data_3KM9 # _model_server_result.job_id nHXHYV4wsSrgXCKcmniEsw _model_server_result.datetime_utc '2024-11-30 09:39:22' _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 3km9 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"J","auth_seq_id":1680}' # _entry.id 3KM9 # _exptl.entry_id 3KM9 _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 120 _cell.entry_id 3KM9 _cell.length_a 144.79 _cell.length_b 144.79 _cell.length_c 245.28 _cell.Z_PDB 6 _cell.pdbx_unique_axis ? # _symmetry.entry_id 3KM9 _symmetry.cell_setting ? _symmetry.Int_Tables_number 144 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 31' # loop_ _pdbx_struct_assembly.method_details _pdbx_struct_assembly.oligomeric_details _pdbx_struct_assembly.oligomeric_count _pdbx_struct_assembly.details _pdbx_struct_assembly.id ? dimeric 2 author_defined_assembly 1 ? dimeric 2 author_defined_assembly 2 # loop_ _pdbx_struct_assembly_gen.asym_id_list _pdbx_struct_assembly_gen.assembly_id _pdbx_struct_assembly_gen.oper_expression A,B,E,G,H,I,J 1 1 C,D,F,K,L,M 2 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 J N N ? 5 M 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 E NAG 1 C 1 NAG D 2001 NAG 3 n E NAG 2 C 2 NAG D 2002 NAG 3 n F NAG 1 D 1 NAG F 2001 NAG 3 n F NAG 2 D 2 NAG F 2002 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 567 A CYS 567 1_555 A SG CYS 810 A CYS 810 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.036 ? disulf ? disulf2 A SG CYS 634 A CYS 634 1_555 A SG CYS 669 A CYS 669 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.039 ? disulf ? disulf3 A SG CYS 698 A CYS 698 1_555 A SG CYS 724 A CYS 724 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.283 ? disulf ? disulf4 A SG CYS 699 A CYS 699 1_555 A SG CYS 731 A CYS 731 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.026 ? disulf ? disulf5 A SG CYS 711 A CYS 711 1_555 A SG CYS 732 A CYS 732 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.033 ? disulf ? disulf6 A SG CYS 856 A CYS 856 1_555 A SG CYS 883 A CYS 883 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.032 ? disulf ? disulf7 A SG CYS 1101 A CYS 1101 1_555 A SG CYS 1159 A CYS 1159 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.047 ? disulf ? disulf8 A SG CYS 1375 A CYS 1375 1_555 A SG CYS 1505 A CYS 1505 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.03 ? disulf ? disulf9 A SG CYS 1405 A CYS 1405 1_555 A SG CYS 1474 A CYS 1474 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.035 ? disulf ? disulf10 C SG CYS 567 B CYS 567 1_555 C SG CYS 810 B CYS 810 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.034 ? disulf ? disulf11 C SG CYS 634 B CYS 634 1_555 C SG CYS 669 B CYS 669 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.032 ? disulf ? disulf12 C SG CYS 698 B CYS 698 1_555 C SG CYS 724 B CYS 724 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.039 ? disulf ? disulf13 C SG CYS 699 B CYS 699 1_555 C SG CYS 731 B CYS 731 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.024 ? disulf ? disulf14 C SG CYS 711 B CYS 711 1_555 C SG CYS 732 B CYS 732 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.036 ? disulf ? disulf15 C SG CYS 856 B CYS 856 1_555 C SG CYS 883 B CYS 883 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.036 ? disulf ? disulf16 C SG CYS 1101 B CYS 1101 1_555 C SG CYS 1159 B CYS 1159 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.045 ? disulf ? disulf17 C SG CYS 1375 B CYS 1375 1_555 C SG CYS 1505 B CYS 1505 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.027 ? disulf ? disulf18 C SG CYS 1405 B CYS 1405 1_555 C SG CYS 1474 B CYS 1474 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.039 ? covale ? covale1 A ND2 ASN 741 A ASN 741 1_555 J C1 NAG . A NAG 1680 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.451 ? covale ? covale2 A ND2 ASN 911 A ASN 911 1_555 E C1 NAG . C NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.441 ? covale ? covale3 C ND2 ASN 741 B ASN 741 1_555 M C1 NAG . B NAG 1679 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.452 ? covale ? covale4 C ND2 ASN 911 B ASN 911 1_555 F C1 NAG . D NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.442 ? covale ? covale5 E O4 NAG . C NAG 1 1_555 E C1 NAG . C NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.373 ? covale ? covale6 F O4 NAG . D NAG 1 1_555 F C1 NAG . D NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.372 ? metalc ? metalc1 A OE1 GLU 247 A GLU 247 1_555 G CD CD . A CD 1677 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.365 ? metalc ? metalc2 A OD2 ASP 264 A ASP 264 1_555 I CD CD . A CD 1679 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.234 ? metalc ? metalc3 A OD1 ASP 471 A ASP 471 1_555 H CD CD . A CD 1678 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.293 ? metalc ? metalc4 A OD2 ASP 471 A ASP 471 1_555 H CD CD . A CD 1678 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.424 ? metalc ? metalc5 A OE1 GLU 480 A GLU 480 1_555 H CD CD . A CD 1678 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.307 ? metalc ? metalc6 A OE2 GLU 480 A GLU 480 1_555 H CD CD . A CD 1678 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.446 ? metalc ? metalc7 A ND1 HIS 753 A HIS 753 1_555 I CD CD . A CD 1679 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.423 ? metalc ? metalc8 G CD CD . A CD 1677 1_555 C OE1 GLU 247 B GLU 247 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.354 ? metalc ? metalc9 C OD2 ASP 264 B ASP 264 1_555 L CD CD . B CD 1678 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.455 ? metalc ? metalc10 C OD1 ASP 471 B ASP 471 1_555 K CD CD . B CD 1677 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.311 ? metalc ? metalc11 C OD2 ASP 471 B ASP 471 1_555 K CD CD . B CD 1677 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.433 ? metalc ? metalc12 C OE1 GLU 480 B GLU 480 1_555 K CD CD . B CD 1677 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.361 ? metalc ? metalc13 C OE2 GLU 480 B GLU 480 1_555 K CD CD . B CD 1677 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.417 ? metalc ? metalc14 C ND1 HIS 753 B HIS 753 1_555 L CD CD . B CD 1678 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.321 ? # _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 3KM9 _atom_sites.fract_transf_matrix[1][1] 0.006907 _atom_sites.fract_transf_matrix[1][2] 0.003988 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.007975 _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] 0.004077 _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 G 4 CD A 1 1677 1 CD CD . H 4 CD A 1 1678 2 CD CD . I 4 CD A 1 1679 3 CD CD . J 5 NAG A 1 1680 1 NAG NAG . K 4 CD B 1 1677 2 CD CD . L 4 CD B 1 1678 3 CD CD . M 5 NAG B 1 1679 1 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 . . . J 5 68.315 14.014 20.244 1 301.45 ? C1 NAG 1680 A 1 HETATM 2 C C2 NAG . . . J 5 68.609 13.892 21.757 1 301.45 ? C2 NAG 1680 A 1 HETATM 3 C C3 NAG . . . J 5 69.027 15.192 22.447 1 301.45 ? C3 NAG 1680 A 1 HETATM 4 C C4 NAG . . . J 5 69.924 16.04 21.552 1 301.45 ? C4 NAG 1680 A 1 HETATM 5 C C5 NAG . . . J 5 69.236 16.209 20.21 1 301.45 ? C5 NAG 1680 A 1 HETATM 6 C C6 NAG . . . J 5 69.953 17.234 19.334 1 301.45 ? C6 NAG 1680 A 1 HETATM 7 C C7 NAG . . . J 5 67.577 12.814 23.69 1 301.45 ? C7 NAG 1680 A 1 HETATM 8 C C8 NAG . . . J 5 66.555 13.237 24.699 1 301.45 ? C8 NAG 1680 A 1 HETATM 9 N N2 NAG . . . J 5 67.465 13.35 22.478 1 301.45 ? N2 NAG 1680 A 1 HETATM 10 O O3 NAG . . . J 5 69.688 14.867 23.654 1 301.45 ? O3 NAG 1680 A 1 HETATM 11 O O4 NAG . . . J 5 70.148 17.318 22.104 1 301.45 ? O4 NAG 1680 A 1 HETATM 12 O O5 NAG . . . J 5 69.162 14.946 19.583 1 301.45 ? O5 NAG 1680 A 1 HETATM 13 O O6 NAG . . . J 5 71.258 16.796 19.03 1 301.45 ? O6 NAG 1680 A 1 HETATM 14 O O7 NAG . . . J 5 68.457 12.015 23.994 1 301.45 ? O7 NAG 1680 A 1 # _model_server_stats.io_time_ms 167 _model_server_stats.parse_time_ms 13 _model_server_stats.create_model_time_ms 26 _model_server_stats.query_time_ms 293 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 14 #