data_3TVM # _model_server_result.job_id nAXX5jamxg7MZrtXAhIJHA _model_server_result.datetime_utc '2025-01-10 10:33:02' _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":"M","auth_seq_id":508}' # _entry.id 3TVM # _exptl.entry_id 3TVM _exptl.method 'X-RAY DIFFRACTION' # _entity.details glycosphingolipid _entity.formula_weight 221.208 _entity.id 7 _entity.src_method syn _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 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 # loop_ _struct_asym.details _struct_asym.entity_id _struct_asym.id _struct_asym.pdbx_modified _struct_asym.pdbx_blank_PDB_chainid_flag ? 7 M N N ? 7 P N 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 '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 445 n n C1 O1 NAG sing 446 n n C1 O5 NAG sing 447 n n C1 H1 NAG sing 448 n n C2 C3 NAG sing 449 n n C2 N2 NAG sing 450 n n C2 H2 NAG sing 451 n n C3 C4 NAG sing 452 n n C3 O3 NAG sing 453 n n C3 H3 NAG sing 454 n n C4 C5 NAG sing 455 n n C4 O4 NAG sing 456 n n C4 H4 NAG sing 457 n n C5 C6 NAG sing 458 n n C5 O5 NAG sing 459 n n C5 H5 NAG sing 460 n n C6 O6 NAG sing 461 n n C6 H61 NAG sing 462 n n C6 H62 NAG sing 463 n n C7 C8 NAG sing 464 n n C7 N2 NAG sing 465 n n C7 O7 NAG doub 466 n n C8 H81 NAG sing 467 n n C8 H82 NAG sing 468 n n C8 H83 NAG sing 469 n n N2 HN2 NAG sing 470 n n O1 HO1 NAG sing 471 n n O3 HO3 NAG sing 472 n n O4 HO4 NAG sing 473 n n O6 HO6 NAG sing 474 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 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 NAG . . . M 7 13.45 0.071 7.521 1 67.77 ? C1 NAG 508 A 1 HETATM 2 C C2 NAG . . . M 7 12.723 0.351 6.198 1 73.45 ? C2 NAG 508 A 1 HETATM 3 C C3 NAG . . . M 7 11.685 1.475 6.305 1 76.01 ? C3 NAG 508 A 1 HETATM 4 C C4 NAG . . . M 7 10.87 1.405 7.596 1 74.47 ? C4 NAG 508 A 1 HETATM 5 C C5 NAG . . . M 7 11.824 1.279 8.781 1 69.57 ? C5 NAG 508 A 1 HETATM 6 C C6 NAG . . . M 7 11.1 1.275 10.127 1 68.46 ? C6 NAG 508 A 1 HETATM 7 C C7 NAG . . . M 7 14.293 -0.197 4.376 1 76.01 ? C7 NAG 508 A 1 HETATM 8 C C8 NAG . . . M 7 15.243 0.364 3.356 1 77.26 ? C8 NAG 508 A 1 HETATM 9 N N2 NAG . . . M 7 13.678 0.697 5.156 1 75.02 ? N2 NAG 508 A 1 HETATM 10 O O3 NAG . . . M 7 10.82 1.406 5.193 1 81.25 ? O3 NAG 508 A 1 HETATM 11 O O4 NAG . . . M 7 10.059 2.553 7.727 1 76.71 ? O4 NAG 508 A 1 HETATM 12 O O5 NAG . . . M 7 12.557 0.079 8.624 1 67.48 ? O5 NAG 508 A 1 HETATM 13 O O6 NAG . . . M 7 10.4 0.062 10.304 1 69.41 ? O6 NAG 508 A 1 HETATM 14 O O7 NAG . . . M 7 14.122 -1.416 4.46 1 75.87 ? O7 NAG 508 A 1 # _model_server_stats.io_time_ms 136 _model_server_stats.parse_time_ms 46 _model_server_stats.create_model_time_ms 125 _model_server_stats.query_time_ms 1348 _model_server_stats.encode_time_ms 20 _model_server_stats.element_count 14 #