data_2RL9 # _model_server_result.job_id u2DHWTwXpAGVysrQ21eZSw _model_server_result.datetime_utc '2024-11-29 11:54:03' _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 2rl9 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"G","auth_seq_id":502}' # _entry.id 2RL9 # _exptl.entry_id 2RL9 _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 221.208 _entity.id 3 _entity.src_method syn _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 2RL9 _cell.length_a 92.628 _cell.length_b 92.628 _cell.length_c 85.594 _cell.Z_PDB 16 _cell.pdbx_unique_axis ? # _symmetry.entry_id 2RL9 _symmetry.cell_setting ? _symmetry.Int_Tables_number 96 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 43 21 2' # _pdbx_struct_assembly.method_details PISA _pdbx_struct_assembly.oligomeric_details dimeric _pdbx_struct_assembly.oligomeric_count 2 _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 _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 ? 3 E N N ? 3 G N N # _pdbx_entity_branch.entity_id 2 _pdbx_entity_branch.type 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 ? 2 2 1 MAN MAN C1 O1 . O2 HO2 . sing 2 ? 2 3 2 M6P MAN C1 O1 . O2 HO2 . 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 2 n C MAN 1 C 1 MAN A 3003 MAN 2 n C MAN 2 C 2 MAN A 3002 MAN 2 n C M6P 3 C 3 M6P A 3001 M6P 2 n D MAN 1 D 1 MAN B 3003 MAN 2 n D MAN 2 D 2 MAN B 3002 MAN 2 n D M6P 3 D 3 M6P B 3004 M6P # 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 6 1_555 A SG CYS 52 A CYS 52 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.031 ? disulf ? disulf2 A SG CYS 106 A CYS 106 1_555 A SG CYS 141 A CYS 141 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.028 ? disulf ? disulf3 A SG CYS 119 A CYS 119 1_555 A SG CYS 153 A CYS 153 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.035 ? disulf ? disulf4 B SG CYS 6 B CYS 6 1_555 B SG CYS 52 B CYS 52 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.04 ? disulf ? disulf5 B SG CYS 106 B CYS 106 1_555 B SG CYS 141 B CYS 141 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.025 ? disulf ? disulf6 B SG CYS 119 B CYS 119 1_555 B SG CYS 153 B CYS 153 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.027 ? covale ? covale1 A ND2 ASN 81 A ASN 81 1_555 E C1 NAG . A NAG 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.45 ? covale ? covale2 C O2 MAN . C MAN 1 1_555 C C1 MAN . C MAN 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.448 sing covale ? covale3 C O2 MAN . C MAN 2 1_555 C C1 M6P . C M6P 3 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.494 ? covale ? covale4 D O2 MAN . D MAN 1 1_555 D C1 MAN . D MAN 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.442 sing covale ? covale5 D O2 MAN . D MAN 2 1_555 D C1 M6P . D M6P 3 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.493 ? metalc ? metalc1 A OD2 ASP 103 A ASP 103 1_555 F MN MN . A MN 3000 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.352 ? metalc ? metalc2 F MN MN . A MN 3000 1_555 C O2P M6P . C M6P 3 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.354 ? metalc ? metalc3 B OD2 ASP 103 B ASP 103 1_555 H MN MN . B MN 3001 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.322 ? metalc ? metalc4 H MN MN . B MN 3001 1_555 D O2P M6P . D M6P 3 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.557 ? # _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 290 n n C1 O1 NAG sing 291 n n C1 O5 NAG sing 292 n n C1 H1 NAG sing 293 n n C2 C3 NAG sing 294 n n C2 N2 NAG sing 295 n n C2 H2 NAG sing 296 n n C3 C4 NAG sing 297 n n C3 O3 NAG sing 298 n n C3 H3 NAG sing 299 n n C4 C5 NAG sing 300 n n C4 O4 NAG sing 301 n n C4 H4 NAG sing 302 n n C5 C6 NAG sing 303 n n C5 O5 NAG sing 304 n n C5 H5 NAG sing 305 n n C6 O6 NAG sing 306 n n C6 H61 NAG sing 307 n n C6 H62 NAG sing 308 n n C7 C8 NAG sing 309 n n C7 N2 NAG sing 310 n n C7 O7 NAG doub 311 n n C8 H81 NAG sing 312 n n C8 H82 NAG sing 313 n n C8 H83 NAG sing 314 n n N2 HN2 NAG sing 315 n n O1 HO1 NAG sing 316 n n O3 HO3 NAG sing 317 n n O4 HO4 NAG sing 318 n n O6 HO6 NAG sing 319 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 2RL9 _atom_sites.fract_transf_matrix[1][1] 0.010796 _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] 0.010796 _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] 0.011683 _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 E 3 NAG A 1 501 501 NAG NAG . F 4 MN A 1 3000 3000 MN MN . G 3 NAG B 1 502 502 NAG NAG . H 4 MN B 1 3001 3001 MN MN . I 5 HOH A 1 2202 2202 HOH HOH . I 5 HOH A 2 2204 2204 HOH HOH . I 5 HOH A 3 2207 2207 HOH HOH . I 5 HOH A 4 2217 2217 HOH HOH . I 5 HOH A 5 2219 2219 HOH HOH . I 5 HOH A 6 2220 2220 HOH HOH . I 5 HOH A 7 2222 2222 HOH HOH . I 5 HOH A 8 2224 2224 HOH HOH . I 5 HOH A 9 2227 2227 HOH HOH . I 5 HOH A 10 2233 2233 HOH HOH . I 5 HOH A 11 2234 2234 HOH HOH . I 5 HOH A 12 2245 2245 HOH HOH . I 5 HOH A 13 2252 2252 HOH HOH . I 5 HOH A 14 2262 2262 HOH HOH . I 5 HOH A 15 2271 2271 HOH HOH . I 5 HOH A 16 2277 2277 HOH HOH . I 5 HOH A 17 2278 2278 HOH HOH . I 5 HOH A 18 3004 3004 HOH HOH . I 5 HOH A 19 3005 3005 HOH HOH . I 5 HOH A 20 3007 3007 HOH HOH . I 5 HOH A 21 3008 3008 HOH HOH . I 5 HOH A 22 3014 3014 HOH HOH . I 5 HOH A 23 3023 3023 HOH HOH . I 5 HOH A 24 3024 3024 HOH HOH . I 5 HOH A 25 3031 3031 HOH HOH . I 5 HOH A 26 3035 3035 HOH HOH . I 5 HOH A 27 3036 3036 HOH HOH . J 5 HOH B 1 3005 3005 HOH HOH . J 5 HOH B 2 3006 3006 HOH HOH . J 5 HOH B 3 3007 3007 HOH HOH . J 5 HOH B 4 3008 3008 HOH HOH . J 5 HOH B 5 3009 3009 HOH HOH . J 5 HOH B 6 3010 3010 HOH HOH . J 5 HOH B 7 3011 3011 HOH HOH . J 5 HOH B 8 3012 3012 HOH HOH . J 5 HOH B 9 3013 3013 HOH HOH . J 5 HOH B 10 3014 3014 HOH HOH . J 5 HOH B 11 3015 3015 HOH HOH . J 5 HOH B 12 3016 3016 HOH HOH . J 5 HOH B 13 3017 3017 HOH HOH . J 5 HOH B 14 3018 3018 HOH HOH . J 5 HOH B 15 3019 3019 HOH HOH . J 5 HOH B 16 3020 3020 HOH HOH . J 5 HOH B 17 3021 3021 HOH HOH . J 5 HOH B 18 3022 3022 HOH HOH . J 5 HOH B 19 3023 3023 HOH HOH . J 5 HOH B 20 3024 3024 HOH HOH . J 5 HOH B 21 3025 3025 HOH HOH . J 5 HOH B 22 3026 3026 HOH HOH . J 5 HOH B 23 3028 3028 HOH HOH . J 5 HOH B 24 3029 3029 HOH HOH . J 5 HOH B 25 3030 3030 HOH HOH . J 5 HOH B 26 3031 3031 HOH HOH . J 5 HOH B 27 3032 3032 HOH HOH . J 5 HOH B 28 3033 3033 HOH HOH . J 5 HOH B 29 3034 3034 HOH HOH . J 5 HOH B 30 3035 3035 HOH HOH . J 5 HOH B 31 3036 3036 HOH HOH . J 5 HOH B 32 3037 3037 HOH HOH . J 5 HOH B 33 3038 3038 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 . . . G 3 11.15 36.181 26.661 1 48.7 ? C1 NAG 502 B 1 HETATM 2 C C2 NAG . . . G 3 11.558 37.348 27.56 1 49.14 ? C2 NAG 502 B 1 HETATM 3 C C3 NAG . . . G 3 11.202 37.061 29.02 1 49.59 ? C3 NAG 502 B 1 HETATM 4 C C4 NAG . . . G 3 9.732 36.653 29.139 1 50.2 ? C4 NAG 502 B 1 HETATM 5 C C5 NAG . . . G 3 9.441 35.476 28.205 1 50.38 ? C5 NAG 502 B 1 HETATM 6 C C6 NAG . . . G 3 7.977 35.085 28.222 1 51.36 ? C6 NAG 502 B 1 HETATM 7 C C7 NAG . . . G 3 13.487 38.222 26.392 1 49.22 ? C7 NAG 502 B 1 HETATM 8 C C8 NAG . . . G 3 14.825 37.743 25.842 1 48.57 ? C8 NAG 502 B 1 HETATM 9 N N2 NAG . . . G 3 12.988 37.57 27.443 1 48.7 ? N2 NAG 502 B 1 HETATM 10 O O3 NAG . . . G 3 11.437 38.22 29.81 1 49.52 ? O3 NAG 502 B 1 HETATM 11 O O4 NAG . . . G 3 9.436 36.293 30.483 1 50.06 ? O4 NAG 502 B 1 HETATM 12 O O5 NAG . . . G 3 9.77 35.825 26.839 1 50.1 ? O5 NAG 502 B 1 HETATM 13 O O6 NAG . . . G 3 7.167 36.074 27.596 1 51.5 ? O6 NAG 502 B 1 HETATM 14 O O7 NAG . . . G 3 12.911 39.175 25.856 1 49.68 ? O7 NAG 502 B 1 # _model_server_stats.io_time_ms 9 _model_server_stats.parse_time_ms 9 _model_server_stats.create_model_time_ms 4 _model_server_stats.query_time_ms 306 _model_server_stats.encode_time_ms 3 _model_server_stats.element_count 14 #