data_5VAN # _model_server_result.job_id BUEhQ9O54XKqQ5aw2s_KnA _model_server_result.datetime_utc '2024-12-02 09:56:56' _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 5van # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"G","auth_seq_id":1006}' # _entry.id 5VAN # _exptl.entry_id 5VAN _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 180.156 _entity.id 5 _entity.src_method man _entity.type non-polymer _entity.pdbx_description alpha-D-mannopyranose _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 5VAN _cell.length_a 48.683 _cell.length_b 144.069 _cell.length_c 215.612 _cell.Z_PDB 4 _cell.pdbx_unique_axis ? # _symmetry.entry_id 5VAN _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 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,K,L,M _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 ? 5 G N N ? 5 H 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 NAG _pdbx_entity_branch_link.comp_id_2 NAG _pdbx_entity_branch_link.atom_id_1 C1 _pdbx_entity_branch_link.leaving_atom_id_1 O1 _pdbx_entity_branch_link.atom_stereo_config_1 . _pdbx_entity_branch_link.atom_id_2 O4 _pdbx_entity_branch_link.leaving_atom_id_2 HO4 _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 NAG 1 C 1 NAG C 3 NAG 3 n C NAG 2 C 2 NAG C 4 NAG # 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 547 A CYS 576 1_555 A SG CYS 596 A CYS 625 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.072 ? disulf ? disulf2 B SG CYS 22 B CYS 22 1_555 B SG CYS 96 B CYS 96 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.102 ? covale ? covale1 A ND2 ASN 182 A ASN 211 1_555 D C1 NAG . A NAG 1001 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.459 ? covale ? covale2 A ND2 ASN 362 A ASN 391 1_555 C C1 NAG . C NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.438 ? covale ? covale3 A ND2 ASN 677 A ASN 706 1_555 F C1 NAG . A NAG 1005 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.448 ? covale ? covale4 C O4 NAG . C NAG 1 1_555 C C1 NAG . C NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.455 ? # _chem_comp.formula 'C6 H12 O6' _chem_comp.formula_weight 180.156 _chem_comp.id MAN _chem_comp.mon_nstd_flag . _chem_comp.name alpha-D-mannopyranose _chem_comp.type 'd-saccharide, alpha linking' _chem_comp.pdbx_synonyms alpha-D-mannose;D-mannose;mannose # 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 MAN sing 242 n n C1 O1 MAN sing 243 n n C1 O5 MAN sing 244 n n C1 H1 MAN sing 245 n n C2 C3 MAN sing 246 n n C2 O2 MAN sing 247 n n C2 H2 MAN sing 248 n n C3 C4 MAN sing 249 n n C3 O3 MAN sing 250 n n C3 H3 MAN sing 251 n n C4 C5 MAN sing 252 n n C4 O4 MAN sing 253 n n C4 H4 MAN sing 254 n n C5 C6 MAN sing 255 n n C5 O5 MAN sing 256 n n C5 H5 MAN sing 257 n n C6 O6 MAN sing 258 n n C6 H61 MAN sing 259 n n C6 H62 MAN sing 260 n n O1 HO1 MAN sing 261 n n O2 HO2 MAN sing 262 n n O3 HO3 MAN sing 263 n n O4 HO4 MAN sing 264 n n O6 HO6 MAN sing 265 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 MAN DManpa 'CONDENSED IUPAC CARBOHYDRATE SYMBOL' GMML 1 MAN a-D-mannopyranose 'COMMON NAME' GMML 1 MAN a-D-Manp 'IUPAC CARBOHYDRATE SYMBOL' PDB-CARE 1 MAN Man 'SNFG CARBOHYDRATE SYMBOL' GMML 1 # _atom_sites.entry_id 5VAN _atom_sites.fract_transf_matrix[1][1] 0.020541 _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] 0.006941 _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] 0.004638 _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 A 1 1001 1 NAG NAG . E 4 NAG A 1 1002 2 NAG NAG . F 4 NAG A 1 1005 5 NAG NAG . G 5 MAN A 1 1006 1 MAN MAN . H 5 MAN A 1 1007 2 MAN MAN . I 6 BGC A 1 1008 1 BGC GLC . J 6 BGC A 1 1009 2 BGC GLC . K 7 MES A 1 1010 1 MES MES . L 8 HOH A 1 1101 63 HOH HOH . L 8 HOH A 2 1102 100 HOH HOH . L 8 HOH A 3 1103 75 HOH HOH . L 8 HOH A 4 1104 47 HOH HOH . L 8 HOH A 5 1105 89 HOH HOH . L 8 HOH A 6 1106 2 HOH HOH . L 8 HOH A 7 1107 15 HOH HOH . L 8 HOH A 8 1108 66 HOH HOH . L 8 HOH A 9 1109 104 HOH HOH . L 8 HOH A 10 1110 3 HOH HOH . L 8 HOH A 11 1111 9 HOH HOH . L 8 HOH A 12 1112 43 HOH HOH . L 8 HOH A 13 1113 70 HOH HOH . L 8 HOH A 14 1114 69 HOH HOH . L 8 HOH A 15 1115 35 HOH HOH . L 8 HOH A 16 1116 5 HOH HOH . L 8 HOH A 17 1117 90 HOH HOH . L 8 HOH A 18 1118 78 HOH HOH . L 8 HOH A 19 1119 22 HOH HOH . L 8 HOH A 20 1120 10 HOH HOH . L 8 HOH A 21 1121 60 HOH HOH . L 8 HOH A 22 1122 36 HOH HOH . L 8 HOH A 23 1123 12 HOH HOH . L 8 HOH A 24 1124 80 HOH HOH . L 8 HOH A 25 1125 7 HOH HOH . L 8 HOH A 26 1126 51 HOH HOH . L 8 HOH A 27 1127 20 HOH HOH . L 8 HOH A 28 1128 14 HOH HOH . L 8 HOH A 29 1129 98 HOH HOH . L 8 HOH A 30 1130 54 HOH HOH . L 8 HOH A 31 1131 103 HOH HOH . L 8 HOH A 32 1132 105 HOH HOH . L 8 HOH A 33 1133 85 HOH HOH . L 8 HOH A 34 1134 41 HOH HOH . L 8 HOH A 35 1135 53 HOH HOH . L 8 HOH A 36 1136 64 HOH HOH . L 8 HOH A 37 1137 67 HOH HOH . L 8 HOH A 38 1138 106 HOH HOH . L 8 HOH A 39 1139 33 HOH HOH . L 8 HOH A 40 1140 17 HOH HOH . L 8 HOH A 41 1141 37 HOH HOH . L 8 HOH A 42 1142 61 HOH HOH . L 8 HOH A 43 1143 16 HOH HOH . L 8 HOH A 44 1144 25 HOH HOH . L 8 HOH A 45 1145 1 HOH HOH . L 8 HOH A 46 1146 72 HOH HOH . L 8 HOH A 47 1147 97 HOH HOH . L 8 HOH A 48 1148 111 HOH HOH . L 8 HOH A 49 1149 13 HOH HOH . L 8 HOH A 50 1150 11 HOH HOH . L 8 HOH A 51 1151 19 HOH HOH . L 8 HOH A 52 1152 110 HOH HOH . L 8 HOH A 53 1153 83 HOH HOH . L 8 HOH A 54 1154 8 HOH HOH . L 8 HOH A 55 1155 46 HOH HOH . L 8 HOH A 56 1156 30 HOH HOH . L 8 HOH A 57 1157 101 HOH HOH . L 8 HOH A 58 1158 109 HOH HOH . L 8 HOH A 59 1159 40 HOH HOH . L 8 HOH A 60 1160 31 HOH HOH . L 8 HOH A 61 1161 82 HOH HOH . L 8 HOH A 62 1162 96 HOH HOH . L 8 HOH A 63 1163 24 HOH HOH . L 8 HOH A 64 1164 81 HOH HOH . L 8 HOH A 65 1165 86 HOH HOH . L 8 HOH A 66 1166 28 HOH HOH . L 8 HOH A 67 1167 56 HOH HOH . L 8 HOH A 68 1168 18 HOH HOH . L 8 HOH A 69 1169 91 HOH HOH . L 8 HOH A 70 1170 52 HOH HOH . L 8 HOH A 71 1171 108 HOH HOH . L 8 HOH A 72 1172 42 HOH HOH . L 8 HOH A 73 1173 74 HOH HOH . L 8 HOH A 74 1174 21 HOH HOH . L 8 HOH A 75 1175 93 HOH HOH . L 8 HOH A 76 1176 88 HOH HOH . L 8 HOH A 77 1177 6 HOH HOH . L 8 HOH A 78 1178 73 HOH HOH . L 8 HOH A 79 1179 58 HOH HOH . L 8 HOH A 80 1180 62 HOH HOH . L 8 HOH A 81 1181 107 HOH HOH . L 8 HOH A 82 1182 4 HOH HOH . L 8 HOH A 83 1183 39 HOH HOH . L 8 HOH A 84 1184 27 HOH HOH . L 8 HOH A 85 1185 38 HOH HOH . L 8 HOH A 86 1186 34 HOH HOH . L 8 HOH A 87 1187 55 HOH HOH . L 8 HOH A 88 1188 32 HOH HOH . L 8 HOH A 89 1189 50 HOH HOH . L 8 HOH A 90 1190 112 HOH HOH . L 8 HOH A 91 1191 48 HOH HOH . L 8 HOH A 92 1192 79 HOH HOH . L 8 HOH A 93 1193 49 HOH HOH . L 8 HOH A 94 1194 71 HOH HOH . L 8 HOH A 95 1195 99 HOH HOH . L 8 HOH A 96 1196 95 HOH HOH . L 8 HOH A 97 1197 57 HOH HOH . L 8 HOH A 98 1198 59 HOH HOH . L 8 HOH A 99 1199 102 HOH HOH . M 8 HOH B 1 201 65 HOH HOH . M 8 HOH B 2 202 29 HOH HOH . M 8 HOH B 3 203 84 HOH HOH . M 8 HOH B 4 204 94 HOH HOH . M 8 HOH B 5 205 92 HOH HOH . M 8 HOH B 6 206 44 HOH HOH . M 8 HOH B 7 207 26 HOH HOH . M 8 HOH B 8 208 68 HOH HOH . M 8 HOH B 9 209 23 HOH HOH . M 8 HOH B 10 210 76 HOH HOH . M 8 HOH B 11 211 77 HOH HOH . M 8 HOH B 12 212 45 HOH HOH . M 8 HOH B 13 213 87 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 MAN . . . G 5 -22.159 -28.347 -27.3 1 95.62 ? C1 MAN 1006 A 1 HETATM 2 C C2 MAN . . . G 5 -21.031 -27.569 -26.539 1 99.63 ? C2 MAN 1006 A 1 HETATM 3 C C3 MAN . . . G 5 -21.588 -26.75 -25.332 1 97.7 ? C3 MAN 1006 A 1 HETATM 4 C C4 MAN . . . G 5 -23.101 -26.936 -25.211 1 96.73 ? C4 MAN 1006 A 1 HETATM 5 C C5 MAN . . . G 5 -23.376 -28.448 -25.149 1 96.21 ? C5 MAN 1006 A 1 HETATM 6 C C6 MAN . . . G 5 -24.813 -28.783 -24.798 1 91.11 ? C6 MAN 1006 A 1 HETATM 7 O O2 MAN . . . G 5 -20.383 -26.63 -27.405 1 101.41 ? O2 MAN 1006 A 1 HETATM 8 O O3 MAN . . . G 5 -21.247 -25.362 -25.383 1 96.33 ? O3 MAN 1006 A 1 HETATM 9 O O4 MAN . . . G 5 -23.606 -26.282 -24.059 1 95.91 ? O4 MAN 1006 A 1 HETATM 10 O O5 MAN . . . G 5 -23.089 -29.038 -26.458 1 97.77 ? O5 MAN 1006 A 1 HETATM 11 O O6 MAN . . . G 5 -25.336 -27.696 -24.034 1 87.25 ? O6 MAN 1006 A 1 # _model_server_stats.io_time_ms 12 _model_server_stats.parse_time_ms 23 _model_server_stats.create_model_time_ms 31 _model_server_stats.query_time_ms 335 _model_server_stats.encode_time_ms 13 _model_server_stats.element_count 11 #