data_3K41 # _model_server_result.job_id Ct3jMIMrAI_Yn7h5cdvZkw _model_server_result.datetime_utc '2024-11-04 00:02:09' _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 3k41 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"E","auth_seq_id":500}' # _entry.id 3K41 # _exptl.entry_id 3K41 _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 260.136 _entity.id 4 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description 6-O-phosphono-beta-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 3K41 _cell.length_a 53.234 _cell.length_b 77.112 _cell.length_c 79.903 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 3K41 _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 _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 ? 4 E N N ? 4 F N N # loop_ _pdbx_entity_branch.entity_id _pdbx_entity_branch.type 2 oligosaccharide 3 oligosaccharide # loop_ _pdbx_entity_branch_link.link_id _pdbx_entity_branch_link.details _pdbx_entity_branch_link.entity_id _pdbx_entity_branch_link.entity_branch_list_num_1 _pdbx_entity_branch_link.entity_branch_list_num_2 _pdbx_entity_branch_link.comp_id_1 _pdbx_entity_branch_link.comp_id_2 _pdbx_entity_branch_link.atom_id_1 _pdbx_entity_branch_link.leaving_atom_id_1 _pdbx_entity_branch_link.atom_stereo_config_1 _pdbx_entity_branch_link.atom_id_2 _pdbx_entity_branch_link.leaving_atom_id_2 _pdbx_entity_branch_link.atom_stereo_config_2 _pdbx_entity_branch_link.value_order 1 ? 2 2 1 NAG NAG C1 O1 . O4 HO4 . sing 2 ? 2 3 2 BMA NAG C1 O1 . O4 HO4 . sing 3 ? 2 4 3 MAN BMA C1 O1 . O6 HO6 . sing 4 ? 3 2 1 NAG NAG C1 O1 . O4 HO4 . 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 2 n C NAG 1 C 1 NAG ? 1299 NAG 2 n C NAG 2 C 2 NAG ? 1300 NAG 2 n C BMA 3 C 3 BMA ? 1301 BMA 2 n C MAN 4 C 4 MAN ? 1302 MAN 3 n D NAG 1 D 1 NAG ? 2299 NAG 3 n D NAG 2 D 2 NAG ? 2300 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 6 A CYS 6 1_555 A SG CYS 52 A CYS 52 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.037 ? disulf ? disulf2 A SG CYS 106 A CYS 106 1_555 A SG CYS 141 A CYS 141 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.021 ? disulf ? disulf3 A SG CYS 119 A CYS 119 1_555 A SG CYS 153 A CYS 153 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.029 ? disulf ? disulf4 B SG CYS 6 B CYS 6 1_555 B SG CYS 52 B CYS 52 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.037 ? disulf ? disulf5 B SG CYS 106 B CYS 106 1_555 B SG CYS 141 B CYS 141 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.028 ? disulf ? disulf6 B SG CYS 119 B CYS 119 1_555 B SG CYS 153 B CYS 153 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.029 ? covale ? covale1 A ND2 ASN 81 A ASN 81 1_555 C C1 NAG . C NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.452 ? covale ? covale2 B ND2 ASN 81 B ASN 81 1_555 D C1 NAG . D NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.45 ? covale ? covale3 C O4 NAG . C NAG 1 1_555 C C1 NAG . C NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.39 ? covale ? covale4 C O4 NAG . C NAG 2 1_555 C C1 BMA . C BMA 3 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.387 ? covale ? covale5 C O6 BMA . C BMA 3 1_555 C C1 MAN . C MAN 4 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.402 ? covale ? covale6 D O4 NAG . D NAG 1 1_555 D C1 NAG . D NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.387 ? # _chem_comp.formula 'C6 H13 O9 P' _chem_comp.formula_weight 260.136 _chem_comp.id M6D _chem_comp.mon_nstd_flag n _chem_comp.name 6-O-phosphono-beta-D-mannopyranose _chem_comp.type 'd-saccharide, beta linking' _chem_comp.pdbx_synonyms beta-D-mannose-6-phosphate;6-O-phosphono-beta-D-mannose;6-O-phosphono-D-mannose;6-O-phosphono-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 C2 C1 M6D sing 242 n n O1 C1 M6D sing 243 n n C1 O5 M6D sing 244 n n C1 H1 M6D sing 245 n n O2 C2 M6D sing 246 n n C2 C3 M6D sing 247 n n C2 H2 M6D sing 248 n n O3 C3 M6D sing 249 n n C3 C4 M6D sing 250 n n C3 H3 M6D sing 251 n n C4 O4 M6D sing 252 n n C4 C5 M6D sing 253 n n C4 H4 M6D sing 254 n n O5 C5 M6D sing 255 n n C5 C6 M6D sing 256 n n C5 H5 M6D sing 257 n n C6 O6 M6D sing 258 n n C6 H61 M6D sing 259 n n C6 H62 M6D sing 260 n n O1 HO1 M6D sing 261 n n O2 HO2 M6D sing 262 n n O3 HO3 M6D sing 263 n n O4 HO4 M6D sing 264 n n O6 P M6D sing 265 n n O3P P M6D doub 266 n n P O1P M6D sing 267 n n P O2P M6D sing 268 n n O1P HO1P M6D sing 269 n n O2P HO2P M6D sing 270 n n # _pdbx_chem_comp_identifier.comp_id M6D _pdbx_chem_comp_identifier.identifier b-D-Manp6PO3 _pdbx_chem_comp_identifier.type 'IUPAC CARBOHYDRATE SYMBOL' _pdbx_chem_comp_identifier.program PDB-CARE _pdbx_chem_comp_identifier.program_version 1 # _atom_sites.entry_id 3K41 _atom_sites.fract_transf_matrix[1][1] 0.018785 _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] 0.012968 _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] 0.012515 _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 4 M6D A 1 500 500 M6D M6D . F 4 M6D B 1 501 501 M6D M6D . G 5 HOH A 1 161 161 HOH WAT . G 5 HOH A 2 162 162 HOH WAT . G 5 HOH A 3 163 11 HOH WAT . G 5 HOH A 4 164 14 HOH WAT . G 5 HOH A 5 165 15 HOH WAT . G 5 HOH A 6 166 17 HOH WAT . G 5 HOH A 7 167 20 HOH WAT . G 5 HOH A 8 168 21 HOH WAT . G 5 HOH A 9 169 24 HOH WAT . G 5 HOH A 10 170 170 HOH WAT . G 5 HOH A 11 171 171 HOH WAT . G 5 HOH A 12 172 27 HOH WAT . G 5 HOH A 13 173 32 HOH WAT . G 5 HOH A 14 174 174 HOH WAT . G 5 HOH A 15 175 175 HOH WAT . G 5 HOH A 16 176 176 HOH WAT . G 5 HOH A 17 177 177 HOH WAT . G 5 HOH A 18 178 33 HOH WAT . G 5 HOH A 19 179 179 HOH WAT . G 5 HOH A 20 180 37 HOH WAT . G 5 HOH A 21 181 40 HOH WAT . G 5 HOH A 22 182 44 HOH WAT . G 5 HOH A 23 183 183 HOH WAT . G 5 HOH A 24 184 184 HOH WAT . G 5 HOH A 25 185 47 HOH WAT . G 5 HOH A 26 186 48 HOH WAT . G 5 HOH A 27 187 50 HOH WAT . G 5 HOH A 28 188 51 HOH WAT . G 5 HOH A 29 189 189 HOH WAT . G 5 HOH A 30 190 56 HOH WAT . G 5 HOH A 31 191 57 HOH WAT . G 5 HOH A 32 192 58 HOH WAT . G 5 HOH A 33 193 61 HOH WAT . G 5 HOH A 34 194 62 HOH WAT . G 5 HOH A 35 195 195 HOH WAT . G 5 HOH A 36 196 70 HOH WAT . G 5 HOH A 37 197 197 HOH WAT . G 5 HOH A 38 198 198 HOH WAT . G 5 HOH A 39 199 72 HOH WAT . G 5 HOH A 40 200 200 HOH WAT . G 5 HOH A 41 201 73 HOH WAT . G 5 HOH A 42 202 74 HOH WAT . G 5 HOH A 43 203 203 HOH WAT . G 5 HOH A 44 204 204 HOH WAT . G 5 HOH A 45 205 205 HOH WAT . G 5 HOH A 46 206 76 HOH WAT . G 5 HOH A 47 207 77 HOH WAT . G 5 HOH A 48 208 79 HOH WAT . G 5 HOH A 49 209 82 HOH WAT . G 5 HOH A 50 210 83 HOH WAT . G 5 HOH A 51 211 87 HOH WAT . G 5 HOH A 52 212 88 HOH WAT . G 5 HOH A 53 213 89 HOH WAT . G 5 HOH A 54 214 91 HOH WAT . G 5 HOH A 55 215 92 HOH WAT . G 5 HOH A 56 216 101 HOH WAT . G 5 HOH A 57 217 105 HOH WAT . G 5 HOH A 58 218 106 HOH WAT . G 5 HOH A 59 219 112 HOH WAT . G 5 HOH A 60 220 114 HOH WAT . G 5 HOH A 61 221 117 HOH WAT . G 5 HOH A 62 222 119 HOH WAT . G 5 HOH A 63 223 122 HOH WAT . G 5 HOH A 64 224 124 HOH WAT . G 5 HOH A 65 225 130 HOH WAT . G 5 HOH A 66 226 134 HOH WAT . G 5 HOH A 67 227 137 HOH WAT . G 5 HOH A 68 228 150 HOH WAT . G 5 HOH A 69 229 151 HOH WAT . G 5 HOH A 70 230 2 HOH WAT . G 5 HOH A 71 231 156 HOH WAT . G 5 HOH A 72 232 157 HOH WAT . G 5 HOH A 73 233 4 HOH WAT . G 5 HOH A 74 234 6 HOH WAT . G 5 HOH A 75 235 8 HOH WAT . H 5 HOH B 1 161 9 HOH WAT . H 5 HOH B 2 162 10 HOH WAT . H 5 HOH B 3 163 163 HOH WAT . H 5 HOH B 4 164 12 HOH WAT . H 5 HOH B 5 165 13 HOH WAT . H 5 HOH B 6 166 166 HOH WAT . H 5 HOH B 7 167 167 HOH WAT . H 5 HOH B 8 168 168 HOH WAT . H 5 HOH B 9 169 169 HOH WAT . H 5 HOH B 10 170 16 HOH WAT . H 5 HOH B 11 171 18 HOH WAT . H 5 HOH B 12 172 172 HOH WAT . H 5 HOH B 13 173 173 HOH WAT . H 5 HOH B 14 174 19 HOH WAT . H 5 HOH B 15 175 22 HOH WAT . H 5 HOH B 16 176 23 HOH WAT . H 5 HOH B 17 177 26 HOH WAT . H 5 HOH B 18 178 178 HOH WAT . H 5 HOH B 19 179 28 HOH WAT . H 5 HOH B 20 180 29 HOH WAT . H 5 HOH B 21 181 34 HOH WAT . H 5 HOH B 22 182 182 HOH WAT . H 5 HOH B 23 183 36 HOH WAT . H 5 HOH B 24 184 38 HOH WAT . H 5 HOH B 25 185 185 HOH WAT . H 5 HOH B 26 186 39 HOH WAT . H 5 HOH B 27 187 187 HOH WAT . H 5 HOH B 28 188 41 HOH WAT . H 5 HOH B 29 189 42 HOH WAT . H 5 HOH B 30 190 190 HOH WAT . H 5 HOH B 31 191 43 HOH WAT . H 5 HOH B 32 192 192 HOH WAT . H 5 HOH B 33 193 193 HOH WAT . H 5 HOH B 34 194 194 HOH WAT . H 5 HOH B 35 195 45 HOH WAT . H 5 HOH B 36 196 196 HOH WAT . H 5 HOH B 37 197 46 HOH WAT . H 5 HOH B 38 198 49 HOH WAT . H 5 HOH B 39 199 199 HOH WAT . H 5 HOH B 40 200 52 HOH WAT . H 5 HOH B 41 201 53 HOH WAT . H 5 HOH B 42 202 202 HOH WAT . H 5 HOH B 43 203 54 HOH WAT . H 5 HOH B 44 204 55 HOH WAT . H 5 HOH B 45 205 59 HOH WAT . H 5 HOH B 46 206 60 HOH WAT . H 5 HOH B 47 207 63 HOH WAT . H 5 HOH B 48 208 65 HOH WAT . H 5 HOH B 49 209 67 HOH WAT . H 5 HOH B 50 210 68 HOH WAT . H 5 HOH B 51 211 69 HOH WAT . H 5 HOH B 52 212 71 HOH WAT . H 5 HOH B 53 213 75 HOH WAT . H 5 HOH B 54 214 78 HOH WAT . H 5 HOH B 55 215 80 HOH WAT . H 5 HOH B 56 216 81 HOH WAT . H 5 HOH B 57 217 84 HOH WAT . H 5 HOH B 58 218 86 HOH WAT . H 5 HOH B 59 219 90 HOH WAT . H 5 HOH B 60 220 93 HOH WAT . H 5 HOH B 61 221 95 HOH WAT . H 5 HOH B 62 222 96 HOH WAT . H 5 HOH B 63 223 103 HOH WAT . H 5 HOH B 64 224 108 HOH WAT . H 5 HOH B 65 225 113 HOH WAT . H 5 HOH B 66 226 115 HOH WAT . H 5 HOH B 67 227 116 HOH WAT . H 5 HOH B 68 228 120 HOH WAT . H 5 HOH B 69 229 121 HOH WAT . H 5 HOH B 70 230 123 HOH WAT . H 5 HOH B 71 231 125 HOH WAT . H 5 HOH B 72 232 127 HOH WAT . H 5 HOH B 73 233 131 HOH WAT . H 5 HOH B 74 234 135 HOH WAT . H 5 HOH B 75 235 138 HOH WAT . H 5 HOH B 76 236 139 HOH WAT . H 5 HOH B 77 237 140 HOH WAT . H 5 HOH B 78 238 141 HOH WAT . H 5 HOH B 79 239 64 HOH WAT . H 5 HOH B 80 240 104 HOH WAT . H 5 HOH B 81 241 155 HOH WAT . H 5 HOH B 82 242 1 HOH WAT . H 5 HOH B 83 243 3 HOH WAT . H 5 HOH B 84 244 158 HOH WAT . H 5 HOH B 85 245 5 HOH WAT . H 5 HOH B 86 246 160 HOH WAT . # 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 M6D . . . E 4 21.444 7.966 25.929 1 23.71 ? C1 M6D 500 A 1 HETATM 2 C C2 M6D . . . E 4 20.686 8.06 24.574 1 22.48 ? C2 M6D 500 A 1 HETATM 3 C C3 M6D . . . E 4 19.163 8.286 24.861 1 21.76 ? C3 M6D 500 A 1 HETATM 4 C C4 M6D . . . E 4 18.615 7.149 25.751 1 21.09 ? C4 M6D 500 A 1 HETATM 5 C C5 M6D . . . E 4 19.418 7.125 27.079 1 23.3 ? C5 M6D 500 A 1 HETATM 6 C C6 M6D . . . E 4 18.962 5.986 27.987 1 23.75 ? C6 M6D 500 A 1 HETATM 7 O O1 M6D . . . E 4 22.793 7.61 25.721 1 26.65 ? O1 M6D 500 A 1 HETATM 8 O O2 M6D . . . E 4 20.864 6.849 23.824 1 18.73 ? O2 M6D 500 A 1 HETATM 9 O O3 M6D . . . E 4 18.419 8.338 23.645 1 20.35 ? O3 M6D 500 A 1 HETATM 10 O O4 M6D . . . E 4 17.225 7.375 25.997 1 22.44 ? O4 M6D 500 A 1 HETATM 11 O O5 M6D . . . E 4 20.843 6.93 26.774 1 22.62 ? O5 M6D 500 A 1 HETATM 12 O O6 M6D . . . E 4 19.644 5.913 29.24 1 25.16 ? O6 M6D 500 A 1 HETATM 13 P P M6D . . . E 4 19.891 4.557 30.036 1 24.53 ? P M6D 500 A 1 HETATM 14 O O1P M6D . . . E 4 18.585 3.874 30.343 1 23.9 ? O1P M6D 500 A 1 HETATM 15 O O2P M6D . . . E 4 20.604 4.823 31.343 1 25.94 ? O2P M6D 500 A 1 HETATM 16 O O3P M6D . . . E 4 20.757 3.62 29.211 1 22.97 ? O3P M6D 500 A 1 # _model_server_stats.io_time_ms 43 _model_server_stats.parse_time_ms 7 _model_server_stats.create_model_time_ms 7 _model_server_stats.query_time_ms 306 _model_server_stats.encode_time_ms 3 _model_server_stats.element_count 16 #