data_3VXF # _model_server_result.job_id 50djpW579dq9WMFcks1AJA _model_server_result.datetime_utc '2025-02-28 04:52:23' _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 3vxf # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"E","auth_seq_id":300}' # _entry.id 3VXF # loop_ _exptl.entry_id _exptl.method 3VXF 'X-RAY DIFFRACTION' 3VXF 'NEUTRON 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 1 _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 3VXF _cell.length_a 80.998 _cell.length_b 107.8 _cell.length_c 45.888 _cell.Z_PDB 4 _cell.pdbx_unique_axis ? # _symmetry.entry_id 3VXF _symmetry.cell_setting ? _symmetry.Int_Tables_number 18 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 21 21 2' # _pdbx_struct_assembly.method_details PISA _pdbx_struct_assembly.oligomeric_details tetrameric _pdbx_struct_assembly.oligomeric_count 4 _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 _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 # _struct_asym.details ? _struct_asym.entity_id 5 _struct_asym.id E _struct_asym.pdbx_modified N _struct_asym.pdbx_blank_PDB_chainid_flag 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 9 L CYS 1 1_555 B SG CYS 119 H CYS 122 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.023 ? disulf ? disulf2 B SG CYS 28 H CYS 42 1_555 B SG CYS 44 H CYS 58 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.022 ? disulf ? disulf3 B SG CYS 173 H CYS 168 1_555 B SG CYS 187 H CYS 182 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.037 ? disulf ? disulf4 B SG CYS 201 H CYS 191 1_555 B SG CYS 231 H CYS 220 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.042 ? covale ? covale1 B ND2 ASN 53 H ASN 60 1_555 E C1 NAG . H NAG 300 1_555 G ? ? ? ? ? ? ? ? ? ? ? 1.741 ? covale ? covale2 D C DPN 1 I DPN 1 1_555 D N PRO 2 I PRO 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.35 sing # _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 260 n n C1 O1 NAG sing 261 n n C1 O5 NAG sing 262 n n C1 H1 NAG sing 263 n n C2 C3 NAG sing 264 n n C2 N2 NAG sing 265 n n C2 H2 NAG sing 266 n n C3 C4 NAG sing 267 n n C3 O3 NAG sing 268 n n C3 H3 NAG sing 269 n n C4 C5 NAG sing 270 n n C4 O4 NAG sing 271 n n C4 H4 NAG sing 272 n n C5 C6 NAG sing 273 n n C5 O5 NAG sing 274 n n C5 H5 NAG sing 275 n n C6 O6 NAG sing 276 n n C6 H61 NAG sing 277 n n C6 H62 NAG sing 278 n n C7 C8 NAG sing 279 n n C7 N2 NAG sing 280 n n C7 O7 NAG doub 281 n n C8 H81 NAG sing 282 n n C8 H82 NAG sing 283 n n C8 H83 NAG sing 284 n n N2 HN2 NAG sing 285 n n O1 HO1 NAG sing 286 n n O3 HO3 NAG sing 287 n n O4 HO4 NAG sing 288 n n O6 HO6 NAG sing 289 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 3VXF _atom_sites.fract_transf_matrix[1][1] 0.012346 _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] 0.009276 _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] 0.021792 _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 5 NAG H 1 300 300 NAG NAG . F 6 DOD L 1 101 1020 DOD DOD . F 6 DOD L 2 102 1029 DOD DOD . F 6 DOD L 3 103 1041 DOD DOD . F 6 DOD L 4 104 1044 DOD DOD . F 6 DOD L 5 105 2001 DOD DOD . F 6 DOD L 6 106 2023 DOD DOD . F 6 DOD L 7 107 2024 DOD DOD . F 6 DOD L 8 108 3018 DOD DOD . F 6 DOD L 9 109 3028 DOD DOD . F 6 DOD L 10 110 3029 DOD DOD . G 6 DOD H 1 1001 1001 DOD DOD . G 6 DOD H 2 1002 1002 DOD DOD . G 6 DOD H 3 1003 1003 DOD DOD . G 6 DOD H 4 1004 1004 DOD DOD . G 6 DOD H 5 1005 1005 DOD DOD . G 6 DOD H 6 1006 1006 DOD DOD . G 6 DOD H 7 1007 1007 DOD DOD . G 6 DOD H 8 1008 1008 DOD DOD . G 6 DOD H 9 1009 1009 DOD DOD . G 6 DOD H 10 1010 1010 DOD DOD . G 6 DOD H 11 1011 1011 DOD DOD . G 6 DOD H 12 1012 1012 DOD DOD . G 6 DOD H 13 1013 1013 DOD DOD . G 6 DOD H 14 1014 1014 DOD DOD . G 6 DOD H 15 1015 1015 DOD DOD . G 6 DOD H 16 1016 1016 DOD DOD . G 6 DOD H 17 1017 1017 DOD DOD . G 6 DOD H 18 1018 1018 DOD DOD . G 6 DOD H 19 1019 1019 DOD DOD . G 6 DOD H 20 1020 1022 DOD DOD . G 6 DOD H 21 1021 1023 DOD DOD . G 6 DOD H 22 1022 1024 DOD DOD . G 6 DOD H 23 1023 1025 DOD DOD . G 6 DOD H 24 1024 1026 DOD DOD . G 6 DOD H 25 1025 1027 DOD DOD . G 6 DOD H 26 1026 1028 DOD DOD . G 6 DOD H 27 1027 1030 DOD DOD . G 6 DOD H 28 1028 1031 DOD DOD . G 6 DOD H 29 1029 1032 DOD DOD . G 6 DOD H 30 1030 1033 DOD DOD . G 6 DOD H 31 1031 1034 DOD DOD . G 6 DOD H 32 1032 1035 DOD DOD . G 6 DOD H 33 1033 1036 DOD DOD . G 6 DOD H 34 1034 1037 DOD DOD . G 6 DOD H 35 1035 1038 DOD DOD . G 6 DOD H 36 1036 1039 DOD DOD . G 6 DOD H 37 1037 1040 DOD DOD . G 6 DOD H 38 1038 1042 DOD DOD . G 6 DOD H 39 1039 1043 DOD DOD . G 6 DOD H 40 1040 1045 DOD DOD . G 6 DOD H 41 1041 1046 DOD DOD . G 6 DOD H 42 1042 1047 DOD DOD . G 6 DOD H 43 1043 1048 DOD DOD . G 6 DOD H 44 1044 1049 DOD DOD . G 6 DOD H 45 1045 1050 DOD DOD . G 6 DOD H 46 1046 1051 DOD DOD . G 6 DOD H 47 1047 1052 DOD DOD . G 6 DOD H 48 1048 1053 DOD DOD . G 6 DOD H 49 1049 1054 DOD DOD . G 6 DOD H 50 1050 1055 DOD DOD . G 6 DOD H 51 1051 1056 DOD DOD . G 6 DOD H 52 1052 1058 DOD DOD . G 6 DOD H 53 1053 1059 DOD DOD . G 6 DOD H 54 1054 1062 DOD DOD . G 6 DOD H 55 1055 1063 DOD DOD . G 6 DOD H 56 1056 1065 DOD DOD . G 6 DOD H 57 1057 1066 DOD DOD . G 6 DOD H 58 1058 1067 DOD DOD . G 6 DOD H 59 1059 1068 DOD DOD . G 6 DOD H 60 1060 1069 DOD DOD . G 6 DOD H 61 1061 1070 DOD DOD . G 6 DOD H 62 1062 1071 DOD DOD . G 6 DOD H 63 1063 1073 DOD DOD . G 6 DOD H 64 1064 1074 DOD DOD . G 6 DOD H 65 1065 1075 DOD DOD . G 6 DOD H 66 1066 2002 DOD DOD . G 6 DOD H 67 1067 2003 DOD DOD . G 6 DOD H 68 1068 2004 DOD DOD . G 6 DOD H 69 1069 2005 DOD DOD . G 6 DOD H 70 1070 2006 DOD DOD . G 6 DOD H 71 1071 2007 DOD DOD . G 6 DOD H 72 1072 2008 DOD DOD . G 6 DOD H 73 1073 2009 DOD DOD . G 6 DOD H 74 1074 2010 DOD DOD . G 6 DOD H 75 1075 2011 DOD DOD . G 6 DOD H 76 1076 2012 DOD DOD . G 6 DOD H 77 1077 2013 DOD DOD . G 6 DOD H 78 1078 2014 DOD DOD . G 6 DOD H 79 1079 2015 DOD DOD . G 6 DOD H 80 1080 2016 DOD DOD . G 6 DOD H 81 1081 2017 DOD DOD . G 6 DOD H 82 1082 2018 DOD DOD . G 6 DOD H 83 1083 2019 DOD DOD . G 6 DOD H 84 1084 2020 DOD DOD . G 6 DOD H 85 1085 2022 DOD DOD . G 6 DOD H 86 1086 2025 DOD DOD . G 6 DOD H 87 1087 2026 DOD DOD . G 6 DOD H 88 1088 2027 DOD DOD . G 6 DOD H 89 1089 2028 DOD DOD . G 6 DOD H 90 1090 2029 DOD DOD . G 6 DOD H 91 1091 2030 DOD DOD . G 6 DOD H 92 1092 2031 DOD DOD . G 6 DOD H 93 1093 2032 DOD DOD . G 6 DOD H 94 1094 2033 DOD DOD . G 6 DOD H 95 1095 2034 DOD DOD . G 6 DOD H 96 1096 2035 DOD DOD . G 6 DOD H 97 1097 2036 DOD DOD . G 6 DOD H 98 1098 2037 DOD DOD . G 6 DOD H 99 1099 2038 DOD DOD . G 6 DOD H 100 1100 2039 DOD DOD . G 6 DOD H 101 1101 3001 DOD DOD . G 6 DOD H 102 1102 3002 DOD DOD . G 6 DOD H 103 1103 3003 DOD DOD . G 6 DOD H 104 1104 3004 DOD DOD . G 6 DOD H 105 1105 3005 DOD DOD . G 6 DOD H 106 1106 3006 DOD DOD . G 6 DOD H 107 1107 3007 DOD DOD . G 6 DOD H 108 1108 3008 DOD DOD . G 6 DOD H 109 1109 3009 DOD DOD . G 6 DOD H 110 1110 3010 DOD DOD . G 6 DOD H 111 1111 3011 DOD DOD . G 6 DOD H 112 1112 3012 DOD DOD . G 6 DOD H 113 1113 3013 DOD DOD . G 6 DOD H 114 1114 3014 DOD DOD . G 6 DOD H 115 1115 3016 DOD DOD . G 6 DOD H 116 1116 3017 DOD DOD . G 6 DOD H 117 1117 3019 DOD DOD . G 6 DOD H 118 1118 3020 DOD DOD . G 6 DOD H 119 1119 3021 DOD DOD . G 6 DOD H 120 1120 3022 DOD DOD . G 6 DOD H 121 1121 3023 DOD DOD . G 6 DOD H 122 1122 3024 DOD DOD . G 6 DOD H 123 1123 3025 DOD DOD . G 6 DOD H 124 1124 3026 DOD DOD . G 6 DOD H 125 1125 3027 DOD DOD . G 6 DOD H 126 1126 3030 DOD DOD . G 6 DOD H 127 1127 3031 DOD DOD . G 6 DOD H 128 1128 3032 DOD DOD . G 6 DOD H 129 1129 3033 DOD DOD . G 6 DOD H 130 1130 3034 DOD DOD . G 6 DOD H 131 1131 3035 DOD DOD . G 6 DOD H 132 1132 3036 DOD DOD . G 6 DOD H 133 1133 3037 DOD DOD . G 6 DOD H 134 1134 3038 DOD DOD . G 6 DOD H 135 1135 3039 DOD DOD . G 6 DOD H 136 1136 3040 DOD DOD . G 6 DOD H 137 1137 3041 DOD DOD . G 6 DOD H 138 1138 3042 DOD DOD . G 6 DOD H 139 1139 3043 DOD DOD . G 6 DOD H 140 1140 3044 DOD DOD . G 6 DOD H 141 1141 3045 DOD DOD . G 6 DOD H 142 1142 3055 DOD DOD . G 6 DOD H 143 1143 1060 DOD DOD . G 6 DOD H 144 1144 1061 DOD DOD . H 6 DOD J 1 101 1021 DOD DOD . H 6 DOD J 2 102 3015 DOD DOD . I 6 DOD I 1 101 1064 DOD DOD . I 6 DOD I 2 102 2021 DOD DOD . # 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 5 5.885 -23.547 -7.64 1 22.07 ? C1 NAG 300 H 1 HETATM 2 C C2 NAG . . . E 5 6.972 -23.802 -8.692 1 21.64 ? C2 NAG 300 H 1 HETATM 3 C C3 NAG . . . E 5 7.74 -22.494 -8.864 1 29.8 ? C3 NAG 300 H 1 HETATM 4 C C4 NAG . . . E 5 6.764 -21.346 -9.178 1 31.56 ? C4 NAG 300 H 1 HETATM 5 C C5 NAG . . . E 5 5.55 -21.333 -8.205 1 31.41 ? C5 NAG 300 H 1 HETATM 6 C C6 NAG . . . E 5 4.406 -20.392 -8.538 1 30.94 ? C6 NAG 300 H 1 HETATM 7 C C7 NAG . . . E 5 7.856 -26.103 -8.671 1 18.64 ? C7 NAG 300 H 1 HETATM 8 C C8 NAG . . . E 5 8.917 -26.995 -8.095 1 21.08 ? C8 NAG 300 H 1 HETATM 9 N N2 NAG . . . E 5 7.918 -24.831 -8.305 1 22 ? N2 NAG 300 H 1 HETATM 10 O O3 NAG . . . E 5 8.665 -22.71 -9.905 1 30.82 ? O3 NAG 300 H 1 HETATM 11 O O4 NAG . . . E 5 7.43 -20.085 -9.281 1 40.38 ? O4 NAG 300 H 1 HETATM 12 O O5 NAG . . . E 5 4.942 -22.627 -8.176 1 28.17 ? O5 NAG 300 H 1 HETATM 13 O O6 NAG . . . E 5 3.565 -20.516 -7.415 1 43.2 ? O6 NAG 300 H 1 HETATM 14 O O7 NAG . . . E 5 6.96 -26.542 -9.381 1 20.28 ? O7 NAG 300 H 1 HETATM 15 H H1 NAG . . . E 5 6.371 -23.132 -6.762 1 29.71 ? H1 NAG 300 H 1 HETATM 16 H H2 NAG . . . E 5 6.487 -24.065 -9.622 1 24.19 ? H2 NAG 300 H 1 HETATM 17 H H3 NAG . . . E 5 8.325 -22.315 -7.962 1 27.4 ? H3 NAG 300 H 1 HETATM 18 H H4 NAG . . . E 5 6.184 -21.644 -10.05 1 23.6 ? H4 NAG 300 H 1 HETATM 19 H H5 NAG . . . E 5 5.936 -21.108 -7.216 1 31.57 ? H5 NAG 300 H 1 HETATM 20 H H61 NAG . . . E 5 4.704 -19.337 -8.611 1 27.84 ? H61 NAG 300 H 1 HETATM 21 H H62 NAG . . . E 5 3.831 -20.689 -9.415 1 36.38 ? H62 NAG 300 H 1 HETATM 22 H H81 NAG . . . E 5 8.947 -27.934 -8.658 1 19.93 ? H81 NAG 300 H 1 HETATM 23 H H82 NAG . . . E 5 8.696 -27.163 -7.029 1 22.5 ? H82 NAG 300 H 1 HETATM 24 H H83 NAG . . . E 5 9.88 -26.481 -8.23 1 19.38 ? H83 NAG 300 H 1 HETATM 25 D DN2 NAG . . . E 5 8.688 -24.541 -7.72 0 22.27 ? DN2 NAG 300 H 1 HETATM 26 D DO3 NAG . . . E 5 9.302 -23.441 -9.661 1 23.25 ? DO3 NAG 300 H 1 # _model_server_stats.io_time_ms 9 _model_server_stats.parse_time_ms 8 _model_server_stats.create_model_time_ms 6 _model_server_stats.query_time_ms 297 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 26 #