETATM 7 C C7 NAG . . . O 5 2.923 23.684 21.397 1 88.12 ? C7 NAG 331 E 1 HETATM 8 C C8 NAG . . . O 5 2.322 23.941 20.045 1 86.15 ? C8 NAG 331 E 1 HETATM 9 N N2 NAG . . . O 5 2.141 23.042 22.277 1 86.33 ? N2 NAG 331 E 1 HETATM 10 O O3 NAG . . . O 5 1.399 24.52 24.703 1 87.29 ? O3 NAG 331 E 1 HETATM 11 O O4 NAG . . . O 5 3.792 24.827 26.445 1 88.62 ? O4 NAG 331 E 1 HETATM 12 O O5 NAG . . . O 5 3.962 21.444 25.091 1 80.26 ? O5 NAG 331 E 1 HETATM 13 O O6 NAG . . . O 5 3.73 21.185 27.733 1 83.11 ? O6 NAG 331 E 1 HETATM 14 O O7 NAG . . . O 5 4.074 24.06 21.633 1 89.38 ? O7 NAG 331 E 1 # _model_server_stats.io_time_ms 13 _model_server_stats.parse_time_ms 14 _model_server_stats.create_model_time_ms 21 _model_server_stats.query_time_ms 320 _model_server_stats.encode_time_ms 17 _model_server_stats.element_count 14 #