data_3ZP2 # _model_server_result.job_id 2YzdQOUYw9iFadjNk2gCFg _model_server_result.datetime_utc '2024-11-23 12:20:48' _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 3zp2 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"E","auth_seq_id":421}' # _entry.id 3ZP2 # _exptl.entry_id 3ZP2 _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 221.208 _entity.id 4 _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 3ZP2 _cell.length_a 101.18 _cell.length_b 101.18 _cell.length_c 449.34 _cell.Z_PDB 18 _cell.pdbx_unique_axis ? # _symmetry.entry_id 3ZP2 _symmetry.cell_setting ? _symmetry.Int_Tables_number 155 _symmetry.space_group_name_Hall . _symmetry.space_group_name_H-M 'H 3 2' # _pdbx_struct_assembly.method_details PISA _pdbx_struct_assembly.oligomeric_details hexameric _pdbx_struct_assembly.oligomeric_count 6 _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 _pdbx_struct_assembly_gen.assembly_id 1 _pdbx_struct_assembly_gen.oper_expression 1,2,3 # loop_ _pdbx_struct_oper_list.id _pdbx_struct_oper_list.type _pdbx_struct_oper_list.name _pdbx_struct_oper_list.symmetry_operation _pdbx_struct_oper_list.matrix[1][1] _pdbx_struct_oper_list.matrix[1][2] _pdbx_struct_oper_list.matrix[1][3] _pdbx_struct_oper_list.matrix[2][1] _pdbx_struct_oper_list.matrix[2][2] _pdbx_struct_oper_list.matrix[2][3] _pdbx_struct_oper_list.matrix[3][1] _pdbx_struct_oper_list.matrix[3][2] _pdbx_struct_oper_list.matrix[3][3] _pdbx_struct_oper_list.vector[1] _pdbx_struct_oper_list.vector[2] _pdbx_struct_oper_list.vector[3] 1 'identity operation' 1_555 x,y,z 1 0 0 0 1 0 0 0 1 0 0 0 2 'crystal symmetry operation' 2_565 -y,x-y+1,z -0.5 -0.866025 0 0.866025 -0.5 0 0 0 1 -50.59 87.62445 0 3 'crystal symmetry operation' 3_455 -x+y-1,-x,z -0.5 0.866025 0 -0.866025 -0.5 0 0 0 1 -101.18 0 0 # loop_ _struct_asym.details _struct_asym.entity_id _struct_asym.id _struct_asym.pdbx_modified _struct_asym.pdbx_blank_PDB_chainid_flag ? 4 D N N ? 4 E 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 SIA _pdbx_entity_branch_link.comp_id_2 GAL _pdbx_entity_branch_link.atom_id_1 C2 _pdbx_entity_branch_link.leaving_atom_id_1 O2 _pdbx_entity_branch_link.atom_stereo_config_1 . _pdbx_entity_branch_link.atom_id_2 O6 _pdbx_entity_branch_link.leaving_atom_id_2 HO6 _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 C GAL 1 A 1 GAL E 1327 GAL 3 n C SIA 2 A 2 SIA E 1326 SIA # 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 4 E CYS 8 1_555 B SG CYS 137 F CYS 137 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.134 ? disulf ? disulf2 A SG CYS 42 E CYS 46 1_555 A SG CYS 274 E CYS 278 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.058 ? disulf ? disulf3 A SG CYS 55 E CYS 59 1_555 A SG CYS 67 E CYS 71 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.071 ? disulf ? disulf4 A SG CYS 90 E CYS 94 1_555 A SG CYS 135 E CYS 139 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.178 ? disulf ? disulf5 A SG CYS 278 E CYS 282 1_555 A SG CYS 302 E CYS 306 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.064 ? disulf ? disulf6 B SG CYS 144 F CYS 144 1_555 B SG CYS 148 F CYS 148 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.939 ? covale ? covale1 A ND2 ASN 23 E ASN 27 1_555 D C1 NAG . F NAG 411 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.633 ? covale ? covale2 A ND2 ASN 165 E ASN 169 1_555 E C1 NAG . F NAG 421 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.428 ? covale ? covale3 C O6 GAL . A GAL 1 1_555 C C2 SIA . A SIA 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.45 ? # _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 261 n n C1 O1 NAG sing 262 n n C1 O5 NAG sing 263 n n C1 H1 NAG sing 264 n n C2 C3 NAG sing 265 n n C2 N2 NAG sing 266 n n C2 H2 NAG sing 267 n n C3 C4 NAG sing 268 n n C3 O3 NAG sing 269 n n C3 H3 NAG sing 270 n n C4 C5 NAG sing 271 n n C4 O4 NAG sing 272 n n C4 H4 NAG sing 273 n n C5 C6 NAG sing 274 n n C5 O5 NAG sing 275 n n C5 H5 NAG sing 276 n n C6 O6 NAG sing 277 n n C6 H61 NAG sing 278 n n C6 H62 NAG sing 279 n n C7 C8 NAG sing 280 n n C7 N2 NAG sing 281 n n C7 O7 NAG doub 282 n n C8 H81 NAG sing 283 n n C8 H82 NAG sing 284 n n C8 H83 NAG sing 285 n n N2 HN2 NAG sing 286 n n O1 HO1 NAG sing 287 n n O3 HO3 NAG sing 288 n n O4 HO4 NAG sing 289 n n O6 HO6 NAG sing 290 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 3ZP2 _atom_sites.fract_transf_matrix[1][1] 0.009883 _atom_sites.fract_transf_matrix[1][2] 0.005706 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.011412 _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] 0.002225 _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 D 4 NAG F 1 411 411 NAG NAG . E 4 NAG F 1 421 421 NAG NAG . F 5 HOH E 1 2001 2001 HOH HOH . F 5 HOH E 2 2002 2002 HOH HOH . F 5 HOH E 3 2003 2003 HOH HOH . F 5 HOH E 4 2004 2004 HOH HOH . F 5 HOH E 5 2005 2005 HOH HOH . F 5 HOH E 6 2006 2006 HOH HOH . F 5 HOH E 7 2007 2007 HOH HOH . F 5 HOH E 8 2008 2008 HOH HOH . F 5 HOH E 9 2009 2009 HOH HOH . F 5 HOH E 10 2010 2010 HOH HOH . F 5 HOH E 11 2011 2011 HOH HOH . F 5 HOH E 12 2012 2012 HOH HOH . F 5 HOH E 13 2013 2013 HOH HOH . F 5 HOH E 14 2014 2014 HOH HOH . F 5 HOH E 15 2015 2015 HOH HOH . F 5 HOH E 16 2016 2016 HOH HOH . F 5 HOH E 17 2017 2017 HOH HOH . F 5 HOH E 18 2018 2018 HOH HOH . F 5 HOH E 19 2019 2019 HOH HOH . F 5 HOH E 20 2020 2020 HOH HOH . F 5 HOH E 21 2021 2021 HOH HOH . F 5 HOH E 22 2022 2022 HOH HOH . F 5 HOH E 23 2023 2023 HOH HOH . F 5 HOH E 24 2024 2024 HOH HOH . F 5 HOH E 25 2025 2025 HOH HOH . F 5 HOH E 26 2026 2026 HOH HOH . F 5 HOH E 27 2027 2027 HOH HOH . F 5 HOH E 28 2028 2028 HOH HOH . F 5 HOH E 29 2029 2029 HOH HOH . F 5 HOH E 30 2030 2030 HOH HOH . F 5 HOH E 31 2031 2031 HOH HOH . F 5 HOH E 32 2032 2032 HOH HOH . F 5 HOH E 33 2033 2033 HOH HOH . F 5 HOH E 34 2034 2034 HOH HOH . F 5 HOH E 35 2035 2035 HOH HOH . F 5 HOH E 36 2036 2036 HOH HOH . F 5 HOH E 37 2037 2037 HOH HOH . F 5 HOH E 38 2038 2038 HOH HOH . F 5 HOH E 39 2039 2039 HOH HOH . F 5 HOH E 40 2040 2040 HOH HOH . F 5 HOH E 41 2041 2041 HOH HOH . F 5 HOH E 42 2042 2042 HOH HOH . F 5 HOH E 43 2043 2043 HOH HOH . F 5 HOH E 44 2044 2044 HOH HOH . F 5 HOH E 45 2045 2045 HOH HOH . F 5 HOH E 46 2046 2046 HOH HOH . F 5 HOH E 47 2047 2047 HOH HOH . F 5 HOH E 48 2048 2048 HOH HOH . F 5 HOH E 49 2049 2049 HOH HOH . F 5 HOH E 50 2050 2050 HOH HOH . F 5 HOH E 51 2051 2051 HOH HOH . F 5 HOH E 52 2052 2052 HOH HOH . F 5 HOH E 53 2053 2053 HOH HOH . F 5 HOH E 54 2054 2054 HOH HOH . F 5 HOH E 55 2055 2055 HOH HOH . F 5 HOH E 56 2056 2056 HOH HOH . F 5 HOH E 57 2057 2057 HOH HOH . F 5 HOH E 58 2058 2058 HOH HOH . F 5 HOH E 59 2059 2059 HOH HOH . F 5 HOH E 60 2060 2060 HOH HOH . F 5 HOH E 61 2061 2061 HOH HOH . F 5 HOH E 62 2062 2062 HOH HOH . F 5 HOH E 63 2063 2063 HOH HOH . F 5 HOH E 64 2064 2064 HOH HOH . F 5 HOH E 65 2065 2065 HOH HOH . F 5 HOH E 66 2066 2066 HOH HOH . F 5 HOH E 67 2067 2067 HOH HOH . F 5 HOH E 68 2068 2068 HOH HOH . F 5 HOH E 69 2069 2069 HOH HOH . F 5 HOH E 70 2070 2070 HOH HOH . F 5 HOH E 71 2071 2071 HOH HOH . F 5 HOH E 72 2072 2072 HOH HOH . F 5 HOH E 73 2073 2073 HOH HOH . F 5 HOH E 74 2074 2074 HOH HOH . F 5 HOH E 75 2075 2075 HOH HOH . F 5 HOH E 76 2076 2076 HOH HOH . F 5 HOH E 77 2077 2077 HOH HOH . F 5 HOH E 78 2078 2078 HOH HOH . F 5 HOH E 79 2079 2079 HOH HOH . F 5 HOH E 80 2080 2080 HOH HOH . F 5 HOH E 81 2081 2081 HOH HOH . F 5 HOH E 82 2082 2082 HOH HOH . F 5 HOH E 83 2083 2083 HOH HOH . F 5 HOH E 84 2084 2084 HOH HOH . F 5 HOH E 85 2085 2085 HOH HOH . F 5 HOH E 86 2086 2086 HOH HOH . F 5 HOH E 87 2087 2087 HOH HOH . F 5 HOH E 88 2088 2088 HOH HOH . F 5 HOH E 89 2089 2089 HOH HOH . G 5 HOH F 1 2001 2001 HOH HOH . G 5 HOH F 2 2002 2002 HOH HOH . G 5 HOH F 3 2003 2003 HOH HOH . G 5 HOH F 4 2004 2004 HOH HOH . G 5 HOH F 5 2005 2005 HOH HOH . G 5 HOH F 6 2006 2006 HOH HOH . G 5 HOH F 7 2007 2007 HOH HOH . G 5 HOH F 8 2008 2008 HOH HOH . G 5 HOH F 9 2009 2009 HOH HOH . G 5 HOH F 10 2010 2010 HOH HOH . G 5 HOH F 11 2011 2011 HOH HOH . G 5 HOH F 12 2012 2012 HOH HOH . G 5 HOH F 13 2013 2013 HOH HOH . G 5 HOH F 14 2014 2014 HOH HOH . G 5 HOH F 15 2015 2015 HOH HOH . G 5 HOH F 16 2016 2016 HOH HOH . G 5 HOH F 17 2017 2017 HOH HOH . G 5 HOH F 18 2018 2018 HOH HOH . G 5 HOH F 19 2019 2019 HOH HOH . G 5 HOH F 20 2020 2020 HOH HOH . G 5 HOH F 21 2021 2021 HOH HOH . G 5 HOH F 22 2022 2022 HOH HOH . G 5 HOH F 23 2023 2023 HOH HOH . G 5 HOH F 24 2024 2024 HOH HOH . G 5 HOH F 25 2025 2025 HOH HOH . G 5 HOH F 26 2026 2026 HOH HOH . G 5 HOH F 27 2027 2027 HOH HOH . G 5 HOH F 28 2028 2028 HOH HOH . G 5 HOH F 29 2029 2029 HOH HOH . G 5 HOH F 30 2030 2030 HOH HOH . G 5 HOH F 31 2031 2031 HOH HOH . G 5 HOH F 32 2032 2032 HOH HOH . G 5 HOH F 33 2033 2033 HOH HOH . G 5 HOH F 34 2034 2034 HOH HOH . G 5 HOH F 35 2035 2035 HOH HOH . G 5 HOH F 36 2036 2036 HOH HOH . G 5 HOH F 37 2037 2037 HOH HOH . G 5 HOH F 38 2038 2038 HOH HOH . G 5 HOH F 39 2039 2039 HOH HOH . G 5 HOH F 40 2040 2040 HOH HOH . G 5 HOH F 41 2041 2041 HOH HOH . G 5 HOH F 42 2042 2042 HOH HOH . G 5 HOH F 43 2043 2043 HOH HOH . G 5 HOH F 44 2044 2044 HOH HOH . G 5 HOH F 45 2045 2045 HOH HOH . G 5 HOH F 46 2046 2046 HOH HOH . G 5 HOH F 47 2047 2047 HOH HOH . G 5 HOH F 48 2048 2048 HOH HOH . G 5 HOH F 49 2049 2049 HOH HOH . G 5 HOH F 50 2050 2050 HOH HOH . G 5 HOH F 51 2051 2051 HOH HOH . G 5 HOH F 52 2052 2052 HOH HOH . G 5 HOH F 53 2053 2053 HOH HOH . G 5 HOH F 54 2054 2054 HOH HOH . G 5 HOH F 55 2055 2055 HOH HOH . G 5 HOH F 56 2056 2056 HOH HOH . G 5 HOH F 57 2059 2059 HOH HOH . G 5 HOH F 58 2060 2060 HOH HOH . G 5 HOH F 59 2061 2061 HOH HOH . G 5 HOH F 60 2063 2063 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 . . . E 4 -45.196 58.387 88.86 1 89.05 ? C1 NAG 421 F 1 HETATM 2 C C2 NAG . . . E 4 -46.607 58.538 89.396 1 89.74 ? C2 NAG 421 F 1 HETATM 3 C C3 NAG . . . E 4 -47.312 59.667 88.674 1 89.63 ? C3 NAG 421 F 1 HETATM 4 C C4 NAG . . . E 4 -46.54 60.942 88.919 1 89.22 ? C4 NAG 421 F 1 HETATM 5 C C5 NAG . . . E 4 -45.131 60.733 88.392 1 89.61 ? C5 NAG 421 F 1 HETATM 6 C C6 NAG . . . E 4 -44.285 61.979 88.59 1 89.55 ? C6 NAG 421 F 1 HETATM 7 C C7 NAG . . . E 4 -48.416 57.086 90.013 1 91.3 ? C7 NAG 421 F 1 HETATM 8 C C8 NAG . . . E 4 -49.081 55.756 89.863 1 90.93 ? C8 NAG 421 F 1 HETATM 9 N N2 NAG . . . E 4 -47.36 57.319 89.246 1 90.79 ? N2 NAG 421 F 1 HETATM 10 O O3 NAG . . . E 4 -48.642 59.815 89.162 1 90.2 ? O3 NAG 421 F 1 HETATM 11 O O4 NAG . . . E 4 -47.195 62.023 88.253 1 88.8 ? O4 NAG 421 F 1 HETATM 12 O O5 NAG . . . E 4 -44.515 59.622 89.053 1 89.52 ? O5 NAG 421 F 1 HETATM 13 O O6 NAG . . . E 4 -44.745 62.691 89.743 1 89.78 ? O6 NAG 421 F 1 HETATM 14 O O7 NAG . . . E 4 -48.82 57.914 90.801 1 91.95 ? O7 NAG 421 F 1 # _model_server_stats.io_time_ms 15 _model_server_stats.parse_time_ms 10 _model_server_stats.create_model_time_ms 18 _model_server_stats.query_time_ms 286 _model_server_stats.encode_time_ms 5 _model_server_stats.element_count 14 #