data_5KXI # _model_server_result.job_id LZDij6M_oYDHFm0abHzk6A _model_server_result.datetime_utc '2024-12-13 17:36:15' _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 5kxi # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"J","auth_seq_id":500}' # _entry.id 5KXI # _exptl.entry_id 5KXI _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 5 _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 5KXI _cell.length_a 127.099 _cell.length_b 132.633 _cell.length_c 202.44 _cell.Z_PDB 12 _cell.pdbx_unique_axis ? # _symmetry.entry_id 5KXI _symmetry.cell_setting ? _symmetry.Int_Tables_number 19 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 21 21 21' # _pdbx_struct_assembly.method_details PISA _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 _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 F N N ? 3 I N N ? 3 J N N ? 3 K N N ? 3 M N N # 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 135 A CYS 135 1_555 A SG CYS 149 A CYS 149 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.035 ? disulf ? disulf2 A SG CYS 199 A CYS 199 1_555 A SG CYS 200 A CYS 200 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.046 ? disulf ? disulf3 B SG CYS 130 B CYS 130 1_555 B SG CYS 144 B CYS 144 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.034 ? disulf ? disulf4 C SG CYS 130 C CYS 130 1_555 C SG CYS 144 C CYS 144 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.035 ? disulf ? disulf5 D SG CYS 135 D CYS 135 1_555 D SG CYS 149 D CYS 149 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.033 ? disulf ? disulf6 D SG CYS 199 D CYS 199 1_555 D SG CYS 200 D CYS 200 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.047 ? disulf ? disulf7 E SG CYS 130 E CYS 130 1_555 E SG CYS 144 E CYS 144 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.035 ? covale ? covale1 A ND2 ASN 148 A ASN 148 1_555 F C1 NAG . A NAG 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.433 ? covale ? covale2 B ND2 ASN 143 B ASN 143 1_555 I C1 NAG . B NAG 500 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.437 ? covale ? covale3 C ND2 ASN 143 C ASN 143 1_555 J C1 NAG . C NAG 500 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.442 ? covale ? covale4 D ND2 ASN 148 D ASN 148 1_555 K C1 NAG . D NAG 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.437 ? covale ? covale5 E ND2 ASN 143 E ASN 143 1_555 M C1 NAG . E NAG 500 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.44 ? metalc ? metalc1 H NA NA . A NA 403 1_555 N O HOH . A HOH 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.445 ? metalc ? metalc2 H NA NA . A NA 403 1_555 O O HOH . B HOH 601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.64 ? metalc ? metalc3 H NA NA . A NA 403 1_555 P O HOH . C HOH 601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.435 ? metalc ? metalc4 H NA NA . A NA 403 1_555 Q O HOH . D HOH 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.448 ? metalc ? metalc5 H NA NA . A NA 403 1_555 R O HOH . E HOH 601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.443 ? # _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 237 n n C1 O1 NAG sing 238 n n C1 O5 NAG sing 239 n n C1 H1 NAG sing 240 n n C2 C3 NAG sing 241 n n C2 N2 NAG sing 242 n n C2 H2 NAG sing 243 n n C3 C4 NAG sing 244 n n C3 O3 NAG sing 245 n n C3 H3 NAG sing 246 n n C4 C5 NAG sing 247 n n C4 O4 NAG sing 248 n n C4 H4 NAG sing 249 n n C5 C6 NAG sing 250 n n C5 O5 NAG sing 251 n n C5 H5 NAG sing 252 n n C6 O6 NAG sing 253 n n C6 H61 NAG sing 254 n n C6 H62 NAG sing 255 n n C7 C8 NAG sing 256 n n C7 N2 NAG sing 257 n n C7 O7 NAG doub 258 n n C8 H81 NAG sing 259 n n C8 H82 NAG sing 260 n n C8 H83 NAG sing 261 n n N2 HN2 NAG sing 262 n n O1 HO1 NAG sing 263 n n O3 HO3 NAG sing 264 n n O4 HO4 NAG sing 265 n n O6 HO6 NAG sing 266 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 5KXI _atom_sites.fract_transf_matrix[1][1] 0.007868 _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] 0.00754 _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] 0.00494 _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 F 3 NAG A 1 401 500 NAG NAG . G 4 NCT A 1 402 600 NCT NCT . H 5 NA A 1 403 1 NA NA . I 3 NAG B 1 500 500 NAG NAG . J 3 NAG C 1 500 500 NAG NAG . K 3 NAG D 1 401 500 NAG NAG . L 4 NCT D 1 402 600 NCT NCT . M 3 NAG E 1 500 500 NAG NAG . N 6 HOH A 1 501 2 HOH HOH . O 6 HOH B 1 601 3 HOH HOH . P 6 HOH C 1 601 4 HOH HOH . Q 6 HOH D 1 501 5 HOH HOH . R 6 HOH E 1 601 1 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 3 37.963 12.98 -54.215 1 136.4 ? C1 NAG 500 C 1 HETATM 2 C C2 NAG . . . J 3 37.28 13.913 -55.167 1 136.4 ? C2 NAG 500 C 1 HETATM 3 C C3 NAG . . . J 3 38.195 14.967 -55.675 1 136.4 ? C3 NAG 500 C 1 HETATM 4 C C4 NAG . . . J 3 38.794 15.683 -54.528 1 136.4 ? C4 NAG 500 C 1 HETATM 5 C C5 NAG . . . J 3 39.609 14.72 -53.743 1 136.4 ? C5 NAG 500 C 1 HETATM 6 C C6 NAG . . . J 3 40.152 15.349 -52.506 1 136.4 ? C6 NAG 500 C 1 HETATM 7 C C7 NAG . . . J 3 35.685 12.338 -56.321 1 136.4 ? C7 NAG 500 C 1 HETATM 8 C C8 NAG . . . J 3 35.329 11.608 -57.571 1 136.4 ? C8 NAG 500 C 1 HETATM 9 N N2 NAG . . . J 3 36.823 13.204 -56.327 1 136.4 ? N2 NAG 500 C 1 HETATM 10 O O3 NAG . . . J 3 37.438 15.872 -56.38 1 136.4 ? O3 NAG 500 C 1 HETATM 11 O O4 NAG . . . J 3 39.6 16.704 -54.976 1 136.4 ? O4 NAG 500 C 1 HETATM 12 O O5 NAG . . . J 3 38.949 13.546 -53.419 1 136.4 ? O5 NAG 500 C 1 HETATM 13 O O6 NAG . . . J 3 39.279 15.017 -51.494 1 136.4 ? O6 NAG 500 C 1 HETATM 14 O O7 NAG . . . J 3 34.956 12.275 -55.344 1 136.4 ? O7 NAG 500 C 1 # _model_server_stats.io_time_ms 38 _model_server_stats.parse_time_ms 46 _model_server_stats.create_model_time_ms 167 _model_server_stats.query_time_ms 425 _model_server_stats.encode_time_ms 6 _model_server_stats.element_count 14 #