data_7DPM # _model_server_result.job_id 9EbiN9qTctCXIyzlMfaEZA _model_server_result.datetime_utc '2024-11-21 11:19:53' _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 7dpm # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"N","auth_seq_id":601}' # _entry.id 7DPM # _exptl.entry_id 7DPM _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 221.208 _entity.id 5 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description 2-acetamido-2-deoxy-beta-D-glucopyranose _entity.pdbx_number_of_molecules 3 _entity.pdbx_parent_entity_id . _entity.pdbx_mutation ? _entity.pdbx_fragment ? _entity.pdbx_ec ? # _cell.angle_alpha 90 _cell.angle_beta 95.88 _cell.angle_gamma 90 _cell.entry_id 7DPM _cell.length_a 147.13 _cell.length_b 153.83 _cell.length_c 172.69 _cell.Z_PDB 16 _cell.pdbx_unique_axis ? # _symmetry.entry_id 7DPM _symmetry.cell_setting ? _symmetry.Int_Tables_number 5 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'C 1 2 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 ? trimeric 3 author_defined_assembly 1 ? trimeric 3 author_defined_assembly 2 ? trimeric 3 author_defined_assembly 3 ? trimeric 3 author_defined_assembly 4 # loop_ _pdbx_struct_assembly_gen.asym_id_list _pdbx_struct_assembly_gen.assembly_id _pdbx_struct_assembly_gen.oper_expression A,B,C,M,Q,R,S 1 1 D,E,F,N,T,U 2 1 G,H,I,O,V,W,X 3 1 J,K,L,P,Y 4 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 N N N ? 5 O N N ? 5 P N N # _pdbx_entity_branch.entity_id 4 _pdbx_entity_branch.type 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 ? 4 2 1 NAG NAG C1 O1 . O4 HO4 . sing 2 ? 4 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 4 n M NAG 1 M 1 NAG C 601 NAG 4 n M NAG 2 M 2 NAG C 701 NAG 4 n M FUC 3 M 3 FUC C 801 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 22 A CYS 22 1_555 A SG CYS 96 A CYS 96 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.039 ? disulf ? disulf2 A SG CYS 154 A CYS 154 1_555 A SG CYS 210 A CYS 210 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.042 ? disulf ? disulf3 A SG CYS 230 A CYS 230 1_555 B SG CYS 214 B CYS 214 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.032 ? disulf ? disulf4 B SG CYS 23 B CYS 23 1_555 B SG CYS 88 B CYS 88 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.05 ? disulf ? disulf5 B SG CYS 134 B CYS 134 1_555 B SG CYS 194 B CYS 194 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.029 ? disulf ? disulf6 C SG CYS 18 C CYS 336 1_555 C SG CYS 43 C CYS 361 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.039 ? disulf ? disulf7 C SG CYS 61 C CYS 379 1_555 C SG CYS 114 C CYS 432 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.05 ? disulf ? disulf8 C SG CYS 73 C CYS 391 1_555 C SG CYS 207 C CYS 525 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.04 ? disulf ? disulf9 C SG CYS 162 C CYS 480 1_555 C SG CYS 170 C CYS 488 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.039 ? disulf ? disulf10 D SG CYS 22 D CYS 22 1_555 D SG CYS 96 D CYS 96 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.036 ? disulf ? disulf11 D SG CYS 154 D CYS 154 1_555 D SG CYS 210 D CYS 210 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.034 ? disulf ? disulf12 E SG CYS 23 E CYS 23 1_555 E SG CYS 88 E CYS 88 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.033 ? disulf ? disulf13 E SG CYS 134 E CYS 134 1_555 E SG CYS 194 E CYS 194 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.038 ? disulf ? disulf14 F SG CYS 18 F CYS 336 1_555 F SG CYS 43 F CYS 361 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.035 ? disulf ? disulf15 F SG CYS 61 F CYS 379 1_555 F SG CYS 114 F CYS 432 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.049 ? disulf ? disulf16 F SG CYS 73 F CYS 391 1_555 F SG CYS 207 F CYS 525 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.034 ? disulf ? disulf17 F SG CYS 162 F CYS 480 1_555 F SG CYS 170 F CYS 488 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.033 ? disulf ? disulf18 G SG CYS 22 G CYS 22 1_555 G SG CYS 96 G CYS 96 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.032 ? disulf ? disulf19 G SG CYS 154 G CYS 154 1_555 G SG CYS 210 G CYS 210 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.031 ? disulf ? disulf20 H SG CYS 23 H CYS 23 1_555 H SG CYS 88 H CYS 88 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.046 ? disulf ? disulf21 H SG CYS 134 H CYS 134 1_555 H SG CYS 194 H CYS 194 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.034 ? disulf ? disulf22 I SG CYS 18 I CYS 336 1_555 I SG CYS 43 I CYS 361 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.039 ? disulf ? disulf23 I SG CYS 61 I CYS 379 1_555 I SG CYS 114 I CYS 432 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.038 ? disulf ? disulf24 I SG CYS 162 I CYS 480 1_555 I SG CYS 170 I CYS 488 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.033 ? disulf ? disulf25 J SG CYS 22 J CYS 22 1_555 J SG CYS 96 J CYS 96 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.037 ? disulf ? disulf26 J SG CYS 154 J CYS 154 1_555 J SG CYS 210 J CYS 210 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.028 ? disulf ? disulf27 K SG CYS 23 K CYS 23 1_555 K SG CYS 88 K CYS 88 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.039 ? disulf ? disulf28 K SG CYS 134 K CYS 134 1_555 K SG CYS 194 K CYS 194 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.036 ? disulf ? disulf29 L SG CYS 18 L CYS 336 1_555 L SG CYS 43 L CYS 361 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.034 ? disulf ? disulf30 L SG CYS 61 L CYS 379 1_555 L SG CYS 114 L CYS 432 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.039 ? disulf ? disulf31 L SG CYS 73 L CYS 391 1_555 L SG CYS 207 L CYS 525 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.03 ? disulf ? disulf32 L SG CYS 162 L CYS 480 1_555 L SG CYS 170 L CYS 488 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.032 ? covale ? covale1 C ND2 ASN 25 C ASN 343 1_555 M C1 NAG . M NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.453 ? covale ? covale2 F ND2 ASN 25 F ASN 343 1_555 N C1 NAG . F NAG 601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.438 ? covale ? covale3 I ND2 ASN 25 I ASN 343 1_555 O C1 NAG . I NAG 601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.446 ? covale ? covale4 L ND2 ASN 25 L ASN 343 1_555 P C1 NAG . L NAG 601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.439 ? covale ? covale5 M O4 NAG . M NAG 1 1_555 M C1 NAG . M NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.438 ? covale ? covale6 M O6 NAG . M NAG 1 1_555 M C1 FUC . M FUC 3 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.437 ? # _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 7DPM _atom_sites.fract_transf_matrix[1][1] 0.006797 _atom_sites.fract_transf_matrix[1][2] 0 _atom_sites.fract_transf_matrix[1][3] 0.0007 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.006501 _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] 0.005821 _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 N 5 NAG F 1 601 601 NAG NAG . O 5 NAG I 1 601 601 NAG NAG . P 5 NAG L 1 601 601 NAG NAG . Q 6 HOH A 1 301 4 HOH HOH . Q 6 HOH A 2 302 38 HOH HOH . Q 6 HOH A 3 303 37 HOH HOH . Q 6 HOH A 4 304 13 HOH HOH . Q 6 HOH A 5 305 45 HOH HOH . Q 6 HOH A 6 306 6 HOH HOH . Q 6 HOH A 7 307 27 HOH HOH . Q 6 HOH A 8 308 5 HOH HOH . Q 6 HOH A 9 309 26 HOH HOH . Q 6 HOH A 10 310 10 HOH HOH . R 6 HOH B 1 301 35 HOH HOH . R 6 HOH B 2 302 12 HOH HOH . R 6 HOH B 3 303 39 HOH HOH . R 6 HOH B 4 304 15 HOH HOH . R 6 HOH B 5 305 9 HOH HOH . R 6 HOH B 6 306 28 HOH HOH . R 6 HOH B 7 307 44 HOH HOH . R 6 HOH B 8 308 16 HOH HOH . R 6 HOH B 9 309 11 HOH HOH . S 6 HOH C 1 601 29 HOH HOH . S 6 HOH C 2 602 3 HOH HOH . S 6 HOH C 3 603 24 HOH HOH . S 6 HOH C 4 604 33 HOH HOH . S 6 HOH C 5 605 22 HOH HOH . S 6 HOH C 6 606 8 HOH HOH . S 6 HOH C 7 607 21 HOH HOH . S 6 HOH C 8 608 1 HOH HOH . S 6 HOH C 9 609 17 HOH HOH . S 6 HOH C 10 610 30 HOH HOH . T 6 HOH D 1 301 32 HOH HOH . U 6 HOH F 1 701 19 HOH HOH . U 6 HOH F 2 702 18 HOH HOH . U 6 HOH F 3 703 14 HOH HOH . U 6 HOH F 4 704 36 HOH HOH . U 6 HOH F 5 705 25 HOH HOH . U 6 HOH F 6 706 40 HOH HOH . V 6 HOH G 1 301 23 HOH HOH . W 6 HOH H 1 301 34 HOH HOH . W 6 HOH H 2 302 41 HOH HOH . W 6 HOH H 3 303 42 HOH HOH . X 6 HOH I 1 701 7 HOH HOH . X 6 HOH I 2 702 43 HOH HOH . Y 6 HOH L 1 701 2 HOH HOH . Y 6 HOH L 2 702 31 HOH HOH . Y 6 HOH L 3 703 20 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 . . . N 5 33.86 33.851 63.64 1 83.91 ? C1 NAG 601 F 1 HETATM 2 C C2 NAG . . . N 5 32.735 33.413 62.689 1 85.23 ? C2 NAG 601 F 1 HETATM 3 C C3 NAG . . . N 5 31.434 34.163 63.002 1 86.77 ? C3 NAG 601 F 1 HETATM 4 C C4 NAG . . . N 5 31.092 34.063 64.483 1 92.34 ? C4 NAG 601 F 1 HETATM 5 C C5 NAG . . . N 5 32.278 34.534 65.318 1 93.92 ? C5 NAG 601 F 1 HETATM 6 C C6 NAG . . . N 5 32.053 34.399 66.809 1 100.27 ? C6 NAG 601 F 1 HETATM 7 C C7 NAG . . . N 5 32.772 32.84 60.29 1 86.38 ? C7 NAG 601 F 1 HETATM 8 C C8 NAG . . . N 5 33.287 33.234 58.94 1 83.35 ? C8 NAG 601 F 1 HETATM 9 N N2 NAG . . . N 5 33.132 33.633 61.306 1 86.07 ? N2 NAG 601 F 1 HETATM 10 O O3 NAG . . . N 5 30.366 33.616 62.236 1 84.63 ? O3 NAG 601 F 1 HETATM 11 O O4 NAG . . . N 5 29.939 34.843 64.783 1 93.26 ? O4 NAG 601 F 1 HETATM 12 O O5 NAG . . . N 5 33.424 33.736 64.995 1 85.75 ? O5 NAG 601 F 1 HETATM 13 O O6 NAG . . . N 5 32.9 33.422 67.401 1 93.09 ? O6 NAG 601 F 1 HETATM 14 O O7 NAG . . . N 5 32.06 31.854 60.451 1 87.86 ? O7 NAG 601 F 1 # _model_server_stats.io_time_ms 77 _model_server_stats.parse_time_ms 11 _model_server_stats.create_model_time_ms 22 _model_server_stats.query_time_ms 287 _model_server_stats.encode_time_ms 5 _model_server_stats.element_count 14 #