data_5OJM # _model_server_result.job_id 959gkIXkWJ556G4DDfeHdQ _model_server_result.datetime_utc '2024-12-22 12:27:15' _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 5ojm # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"P","auth_seq_id":501}' # _entry.id 5OJM # _exptl.entry_id 5OJM _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 5 _entity.pdbx_parent_entity_id . _entity.pdbx_mutation ? _entity.pdbx_fragment ? _entity.pdbx_ec ? # _cell.angle_alpha 90 _cell.angle_beta 102.25 _cell.angle_gamma 90 _cell.entry_id 5OJM _cell.length_a 177.35 _cell.length_b 139.94 _cell.length_c 191.5 _cell.Z_PDB 20 _cell.pdbx_unique_axis ? # _symmetry.entry_id 5OJM _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 decameric _pdbx_struct_assembly.oligomeric_count 10 _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,P,Q,R,S,T _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 P N N ? 5 Q N N ? 5 R N N ? 5 S N N ? 5 T 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 NAG NAG C1 O1 . O4 HO4 . sing 2 ? 3 3 2 BMA NAG C1 O1 . O4 HO4 . sing 3 ? 3 4 3 MAN BMA C1 O1 . O3 HO3 . sing 4 ? 3 5 3 MAN BMA C1 O1 . O6 HO6 . sing 5 ? 4 2 1 NAG NAG C1 O1 . O4 HO4 . sing 6 ? 4 3 2 BMA NAG C1 O1 . O4 HO4 . sing 7 ? 4 4 3 MAN BMA C1 O1 . O6 HO6 . sing 8 ? 4 5 4 MAN MAN C1 O1 . O3 HO3 . sing 9 ? 4 6 3 MAN BMA C1 O1 . 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 K NAG 1 F 1 NAG A 3000 NAG 3 n K NAG 2 F 2 NAG A 3001 NAG 3 n K BMA 3 F 3 BMA A 3002 BMA 3 n K MAN 4 F 4 MAN A 3008 MAN 3 n K MAN 5 F 5 MAN A 3003 MAN 3 n L NAG 1 G 1 NAG B 3000 NAG 3 n L NAG 2 G 2 NAG B 3001 NAG 3 n L BMA 3 G 3 BMA B 3002 BMA 3 n L MAN 4 G 4 MAN B 3008 MAN 3 n L MAN 5 G 5 MAN B 3003 MAN 3 n M NAG 1 H 1 NAG C 3000 NAG 3 n M NAG 2 H 2 NAG C 3001 NAG 3 n M BMA 3 H 3 BMA C 3002 BMA 3 n M MAN 4 H 4 MAN C 3008 MAN 3 n M MAN 5 H 5 MAN C 3003 MAN 4 n N NAG 1 I 1 NAG D 3000 NAG 4 n N NAG 2 I 2 NAG D 3001 NAG 4 n N BMA 3 I 3 BMA D 3002 BMA 4 n N MAN 4 I 4 MAN D 3003 MAN 4 n N MAN 5 I 5 MAN D 3006 MAN 4 n N MAN 6 I 6 MAN D 3008 MAN 4 n O NAG 1 J 1 NAG E 3000 NAG 4 n O NAG 2 J 2 NAG E 3001 NAG 4 n O BMA 3 J 3 BMA E 3002 BMA 4 n O MAN 4 J 4 MAN E 3003 MAN 4 n O MAN 5 J 5 MAN E 3006 MAN 4 n O MAN 6 J 6 MAN E 3008 MAN # 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 167 A CYS 136 1_555 A SG CYS 181 A CYS 150 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.035 ? disulf ? disulf2 B SG CYS 167 B CYS 136 1_555 B SG CYS 181 B CYS 150 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.052 ? disulf ? disulf3 C SG CYS 167 C CYS 136 1_555 C SG CYS 181 C CYS 150 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.05 ? disulf ? disulf4 D SG CYS 167 D CYS 136 1_555 D SG CYS 181 D CYS 150 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.049 ? disulf ? disulf5 E SG CYS 167 E CYS 136 1_555 E SG CYS 181 E CYS 150 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.05 ? disulf ? disulf6 F SG CYS 22 K CYS 22 1_555 F SG CYS 96 K CYS 96 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.038 ? disulf ? disulf7 G SG CYS 22 L CYS 22 1_555 G SG CYS 96 L CYS 96 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.039 ? disulf ? disulf8 H SG CYS 22 M CYS 22 1_555 H SG CYS 96 M CYS 96 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.041 ? disulf ? disulf9 I SG CYS 22 N CYS 22 1_555 I SG CYS 96 N CYS 96 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.032 ? disulf ? disulf10 J SG CYS 22 O CYS 22 1_555 J SG CYS 96 O CYS 96 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.036 ? covale ? covale1 A ND2 ASN 111 A ASN 80 1_555 P C1 NAG . A NAG 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.44 ? covale ? covale2 A ND2 ASN 180 A ASN 149 1_555 K C1 NAG . F NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.445 ? covale ? covale3 B ND2 ASN 111 B ASN 80 1_555 Q C1 NAG . B NAG 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.445 ? covale ? covale4 B ND2 ASN 180 B ASN 149 1_555 L C1 NAG . G NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.44 ? covale ? covale5 C ND2 ASN 111 C ASN 80 1_555 R C1 NAG . C NAG 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.441 ? covale ? covale6 C ND2 ASN 180 C ASN 149 1_555 M C1 NAG . H NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.441 ? covale ? covale7 D ND2 ASN 111 D ASN 80 1_555 S C1 NAG . D NAG 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.444 ? covale ? covale8 D ND2 ASN 180 D ASN 149 1_555 N C1 NAG . I NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.449 ? covale ? covale9 E ND2 ASN 111 E ASN 80 1_555 T C1 NAG . E NAG 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.441 ? covale ? covale10 E ND2 ASN 180 E ASN 149 1_555 O C1 NAG . J NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.437 ? covale ? covale11 K O4 NAG . F NAG 1 1_555 K C1 NAG . F NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.377 ? covale ? covale12 K O4 NAG . F NAG 2 1_555 K C1 BMA . F BMA 3 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.377 ? covale ? covale13 K O3 BMA . F BMA 3 1_555 K C1 MAN . F MAN 4 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.378 ? covale ? covale14 K O6 BMA . F BMA 3 1_555 K C1 MAN . F MAN 5 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.385 ? covale ? covale15 L O4 NAG . G NAG 1 1_555 L C1 NAG . G NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.377 ? covale ? covale16 L O4 NAG . G NAG 2 1_555 L C1 BMA . G BMA 3 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.381 ? covale ? covale17 L O3 BMA . G BMA 3 1_555 L C1 MAN . G MAN 4 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.377 ? covale ? covale18 L O6 BMA . G BMA 3 1_555 L C1 MAN . G MAN 5 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.381 ? covale ? covale19 M O4 NAG . H NAG 1 1_555 M C1 NAG . H NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.375 ? covale ? covale20 M O4 NAG . H NAG 2 1_555 M C1 BMA . H BMA 3 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.378 ? covale ? covale21 M O3 BMA . H BMA 3 1_555 M C1 MAN . H MAN 4 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.379 ? covale ? covale22 M O6 BMA . H BMA 3 1_555 M C1 MAN . H MAN 5 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.385 ? covale ? covale23 N O4 NAG . I NAG 1 1_555 N C1 NAG . I NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.376 ? covale ? covale24 N O4 NAG . I NAG 2 1_555 N C1 BMA . I BMA 3 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.376 ? covale ? covale25 N O6 BMA . I BMA 3 1_555 N C1 MAN . I MAN 4 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.384 ? covale ? covale26 N O3 BMA . I BMA 3 1_555 N C1 MAN . I MAN 6 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.381 ? covale ? covale27 N O3 MAN . I MAN 4 1_555 N C1 MAN . I MAN 5 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.381 ? covale ? covale28 O O4 NAG . J NAG 1 1_555 O C1 NAG . J NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.376 ? covale ? covale29 O O4 NAG . J NAG 2 1_555 O C1 BMA . J BMA 3 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.374 ? covale ? covale30 O O6 BMA . J BMA 3 1_555 O C1 MAN . J MAN 4 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.385 ? covale ? covale31 O O3 BMA . J BMA 3 1_555 O C1 MAN . J MAN 6 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.378 ? covale ? covale32 O O3 MAN . J MAN 4 1_555 O C1 MAN . J MAN 5 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.376 ? # _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 283 n n C1 O1 NAG sing 284 n n C1 O5 NAG sing 285 n n C1 H1 NAG sing 286 n n C2 C3 NAG sing 287 n n C2 N2 NAG sing 288 n n C2 H2 NAG sing 289 n n C3 C4 NAG sing 290 n n C3 O3 NAG sing 291 n n C3 H3 NAG sing 292 n n C4 C5 NAG sing 293 n n C4 O4 NAG sing 294 n n C4 H4 NAG sing 295 n n C5 C6 NAG sing 296 n n C5 O5 NAG sing 297 n n C5 H5 NAG sing 298 n n C6 O6 NAG sing 299 n n C6 H61 NAG sing 300 n n C6 H62 NAG sing 301 n n C7 C8 NAG sing 302 n n C7 N2 NAG sing 303 n n C7 O7 NAG doub 304 n n C8 H81 NAG sing 305 n n C8 H82 NAG sing 306 n n C8 H83 NAG sing 307 n n N2 HN2 NAG sing 308 n n O1 HO1 NAG sing 309 n n O3 HO3 NAG sing 310 n n O4 HO4 NAG sing 311 n n O6 HO6 NAG sing 312 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 5OJM _atom_sites.fract_transf_matrix[1][1] 0.005639 _atom_sites.fract_transf_matrix[1][2] 0 _atom_sites.fract_transf_matrix[1][3] 0.001224 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.007146 _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] 0.005344 _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 P 5 NAG A 1 501 2000 NAG NAG . Q 5 NAG B 1 501 2000 NAG NAG . R 5 NAG C 1 501 2000 NAG NAG . S 5 NAG D 1 501 2000 NAG NAG . T 5 NAG E 1 501 2000 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 . . . P 5 -7.342 -166.409 370.203 1 141.74 ? C1 NAG 501 A 1 HETATM 2 C C2 NAG . . . P 5 -6.03 -166.085 370.927 1 148.04 ? C2 NAG 501 A 1 HETATM 3 C C3 NAG . . . P 5 -5.197 -167.357 371.129 1 149.48 ? C3 NAG 501 A 1 HETATM 4 C C4 NAG . . . P 5 -6.036 -168.49 371.724 1 144.7 ? C4 NAG 501 A 1 HETATM 5 C C5 NAG . . . P 5 -7.312 -168.681 370.912 1 142.14 ? C5 NAG 501 A 1 HETATM 6 C C6 NAG . . . P 5 -8.239 -169.727 371.486 1 135.87 ? C6 NAG 501 A 1 HETATM 7 C C7 NAG . . . P 5 -4.383 -164.244 370.736 1 128.46 ? C7 NAG 501 A 1 HETATM 8 C C8 NAG . . . P 5 -3.823 -163.184 369.831 1 122.7 ? C8 NAG 501 A 1 HETATM 9 N N2 NAG . . . P 5 -5.269 -165.09 370.176 1 140.58 ? N2 NAG 501 A 1 HETATM 10 O O3 NAG . . . P 5 -4.117 -167.063 372.008 1 146.89 ? O3 NAG 501 A 1 HETATM 11 O O4 NAG . . . P 5 -5.291 -169.702 371.716 1 146.5 ? O4 NAG 501 A 1 HETATM 12 O O5 NAG . . . P 5 -8.035 -167.447 370.899 1 147.82 ? O5 NAG 501 A 1 HETATM 13 O O6 NAG . . . P 5 -8.496 -169.491 372.862 1 137.52 ? O6 NAG 501 A 1 HETATM 14 O O7 NAG . . . P 5 -4.028 -164.352 371.905 1 126.46 ? O7 NAG 501 A 1 # _model_server_stats.io_time_ms 66 _model_server_stats.parse_time_ms 36 _model_server_stats.create_model_time_ms 191 _model_server_stats.query_time_ms 478 _model_server_stats.encode_time_ms 5 _model_server_stats.element_count 14 #