data_5O4O # _model_server_result.job_id DGY2Q5tqOdcVheJ1KPV4qQ _model_server_result.datetime_utc '2024-11-02 00:30:42' _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 5o4o # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"H","auth_seq_id":705}' # _entry.id 5O4O # _exptl.entry_id 5O4O _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 221.208 _entity.id 5 _entity.src_method man _entity.type non-polymer _entity.pdbx_description 2-acetamido-2-deoxy-beta-D-glucopyranose _entity.pdbx_number_of_molecules 4 _entity.pdbx_parent_entity_id . _entity.pdbx_mutation ? _entity.pdbx_fragment ? _entity.pdbx_ec ? # _cell.angle_alpha 90 _cell.angle_beta 97.91 _cell.angle_gamma 90 _cell.entry_id 5O4O _cell.length_a 64.38 _cell.length_b 144.02 _cell.length_c 218.756 _cell.Z_PDB 4 _cell.pdbx_unique_axis ? # _symmetry.entry_id 5O4O _symmetry.cell_setting ? _symmetry.Int_Tables_number 5 _symmetry.space_group_name_Hall . _symmetry.space_group_name_H-M 'I 1 2 1' # _pdbx_struct_assembly.method_details PISA _pdbx_struct_assembly.oligomeric_details trimeric _pdbx_struct_assembly.oligomeric_count 3 _pdbx_struct_assembly.details software_defined_assembly _pdbx_struct_assembly.id 1 # _pdbx_struct_assembly_gen.asym_id_list A,B,C,D,E,F,G,H,I _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 F N N ? 5 G N N ? 5 H N N ? 5 I N N # _pdbx_entity_branch.entity_id 4 _pdbx_entity_branch.type oligosaccharide # _pdbx_entity_branch_link.link_id 1 _pdbx_entity_branch_link.details ? _pdbx_entity_branch_link.entity_id 4 _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 4 n D NAG 1 D 1 NAG C 1408 NAG 4 n D NAG 2 D 2 NAG C 1409 NAG 4 n E NAG 1 E 1 NAG C 1469 NAG 4 n E NAG 2 E 2 NAG C 1470 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 23 A CYS 23 1_555 A SG CYS 88 A CYS 88 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.032 ? disulf ? disulf2 A SG CYS 134 A CYS 134 1_555 A SG CYS 194 A CYS 194 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.035 ? disulf ? disulf3 B SG CYS 42 B CYS 22 1_555 B SG CYS 116 B CYS 96 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.034 ? disulf ? disulf4 B SG CYS 171 B CYS 151 1_555 B SG CYS 227 B CYS 207 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.032 ? disulf ? disulf5 C SG CYS 305 C CYS 305 1_555 C SG CYS 320 C CYS 320 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.033 ? disulf ? disulf6 C SG CYS 323 C CYS 323 1_555 C SG CYS 327 C CYS 327 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.033 ? disulf ? disulf7 C SG CYS 331 C CYS 331 1_555 C SG CYS 354 C CYS 354 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.032 ? disulf ? disulf8 C SG CYS 463 C CYS 463 1_555 C SG CYS 493 C CYS 493 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.033 ? disulf ? disulf9 C SG CYS 500 C CYS 500 1_555 C SG CYS 509 C CYS 509 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.032 ? disulf ? disulf10 C SG CYS 504 C CYS 504 1_555 C SG CYS 517 C CYS 517 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.032 ? disulf ? disulf11 C SG CYS 520 C CYS 520 1_555 C SG CYS 529 C CYS 529 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.03 ? disulf ? disulf12 C SG CYS 533 C CYS 533 1_555 C SG CYS 549 C CYS 549 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.031 ? disulf ? disulf13 C SG CYS 552 C CYS 552 1_555 C SG CYS 565 C CYS 565 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.026 ? disulf ? disulf14 C SG CYS 556 C CYS 556 1_555 C SG CYS 573 C CYS 573 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.022 ? disulf ? disulf15 C SG CYS 576 C CYS 576 1_555 C SG CYS 585 C CYS 585 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.033 ? disulf ? disulf16 C SG CYS 589 C CYS 589 1_555 C SG CYS 610 C CYS 610 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.033 ? disulf ? disulf17 C SG CYS 613 C CYS 613 1_555 C SG CYS 621 C CYS 621 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.032 ? disulf ? disulf18 C SG CYS 617 C CYS 617 1_555 C SG CYS 629 C CYS 629 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.027 ? covale ? covale1 C ND2 ASN 353 C ASN 353 1_555 F C1 NAG . C NAG 701 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.439 ? covale ? covale2 C ND2 ASN 408 C ASN 408 1_555 D C1 NAG . D NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.435 ? covale ? covale3 C ND2 ASN 414 C ASN 414 1_555 G C1 NAG . C NAG 704 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.439 ? covale ? covale4 C ND2 ASN 437 C ASN 437 1_555 H C1 NAG . C NAG 705 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.437 ? covale ? covale5 C ND2 ASN 469 C ASN 469 1_555 E C1 NAG . E NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.441 ? covale ? covale6 D O4 NAG . D NAG 1 1_555 D C1 NAG . D NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.439 ? covale ? covale7 E O4 NAG . E NAG 1 1_555 E C1 NAG . E NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.444 ? # _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 235 n n C1 O1 NAG sing 236 n n C1 O5 NAG sing 237 n n C1 H1 NAG sing 238 n n C2 C3 NAG sing 239 n n C2 N2 NAG sing 240 n n C2 H2 NAG sing 241 n n C3 C4 NAG sing 242 n n C3 O3 NAG sing 243 n n C3 H3 NAG sing 244 n n C4 C5 NAG sing 245 n n C4 O4 NAG sing 246 n n C4 H4 NAG sing 247 n n C5 C6 NAG sing 248 n n C5 O5 NAG sing 249 n n C5 H5 NAG sing 250 n n C6 O6 NAG sing 251 n n C6 H61 NAG sing 252 n n C6 H62 NAG sing 253 n n C7 C8 NAG sing 254 n n C7 N2 NAG sing 255 n n C7 O7 NAG doub 256 n n C8 H81 NAG sing 257 n n C8 H82 NAG sing 258 n n C8 H83 NAG sing 259 n n N2 HN2 NAG sing 260 n n O1 HO1 NAG sing 261 n n O3 HO3 NAG sing 262 n n O4 HO4 NAG sing 263 n n O6 HO6 NAG sing 264 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 5O4O _atom_sites.fract_transf_matrix[1][1] 0.015533 _atom_sites.fract_transf_matrix[1][2] 0 _atom_sites.fract_transf_matrix[1][3] 0.002158 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.006943 _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] 0.004615 _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 F 5 NAG C 1 701 1353 NAG NAG . G 5 NAG C 1 704 1414 NAG NAG . H 5 NAG C 1 705 1437 NAG NAG . I 5 NAG C 1 708 1522 NAG NAG . # 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 . . . H 5 7.115 31.499 284.398 1 119.47 ? C1 NAG 705 C 1 HETATM 2 C C2 NAG . . . H 5 7.508 32.095 285.75 1 119.37 ? C2 NAG 705 C 1 HETATM 3 C C3 NAG . . . H 5 7.457 31.025 286.836 1 122.58 ? C3 NAG 705 C 1 HETATM 4 C C4 NAG . . . H 5 6.096 30.343 286.845 1 131.29 ? C4 NAG 705 C 1 HETATM 5 C C5 NAG . . . H 5 5.765 29.811 285.454 1 138.77 ? C5 NAG 705 C 1 HETATM 6 C C6 NAG . . . H 5 4.375 29.227 285.362 1 130.2 ? C6 NAG 705 C 1 HETATM 7 C C7 NAG . . . H 5 9.152 33.821 286.348 1 110.31 ? C7 NAG 705 C 1 HETATM 8 C C8 NAG . . . H 5 10.56 34.305 286.171 1 98.68 ? C8 NAG 705 C 1 HETATM 9 N N2 NAG . . . H 5 8.829 32.702 285.689 1 113.24 ? N2 NAG 705 C 1 HETATM 10 O O3 NAG . . . H 5 7.706 31.625 288.102 1 117.18 ? O3 NAG 705 C 1 HETATM 11 O O4 NAG . . . H 5 6.098 29.265 287.774 1 138.89 ? O4 NAG 705 C 1 HETATM 12 O O5 NAG . . . H 5 5.827 30.88 284.499 1 131.65 ? O5 NAG 705 C 1 HETATM 13 O O6 NAG . . . H 5 3.485 30.106 284.687 1 94.15 ? O6 NAG 705 C 1 HETATM 14 O O7 NAG . . . H 5 8.343 34.414 287.055 1 102.8 ? O7 NAG 705 C 1 # _model_server_stats.io_time_ms 11 _model_server_stats.parse_time_ms 20 _model_server_stats.create_model_time_ms 22 _model_server_stats.query_time_ms 303 _model_server_stats.encode_time_ms 5 _model_server_stats.element_count 14 #