data_2IBX # _model_server_result.job_id e456GjSxyOVBUV1LiDJ2bA _model_server_result.datetime_utc '2024-10-17 03:28:26' _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 2ibx # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"L","auth_seq_id":509}' # _entry.id 2IBX # _exptl.entry_id 2IBX _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 221.208 _entity.id 4 _entity.src_method man _entity.type non-polymer _entity.pdbx_description 2-acetamido-2-deoxy-beta-D-glucopyranose _entity.pdbx_number_of_molecules 6 _entity.pdbx_parent_entity_id . _entity.pdbx_mutation ? _entity.pdbx_fragment ? _entity.pdbx_ec ? # _cell.angle_alpha 90 _cell.angle_beta 111.39 _cell.angle_gamma 90 _cell.entry_id 2IBX _cell.length_a 174.678 _cell.length_b 100.563 _cell.length_c 160.13 _cell.Z_PDB 12 _cell.pdbx_unique_axis ? # _symmetry.entry_id 2IBX _symmetry.cell_setting ? _symmetry.Int_Tables_number 5 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'C 1 2 1' # _pdbx_struct_assembly.method_details PISA _pdbx_struct_assembly.oligomeric_details hexameric _pdbx_struct_assembly.oligomeric_count 6 _pdbx_struct_assembly.details author_and_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 _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 ? 4 J N N ? 4 K N N ? 4 L N N ? 4 M N N ? 4 N N N ? 4 O N N # _pdbx_entity_branch.entity_id 3 _pdbx_entity_branch.type oligosaccharide # _pdbx_entity_branch_link.link_id 1 _pdbx_entity_branch_link.details ? _pdbx_entity_branch_link.entity_id 3 _pdbx_entity_branch_link.entity_branch_list_num_1 2 _pdbx_entity_branch_link.entity_branch_list_num_2 1 _pdbx_entity_branch_link.comp_id_1 NAG _pdbx_entity_branch_link.comp_id_2 NAG _pdbx_entity_branch_link.atom_id_1 C1 _pdbx_entity_branch_link.leaving_atom_id_1 O1 _pdbx_entity_branch_link.atom_stereo_config_1 . _pdbx_entity_branch_link.atom_id_2 O4 _pdbx_entity_branch_link.leaving_atom_id_2 HO4 _pdbx_entity_branch_link.atom_stereo_config_2 . _pdbx_entity_branch_link.value_order 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 S 503 NAG 3 n G NAG 2 G 2 NAG S 504 NAG 3 n H NAG 1 H 1 NAG U 510 NAG 3 n H NAG 2 H 2 NAG U 511 NAG 3 n I NAG 1 I 1 NAG W 517 NAG 3 n I NAG 2 I 2 NAG W 518 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 20 A CYS 8 1_555 B SG CYS 137 B CYS 137 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.063 ? disulf ? disulf2 A SG CYS 58 A CYS 46 1_555 A SG CYS 290 A CYS 278 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.068 ? disulf ? disulf3 A SG CYS 71 A CYS 59 1_555 A SG CYS 83 A CYS 71 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.089 ? disulf ? disulf4 A SG CYS 106 A CYS 94 1_555 A SG CYS 151 A CYS 139 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.109 ? disulf ? disulf5 A SG CYS 294 A CYS 282 1_555 A SG CYS 318 A CYS 306 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.072 ? disulf ? disulf6 B SG CYS 144 B CYS 144 1_555 B SG CYS 148 B CYS 148 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.058 ? disulf ? disulf7 C SG CYS 20 C CYS 8 1_555 D SG CYS 137 D CYS 137 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.076 ? disulf ? disulf8 C SG CYS 58 C CYS 46 1_555 C SG CYS 290 C CYS 278 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.051 ? disulf ? disulf9 C SG CYS 71 C CYS 59 1_555 C SG CYS 83 C CYS 71 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.082 ? disulf ? disulf10 C SG CYS 106 C CYS 94 1_555 C SG CYS 151 C CYS 139 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.107 ? disulf ? disulf11 C SG CYS 294 C CYS 282 1_555 C SG CYS 318 C CYS 306 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.067 ? disulf ? disulf12 D SG CYS 144 D CYS 144 1_555 D SG CYS 148 D CYS 148 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.05 ? disulf ? disulf13 E SG CYS 20 E CYS 8 1_555 F SG CYS 137 F CYS 137 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.094 ? disulf ? disulf14 E SG CYS 58 E CYS 46 1_555 E SG CYS 290 E CYS 278 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.048 ? disulf ? disulf15 E SG CYS 71 E CYS 59 1_555 E SG CYS 83 E CYS 71 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.095 ? disulf ? disulf16 E SG CYS 106 E CYS 94 1_555 E SG CYS 151 E CYS 139 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.106 ? disulf ? disulf17 E SG CYS 294 E CYS 282 1_555 E SG CYS 318 E CYS 306 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.06 ? disulf ? disulf18 F SG CYS 144 F CYS 144 1_555 F SG CYS 148 F CYS 148 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.057 ? covale ? covale1 A ND2 ASN 39 A ASN 27 1_555 J C1 NAG . A NAG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.453 ? covale ? covale2 A ND2 ASN 181 A ASN 169 1_555 G C1 NAG . G NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.432 ? covale ? covale3 C ND2 ASN 39 C ASN 27 1_555 L C1 NAG . C NAG 509 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.458 ? covale ? covale4 C ND2 ASN 181 C ASN 169 1_555 H C1 NAG . H NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.452 ? covale ? covale5 E ND2 ASN 39 E ASN 27 1_555 N C1 NAG . E NAG 516 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.455 ? covale ? covale6 E ND2 ASN 181 E ASN 169 1_555 I C1 NAG . I NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.437 ? covale ? covale7 G O4 NAG . G NAG 1 1_555 G C1 NAG . G NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.441 ? covale ? covale8 H O4 NAG . H NAG 1 1_555 H C1 NAG . H NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.455 ? covale ? covale9 I O4 NAG . I NAG 1 1_555 I C1 NAG . I NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.432 ? # _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 235 n n C1 O1 NAG sing 236 n n C1 O5 NAG sing 237 n n C1 H1 NAG sing 238 n n C2 C3 NAG sing 239 n n C2 N2 NAG sing 240 n n C2 H2 NAG sing 241 n n C3 C4 NAG sing 242 n n C3 O3 NAG sing 243 n n C3 H3 NAG sing 244 n n C4 C5 NAG sing 245 n n C4 O4 NAG sing 246 n n C4 H4 NAG sing 247 n n C5 C6 NAG sing 248 n n C5 O5 NAG sing 249 n n C5 H5 NAG sing 250 n n C6 O6 NAG sing 251 n n C6 H61 NAG sing 252 n n C6 H62 NAG sing 253 n n C7 C8 NAG sing 254 n n C7 N2 NAG sing 255 n n C7 O7 NAG doub 256 n n C8 H81 NAG sing 257 n n C8 H82 NAG sing 258 n n C8 H83 NAG sing 259 n n N2 HN2 NAG sing 260 n n O1 HO1 NAG sing 261 n n O3 HO3 NAG sing 262 n n O4 HO4 NAG sing 263 n n O6 HO6 NAG sing 264 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 2IBX _atom_sites.fract_transf_matrix[1][1] 0.005725 _atom_sites.fract_transf_matrix[1][2] 0 _atom_sites.fract_transf_matrix[1][3] 0.002242 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.009944 _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] 0.006707 _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 4 NAG A 1 502 502 NAG NAG . K 4 NAG B 1 507 507 NAG NAG . L 4 NAG C 1 509 509 NAG NAG . M 4 NAG D 1 514 514 NAG NAG . N 4 NAG E 1 516 516 NAG NAG . O 4 NAG F 1 521 521 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 4 -70.55 54.481 31.935 1 65.39 ? C1 NAG 509 C 1 HETATM 2 C C2 NAG . . . L 4 -69.596 55.577 32.421 1 70.73 ? C2 NAG 509 C 1 HETATM 3 C C3 NAG . . . L 4 -70.12 56.268 33.679 1 70.51 ? C3 NAG 509 C 1 HETATM 4 C C4 NAG . . . L 4 -71.523 56.806 33.397 1 70.8 ? C4 NAG 509 C 1 HETATM 5 C C5 NAG . . . L 4 -72.449 55.669 32.954 1 70.53 ? C5 NAG 509 C 1 HETATM 6 C C6 NAG . . . L 4 -73.845 56.204 32.607 1 71.24 ? C6 NAG 509 C 1 HETATM 7 C C7 NAG . . . L 4 -67.238 55.607 31.872 1 73.94 ? C7 NAG 509 C 1 HETATM 8 C C8 NAG . . . L 4 -65.92 55.835 32.565 1 74.22 ? C8 NAG 509 C 1 HETATM 9 N N2 NAG . . . L 4 -68.23 55.104 32.621 1 73.02 ? N2 NAG 509 C 1 HETATM 10 O O3 NAG . . . L 4 -69.231 57.307 34.035 1 69.69 ? O3 NAG 509 C 1 HETATM 11 O O4 NAG . . . L 4 -72.053 57.457 34.534 1 72.8 ? O4 NAG 509 C 1 HETATM 12 O O5 NAG . . . L 4 -71.887 54.99 31.831 1 69.05 ? O5 NAG 509 C 1 HETATM 13 O O6 NAG . . . L 4 -74.806 55.168 32.674 1 72.51 ? O6 NAG 509 C 1 HETATM 14 O O7 NAG . . . L 4 -67.376 55.882 30.671 1 73.14 ? O7 NAG 509 C 1 # _model_server_stats.io_time_ms 10 _model_server_stats.parse_time_ms 8 _model_server_stats.create_model_time_ms 16 _model_server_stats.query_time_ms 261 _model_server_stats.encode_time_ms 5 _model_server_stats.element_count 14 #