data_3TVM # _model_server_result.job_id i_cuEET6y13WDQo59NuD0A _model_server_result.datetime_utc '2025-01-10 10:22:01' _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 3tvm # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"R","auth_seq_id":287}' # _entry.id 3TVM # _exptl.entry_id 3TVM _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 92.094 _entity.id 10 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description GLYCEROL _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 96.35 _cell.angle_gamma 90 _cell.entry_id 3TVM _cell.length_a 78.97 _cell.length_b 150.57 _cell.length_c 101.96 _cell.Z_PDB 4 _cell.pdbx_unique_axis ? # _symmetry.entry_id 3TVM _symmetry.cell_setting ? _symmetry.Int_Tables_number 4 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 1 21 1' # loop_ _pdbx_struct_assembly.method_details _pdbx_struct_assembly.oligomeric_details _pdbx_struct_assembly.oligomeric_count _pdbx_struct_assembly.details _pdbx_struct_assembly.id ? tetrameric 4 author_defined_assembly 1 ? tetrameric 4 author_defined_assembly 2 # loop_ _pdbx_struct_assembly_gen.asym_id_list _pdbx_struct_assembly_gen.assembly_id _pdbx_struct_assembly_gen.oper_expression A,B,C,D,I,J,M,N,O,S,T,U,V 1 1 E,F,G,H,K,L,P,Q,R,W,X,Y,Z 2 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 10 _struct_asym.id R _struct_asym.pdbx_modified N _struct_asym.pdbx_blank_PDB_chainid_flag N # loop_ _pdbx_entity_branch.entity_id _pdbx_entity_branch.type 5 oligosaccharide 6 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 ? 5 2 1 NAG NAG C1 O1 . O4 HO4 . sing 2 ? 6 2 1 NAG NAG C1 O1 . O4 HO4 . sing 3 ? 6 3 1 FUC NAG C1 O1 . O6 HO6 . 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 5 n I NAG 1 I 1 NAG I 509 NAG 5 n I NAG 2 I 2 NAG I 510 NAG 6 n J NAG 1 J 1 NAG I 511 NAG 6 n J NAG 2 J 2 NAG I 512 NAG 6 n J FUC 3 J 3 FUC I 513 FUC 5 n K NAG 1 K 1 NAG J 515 NAG 5 n K NAG 2 K 2 NAG J 516 NAG 6 n L NAG 1 L 1 NAG J 517 NAG 6 n L NAG 2 L 2 NAG J 518 NAG 6 n L FUC 3 L 3 FUC J 519 FUC # 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 208 A CYS 208 1_555 A SG CYS 263 A CYS 263 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.033 ? disulf ? disulf2 B SG CYS 25 B CYS 25 1_555 B SG CYS 80 B CYS 80 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.028 ? disulf ? disulf3 C SG CYS 24 C CYS 22 1_555 C SG CYS 91 C CYS 90 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.046 ? disulf ? disulf4 C SG CYS 138 C CYS 139 1_555 C SG CYS 188 C CYS 189 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.049 ? disulf ? disulf5 C SG CYS 163 C CYS 164 1_555 D SG CYS 169 D CYS 168 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.042 ? disulf ? disulf6 D SG CYS 24 D CYS 23 1_555 D SG CYS 92 D CYS 91 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.029 ? disulf ? disulf7 D SG CYS 143 D CYS 142 1_555 D SG CYS 208 D CYS 207 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.022 ? disulf ? disulf8 E SG CYS 104 E CYS 104 1_555 E SG CYS 168 E CYS 168 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.043 ? disulf ? disulf9 F SG CYS 25 F CYS 25 1_555 F SG CYS 80 F CYS 80 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.031 ? disulf ? disulf10 G SG CYS 24 G CYS 22 1_555 G SG CYS 91 G CYS 90 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.044 ? disulf ? disulf11 G SG CYS 138 G CYS 139 1_555 G SG CYS 188 G CYS 189 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.045 ? disulf ? disulf12 G SG CYS 163 G CYS 164 1_555 H SG CYS 169 H CYS 168 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.044 ? disulf ? disulf13 H SG CYS 24 H CYS 23 1_555 H SG CYS 92 H CYS 91 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.033 ? disulf ? disulf14 H SG CYS 143 H CYS 142 1_555 H SG CYS 208 H CYS 207 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.031 ? covale ? covale1 A ND2 ASN 20 A ASN 20 1_555 M C1 NAG . A NAG 508 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.444 ? covale ? covale2 A ND2 ASN 42 A ASN 42 1_555 I C1 NAG . I NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.439 ? covale ? covale3 A ND2 ASN 165 A ASN 165 1_555 J C1 NAG . J NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.44 ? covale ? covale4 E ND2 ASN 20 E ASN 20 1_555 P C1 NAG . E NAG 514 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.444 ? covale ? covale5 E ND2 ASN 42 E ASN 42 1_555 K C1 NAG . K NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.438 ? covale ? covale6 E ND2 ASN 165 E ASN 165 1_555 L C1 NAG . L NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.439 ? covale ? covale7 I O4 NAG . I NAG 1 1_555 I C1 NAG . I NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.443 ? covale ? covale8 J O4 NAG . J NAG 1 1_555 J C1 NAG . J NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.443 ? covale ? covale9 J O6 NAG . J NAG 1 1_555 J C1 FUC . J FUC 3 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.451 ? covale ? covale10 K O4 NAG . K NAG 1 1_555 K C1 NAG . K NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.449 ? covale ? covale11 L O4 NAG . L NAG 1 1_555 L C1 NAG . L NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.444 ? covale ? covale12 L O6 NAG . L NAG 1 1_555 L C1 FUC . L FUC 3 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.446 ? # _chem_comp.formula 'C3 H8 O3' _chem_comp.formula_weight 92.094 _chem_comp.id GOL _chem_comp.mon_nstd_flag . _chem_comp.name GLYCEROL _chem_comp.type non-polymer _chem_comp.pdbx_synonyms GLYCERIN;PROPANE-1,2,3-TRIOL # 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 O1 GOL sing 324 n n C1 C2 GOL sing 325 n n C1 H11 GOL sing 326 n n C1 H12 GOL sing 327 n n O1 HO1 GOL sing 328 n n C2 O2 GOL sing 329 n n C2 C3 GOL sing 330 n n C2 H2 GOL sing 331 n n O2 HO2 GOL sing 332 n n C3 O3 GOL sing 333 n n C3 H31 GOL sing 334 n n C3 H32 GOL sing 335 n n O3 HO3 GOL sing 336 n n # _atom_sites.entry_id 3TVM _atom_sites.fract_transf_matrix[1][1] 0.012663 _atom_sites.fract_transf_matrix[1][2] 0 _atom_sites.fract_transf_matrix[1][3] 0.001409 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.006641 _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] 0.009868 _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 M 7 NAG A 1 508 508 NAG NAG . N 8 07P A 1 286 1 07P 07P . O 9 CL D 1 241 1 CL CL . P 7 NAG E 1 514 514 NAG NAG . Q 8 07P E 1 286 2 07P 07P . R 10 GOL E 1 287 2 GOL GOL . S 11 HOH A 1 287 5 HOH HOH . S 11 HOH A 2 288 13 HOH HOH . S 11 HOH A 3 289 17 HOH HOH . S 11 HOH A 4 290 18 HOH HOH . S 11 HOH A 5 291 43 HOH HOH . S 11 HOH A 6 292 44 HOH HOH . S 11 HOH A 7 293 54 HOH HOH . S 11 HOH A 8 294 55 HOH HOH . S 11 HOH A 9 295 60 HOH HOH . T 11 HOH B 1 100 4 HOH HOH . T 11 HOH B 2 101 16 HOH HOH . T 11 HOH B 3 102 30 HOH HOH . T 11 HOH B 4 103 33 HOH HOH . T 11 HOH B 5 104 40 HOH HOH . T 11 HOH B 6 105 47 HOH HOH . U 11 HOH C 1 211 1 HOH HOH . U 11 HOH C 2 212 3 HOH HOH . U 11 HOH C 3 213 10 HOH HOH . U 11 HOH C 4 214 19 HOH HOH . U 11 HOH C 5 215 24 HOH HOH . U 11 HOH C 6 216 25 HOH HOH . U 11 HOH C 7 217 35 HOH HOH . U 11 HOH C 8 218 45 HOH HOH . U 11 HOH C 9 219 46 HOH HOH . U 11 HOH C 10 220 56 HOH HOH . V 11 HOH D 1 242 2 HOH HOH . V 11 HOH D 2 243 11 HOH HOH . V 11 HOH D 3 244 22 HOH HOH . V 11 HOH D 4 245 34 HOH HOH . V 11 HOH D 5 246 41 HOH HOH . V 11 HOH D 6 247 42 HOH HOH . V 11 HOH D 7 248 48 HOH HOH . V 11 HOH D 8 249 49 HOH HOH . V 11 HOH D 9 250 53 HOH HOH . V 11 HOH D 10 251 57 HOH HOH . V 11 HOH D 11 252 58 HOH HOH . V 11 HOH D 12 253 59 HOH HOH . W 11 HOH E 1 288 21 HOH HOH . W 11 HOH E 2 289 27 HOH HOH . W 11 HOH E 3 290 32 HOH HOH . X 11 HOH F 1 100 15 HOH HOH . X 11 HOH F 2 101 31 HOH HOH . X 11 HOH F 3 102 37 HOH HOH . X 11 HOH F 4 103 38 HOH HOH . X 11 HOH F 5 104 39 HOH HOH . Y 11 HOH G 1 211 7 HOH HOH . Y 11 HOH G 2 212 8 HOH HOH . Y 11 HOH G 3 213 9 HOH HOH . Y 11 HOH G 4 214 12 HOH HOH . Y 11 HOH G 5 215 20 HOH HOH . Y 11 HOH G 6 216 26 HOH HOH . Y 11 HOH G 7 217 51 HOH HOH . Z 11 HOH H 1 241 6 HOH HOH . Z 11 HOH H 2 242 14 HOH HOH . Z 11 HOH H 3 243 23 HOH HOH . Z 11 HOH H 4 244 28 HOH HOH . Z 11 HOH H 5 245 29 HOH HOH . Z 11 HOH H 6 246 36 HOH HOH . Z 11 HOH H 7 247 50 HOH HOH . Z 11 HOH H 8 248 52 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 GOL . . . R 10 18.146 23.367 33.993 1 42.45 ? C1 GOL 287 E 1 HETATM 2 O O1 GOL . . . R 10 17.402 22.312 34.559 1 42.18 ? O1 GOL 287 E 1 HETATM 3 C C2 GOL . . . R 10 19.575 23.357 34.532 1 42.82 ? C2 GOL 287 E 1 HETATM 4 O O2 GOL . . . R 10 19.98 22.057 34.883 1 42.61 ? O2 GOL 287 E 1 HETATM 5 C C3 GOL . . . R 10 20.538 23.927 33.502 1 43.19 ? C3 GOL 287 E 1 HETATM 6 O O3 GOL . . . R 10 21.858 23.544 33.819 1 43.29 ? O3 GOL 287 E 1 # _model_server_stats.io_time_ms 132 _model_server_stats.parse_time_ms 25 _model_server_stats.create_model_time_ms 14 _model_server_stats.query_time_ms 317 _model_server_stats.encode_time_ms 4 _model_server_stats.element_count 6 #