data_1O7D # _model_server_result.job_id xiU4voWvc2r1dqyYHwdkVA _model_server_result.datetime_utc '2024-11-05 00:19:32' _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 1o7d # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"J","auth_seq_id":1}' # _entry.id 1O7D # _exptl.entry_id 1O7D _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 221.208 _entity.id 8 _entity.src_method man _entity.type non-polymer _entity.pdbx_description 2-acetamido-2-deoxy-beta-D-glucopyranose _entity.pdbx_number_of_molecules 1 _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 1O7D _cell.length_a 117.88 _cell.length_b 117.88 _cell.length_c 582.04 _cell.Z_PDB 12 _cell.pdbx_unique_axis ? # _symmetry.entry_id 1O7D _symmetry.cell_setting ? _symmetry.Int_Tables_number 178 _symmetry.space_group_name_Hall . _symmetry.space_group_name_H-M 'P 61 2 2' # _pdbx_struct_assembly.method_details PQS _pdbx_struct_assembly.oligomeric_details pentameric _pdbx_struct_assembly.oligomeric_count 5 _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 _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 # _struct_asym.details ? _struct_asym.entity_id 8 _struct_asym.id J _struct_asym.pdbx_modified N _struct_asym.pdbx_blank_PDB_chainid_flag N # loop_ _pdbx_entity_branch.entity_id _pdbx_entity_branch.type 6 oligosaccharide 7 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 ? 6 2 1 NAG NAG C1 O1 . O4 HO4 . sing 2 ? 6 3 2 BMA NAG C1 O1 . O4 HO4 . sing 3 ? 6 4 3 MAN BMA C1 O1 . O6 HO6 . sing 4 ? 6 5 4 MAN MAN C1 O1 . O6 HO6 . sing 5 ? 6 6 5 MAN MAN C1 O1 . O2 HO2 . sing 6 ? 6 7 4 MAN MAN C1 O1 . O3 HO3 . sing 7 ? 6 8 3 MAN BMA C1 O1 . O3 HO3 . sing 8 ? 6 9 8 MAN MAN C1 O1 . O2 HO2 . sing 9 ? 7 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 6 n F NAG 1 F 1 NAG C 1 NDG 6 n F NAG 2 F 2 NAG C 2 NAG 6 n F BMA 3 F 3 BMA C 3 BMA 6 n F MAN 4 F 4 MAN C 16 MAN 6 n F MAN 5 F 5 MAN C 166 MAN 6 n F MAN 6 F 6 MAN C 167 MAN 6 n F MAN 7 F 7 MAN C 163 MAN 6 n F MAN 8 F 8 MAN C 13 MAN 6 n F MAN 9 F 9 MAN C 14 MAN 7 n G NAG 1 G 1 NAG D 1 NAG 7 n G NAG 2 G 2 NAG D 11 NDG 7 n H NAG 1 H 1 NAG D 2 NAG 7 n H NAG 2 H 2 NAG D 21 NAG 7 n I NAG 1 I 1 NAG D 3 NAG 7 n I NAG 2 I 2 NAG D 31 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 6 A CYS 55 1_555 B SG CYS 12 B CYS 358 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.045 ? disulf ? disulf2 B SG CYS 66 B CYS 412 1_555 C SG CYS 42 C CYS 472 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.069 ? covale ? covale1 J C1 NAG . A NAG 1 1_555 A ND2 ASN 84 A ASN 133 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.453 ? covale ? covale2 C ND2 ASN 67 C ASN 497 1_555 F C1 NAG . F NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.438 ? covale ? covale3 D ND2 ASN 43 D ASN 645 1_555 G C1 NAG . G NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.448 ? covale ? covale4 D ND2 ASN 90 D ASN 692 1_555 H C1 NAG . H NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.448 ? covale ? covale5 D ND2 ASN 164 D ASN 766 1_555 I C1 NAG . I NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.464 ? covale ? covale6 F O4 NAG . F NAG 1 1_555 F C1 NAG . F NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.376 ? covale ? covale7 F O4 NAG . F NAG 2 1_555 F C1 BMA . F BMA 3 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.372 ? covale ? covale8 F O6 BMA . F BMA 3 1_555 F C1 MAN . F MAN 4 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.392 ? covale ? covale9 F O3 BMA . F BMA 3 1_555 F C1 MAN . F MAN 8 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.389 ? covale ? covale10 F O6 MAN . F MAN 4 1_555 F C1 MAN . F MAN 5 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.406 ? covale ? covale11 F O3 MAN . F MAN 4 1_555 F C1 MAN . F MAN 7 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.4 ? covale ? covale12 F O2 MAN . F MAN 5 1_555 F C1 MAN . F MAN 6 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.386 ? covale ? covale13 F O2 MAN . F MAN 8 1_555 F C1 MAN . F MAN 9 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.482 ? covale ? covale14 G O4 NAG . G NAG 1 1_555 G C1 NAG . G NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.398 ? covale ? covale15 H O4 NAG . H NAG 1 1_555 H C1 NAG . H NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.387 ? covale ? covale16 I O4 NAG . I NAG 1 1_555 I C1 NAG . I NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.395 ? metalc ? metalc1 K O3 TRS . A TRS 2 1_555 L ZN ZN . A ZN 3 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.26 ? metalc ? metalc2 L ZN ZN . A ZN 3 1_555 A NE2 HIS 23 A HIS 72 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.117 ? metalc ? metalc3 L ZN ZN . A ZN 3 1_555 A OD1 ASP 25 A ASP 74 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.087 ? metalc ? metalc4 L ZN ZN . A ZN 3 1_555 A OD2 ASP 147 A ASP 196 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.663 ? metalc ? metalc5 L ZN ZN . A ZN 3 1_555 C NE2 HIS 16 C HIS 446 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.238 ? # _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 285 n n C1 O1 NAG sing 286 n n C1 O5 NAG sing 287 n n C1 H1 NAG sing 288 n n C2 C3 NAG sing 289 n n C2 N2 NAG sing 290 n n C2 H2 NAG sing 291 n n C3 C4 NAG sing 292 n n C3 O3 NAG sing 293 n n C3 H3 NAG sing 294 n n C4 C5 NAG sing 295 n n C4 O4 NAG sing 296 n n C4 H4 NAG sing 297 n n C5 C6 NAG sing 298 n n C5 O5 NAG sing 299 n n C5 H5 NAG sing 300 n n C6 O6 NAG sing 301 n n C6 H61 NAG sing 302 n n C6 H62 NAG sing 303 n n C7 C8 NAG sing 304 n n C7 N2 NAG sing 305 n n C7 O7 NAG doub 306 n n C8 H81 NAG sing 307 n n C8 H82 NAG sing 308 n n C8 H83 NAG sing 309 n n N2 HN2 NAG sing 310 n n O1 HO1 NAG sing 311 n n O3 HO3 NAG sing 312 n n O4 HO4 NAG sing 313 n n O6 HO6 NAG sing 314 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 1O7D _atom_sites.fract_transf_matrix[1][1] 0.008483 _atom_sites.fract_transf_matrix[1][2] 0.004898 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.009795 _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] 0.001718 _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 8 NAG A 1 1 1 NAG NAG . K 9 TRS A 1 2 2 TRS TRS . L 10 ZN A 1 3 3 ZN ZN . M 11 SO4 A 1 3001 3001 SO4 SO4 . N 11 SO4 E 1 3002 3002 SO4 SO4 . O 12 HOH A 1 2001 2001 HOH HOH . O 12 HOH A 2 2002 2002 HOH HOH . O 12 HOH A 3 2003 2003 HOH HOH . O 12 HOH A 4 2004 2004 HOH HOH . O 12 HOH A 5 2005 2005 HOH HOH . O 12 HOH A 6 2006 2006 HOH HOH . O 12 HOH A 7 2007 2007 HOH HOH . O 12 HOH A 8 2008 2008 HOH HOH . O 12 HOH A 9 2009 2009 HOH HOH . O 12 HOH A 10 2010 2010 HOH HOH . O 12 HOH A 11 2011 2011 HOH HOH . O 12 HOH A 12 2012 2012 HOH HOH . O 12 HOH A 13 2013 2013 HOH HOH . O 12 HOH A 14 2014 2014 HOH HOH . P 12 HOH B 1 2001 2001 HOH HOH . P 12 HOH B 2 2002 2002 HOH HOH . Q 12 HOH C 1 2001 2001 HOH HOH . Q 12 HOH C 2 2002 2002 HOH HOH . Q 12 HOH C 3 2003 2003 HOH HOH . R 12 HOH D 1 2001 2001 HOH HOH . R 12 HOH D 2 2002 2002 HOH HOH . R 12 HOH D 3 2003 2003 HOH HOH . R 12 HOH D 4 2004 2004 HOH HOH . R 12 HOH D 5 2005 2005 HOH HOH . R 12 HOH D 6 2006 2006 HOH HOH . R 12 HOH D 7 2007 2007 HOH HOH . R 12 HOH D 8 2008 2008 HOH HOH . R 12 HOH D 9 2009 2009 HOH HOH . R 12 HOH D 10 2010 2010 HOH HOH . R 12 HOH D 11 2011 2011 HOH HOH . R 12 HOH D 12 2012 2012 HOH HOH . R 12 HOH D 13 2013 2013 HOH HOH . R 12 HOH D 14 2014 2014 HOH HOH . S 12 HOH E 1 2001 2001 HOH HOH . S 12 HOH E 2 2002 2002 HOH HOH . S 12 HOH E 3 2003 2003 HOH HOH . S 12 HOH E 4 2004 2004 HOH HOH . S 12 HOH E 5 2005 2005 HOH HOH . S 12 HOH E 6 2006 2006 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 . . . J 8 73.974 -1.411 134.2 1 57.04 ? C1 NAG 1 A 1 HETATM 2 C C2 NAG . . . J 8 74.937 -1.532 133.001 1 57.04 ? C2 NAG 1 A 1 HETATM 3 C C3 NAG . . . J 8 75.942 -2.666 133.215 1 57.04 ? C3 NAG 1 A 1 HETATM 4 C C4 NAG . . . J 8 76.645 -2.481 134.57 1 57.04 ? C4 NAG 1 A 1 HETATM 5 C C5 NAG . . . J 8 75.574 -2.482 135.644 1 57.04 ? C5 NAG 1 A 1 HETATM 6 C C6 NAG . . . J 8 76.131 -2.373 137.049 1 57.04 ? C6 NAG 1 A 1 HETATM 7 C C7 NAG . . . J 8 74.816 -2.247 130.695 1 57.04 ? C7 NAG 1 A 1 HETATM 8 C C8 NAG . . . J 8 75.7 -1.251 129.946 1 57.04 ? C8 NAG 1 A 1 HETATM 9 N N2 NAG . . . J 8 74.193 -1.776 131.779 1 57.04 ? N2 NAG 1 A 1 HETATM 10 O O3 NAG . . . J 8 76.896 -2.667 132.155 1 57.04 ? O3 NAG 1 A 1 HETATM 11 O O4 NAG . . . J 8 77.579 -3.529 134.809 1 57.04 ? O4 NAG 1 A 1 HETATM 12 O O5 NAG . . . J 8 74.703 -1.358 135.439 1 57.04 ? O5 NAG 1 A 1 HETATM 13 O O6 NAG . . . J 8 75.268 -3.01 137.982 1 57.04 ? O6 NAG 1 A 1 HETATM 14 O O7 NAG . . . J 8 74.714 -3.43 130.294 1 57.04 ? O7 NAG 1 A 1 # _model_server_stats.io_time_ms 9 _model_server_stats.parse_time_ms 8 _model_server_stats.create_model_time_ms 6 _model_server_stats.query_time_ms 294 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 14 #