data_5KZN # _model_server_result.job_id W82qRGflAmzRG3tLIlC4eg _model_server_result.datetime_utc '2024-12-21 15:00:50' _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 5kzn # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"B","auth_seq_id":601}' # _entry.id 5KZN # _exptl.entry_id 5KZN _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 221.208 _entity.id 2 _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 5KZN _cell.length_a 129.85 _cell.length_b 129.85 _cell.length_c 252.483 _cell.Z_PDB 12 _cell.pdbx_unique_axis ? # _symmetry.entry_id 5KZN _symmetry.cell_setting ? _symmetry.Int_Tables_number 179 _symmetry.space_group_name_Hall . _symmetry.space_group_name_H-M 'P 65 2 2' # _pdbx_struct_assembly.method_details PISA _pdbx_struct_assembly.oligomeric_details monomeric _pdbx_struct_assembly.oligomeric_count 1 _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 _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 ? 2 B N N ? 2 C 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 50 A CYS 50 1_555 A SG CYS 92 A CYS 92 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.028 ? disulf ? disulf2 A SG CYS 234 A CYS 234 1_555 A SG CYS 518 A CYS 518 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.046 ? disulf ? disulf3 A SG CYS 355 A CYS 355 1_555 A SG CYS 362 A CYS 362 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.058 ? disulf ? disulf4 A SG CYS 400 A CYS 400 1_555 A SG CYS 407 A CYS 407 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.044 ? disulf ? disulf5 A SG CYS 500 A CYS 500 1_555 A SG CYS 519 A CYS 519 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.049 ? disulf ? disulf6 A SG CYS 504 A CYS 504 1_555 A SG CYS 522 A CYS 522 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.049 ? disulf ? disulf7 A SG CYS 525 A CYS 525 1_555 A SG CYS 537 A CYS 537 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.044 ? covale ? covale1 A ND2 ASN 203 A ASN 203 1_555 B C1 NAG . A NAG 601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.426 ? covale ? covale2 A ND2 ASN 286 A ASN 286 1_555 C C1 NAG . A NAG 602 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.435 ? metalc ? metalc1 A O ILE 72 A ILE 72 1_555 D MG MG . A MG 603 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.522 ? metalc ? metalc2 A O ASP 75 A ASP 75 1_555 D MG MG . A MG 603 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.684 ? metalc ? metalc3 A O LEU 78 A LEU 78 1_555 D MG MG . A MG 603 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.414 ? metalc ? metalc4 A O LEU 79 A LEU 79 1_555 D MG MG . A MG 603 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.559 ? metalc ? metalc5 D MG MG . A MG 603 1_555 E O HOH . A HOH 707 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.587 ? metalc ? metalc6 D MG MG . A MG 603 1_555 E O HOH . A HOH 725 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.747 ? # _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 5KZN _atom_sites.fract_transf_matrix[1][1] 0.007701 _atom_sites.fract_transf_matrix[1][2] 0.004446 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.008893 _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] 0.003961 _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 B 2 NAG A 1 601 1 NAG NAG . C 2 NAG A 1 602 2 NAG NAG . D 3 MG A 1 603 5 MG MG . E 4 HOH A 1 701 31 HOH HOH . E 4 HOH A 2 702 24 HOH HOH . E 4 HOH A 3 703 32 HOH HOH . E 4 HOH A 4 704 30 HOH HOH . E 4 HOH A 5 705 28 HOH HOH . E 4 HOH A 6 706 18 HOH HOH . E 4 HOH A 7 707 19 HOH HOH . E 4 HOH A 8 708 9 HOH HOH . E 4 HOH A 9 709 25 HOH HOH . E 4 HOH A 10 710 12 HOH HOH . E 4 HOH A 11 711 13 HOH HOH . E 4 HOH A 12 712 2 HOH HOH . E 4 HOH A 13 713 33 HOH HOH . E 4 HOH A 14 714 36 HOH HOH . E 4 HOH A 15 715 29 HOH HOH . E 4 HOH A 16 716 20 HOH HOH . E 4 HOH A 17 717 6 HOH HOH . E 4 HOH A 18 718 15 HOH HOH . E 4 HOH A 19 719 3 HOH HOH . E 4 HOH A 20 720 23 HOH HOH . E 4 HOH A 21 721 11 HOH HOH . E 4 HOH A 22 722 1 HOH HOH . E 4 HOH A 23 723 17 HOH HOH . E 4 HOH A 24 724 8 HOH HOH . E 4 HOH A 25 725 21 HOH HOH . E 4 HOH A 26 726 35 HOH HOH . E 4 HOH A 27 727 26 HOH HOH . E 4 HOH A 28 728 22 HOH HOH . E 4 HOH A 29 729 7 HOH HOH . E 4 HOH A 30 730 16 HOH HOH . E 4 HOH A 31 731 4 HOH HOH . E 4 HOH A 32 732 27 HOH HOH . E 4 HOH A 33 733 14 HOH HOH . E 4 HOH A 34 734 10 HOH HOH . E 4 HOH A 35 735 5 HOH HOH . E 4 HOH A 36 736 34 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 . . . B 2 -85.448 79.823 -1.151 1 123.44 ? C1 NAG 601 A 1 HETATM 2 C C2 NAG . . . B 2 -85.13 81.036 -0.268 1 125.79 ? C2 NAG 601 A 1 HETATM 3 C C3 NAG . . . B 2 -84.802 82.268 -1.115 1 125.34 ? C3 NAG 601 A 1 HETATM 4 C C4 NAG . . . B 2 -83.763 81.928 -2.18 1 123.06 ? C4 NAG 601 A 1 HETATM 5 C C5 NAG . . . B 2 -84.292 80.815 -3.086 1 120.11 ? C5 NAG 601 A 1 HETATM 6 C C6 NAG . . . B 2 -83.297 80.373 -4.138 1 115.49 ? C6 NAG 601 A 1 HETATM 7 C C7 NAG . . . B 2 -86.174 81.46 1.958 1 129.55 ? C7 NAG 601 A 1 HETATM 8 C C8 NAG . . . B 2 -87.481 81.536 2.692 1 129.01 ? C8 NAG 601 A 1 HETATM 9 N N2 NAG . . . B 2 -86.26 81.3 0.614 1 128.34 ? N2 NAG 601 A 1 HETATM 10 O O3 NAG . . . B 2 -84.32 83.325 -0.289 1 126.86 ? O3 NAG 601 A 1 HETATM 11 O O4 NAG . . . B 2 -83.429 83.092 -2.934 1 123.41 ? O4 NAG 601 A 1 HETATM 12 O O5 NAG . . . B 2 -84.601 79.646 -2.301 1 121.21 ? O5 NAG 601 A 1 HETATM 13 O O6 NAG . . . B 2 -83.778 79.267 -4.886 1 111.81 ? O6 NAG 601 A 1 HETATM 14 O O7 NAG . . . B 2 -85.097 81.536 2.545 1 129.91 ? O7 NAG 601 A 1 # _model_server_stats.io_time_ms 17 _model_server_stats.parse_time_ms 32 _model_server_stats.create_model_time_ms 5 _model_server_stats.query_time_ms 461 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 14 #