data_5W6U # _model_server_result.job_id sS22pqAMXkEKYHkOtUOeNg _model_server_result.datetime_utc '2024-11-24 20:22:24' _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 5w6u # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"E","auth_seq_id":401}' # _entry.id 5W6U # _exptl.entry_id 5W6U _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 3 _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 5W6U _cell.length_a 166.08 _cell.length_b 166.08 _cell.length_c 166.08 _cell.Z_PDB 24 _cell.pdbx_unique_axis ? # _symmetry.entry_id 5W6U _symmetry.cell_setting ? _symmetry.Int_Tables_number 199 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'I 21 3' # _pdbx_struct_assembly.method_details PISA _pdbx_struct_assembly.oligomeric_details nonameric _pdbx_struct_assembly.oligomeric_count 9 _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,I,J _pdbx_struct_assembly_gen.assembly_id 1 _pdbx_struct_assembly_gen.oper_expression 1,2,3 # loop_ _pdbx_struct_oper_list.id _pdbx_struct_oper_list.type _pdbx_struct_oper_list.name _pdbx_struct_oper_list.symmetry_operation _pdbx_struct_oper_list.matrix[1][1] _pdbx_struct_oper_list.matrix[1][2] _pdbx_struct_oper_list.matrix[1][3] _pdbx_struct_oper_list.matrix[2][1] _pdbx_struct_oper_list.matrix[2][2] _pdbx_struct_oper_list.matrix[2][3] _pdbx_struct_oper_list.matrix[3][1] _pdbx_struct_oper_list.matrix[3][2] _pdbx_struct_oper_list.matrix[3][3] _pdbx_struct_oper_list.vector[1] _pdbx_struct_oper_list.vector[2] _pdbx_struct_oper_list.vector[3] 1 'identity operation' 1_555 x,y,z 1 0 0 0 1 0 0 0 1 0 0 0 2 'crystal symmetry operation' 5_555 z,x,y 0 0 1 1 0 0 0 1 0 0 0 0 3 'crystal symmetry operation' 9_555 y,z,x 0 1 0 0 0 1 1 0 0 0 0 0 # loop_ _struct_asym.details _struct_asym.entity_id _struct_asym.id _struct_asym.pdbx_modified _struct_asym.pdbx_blank_PDB_chainid_flag ? 5 E N N ? 5 F N N ? 5 G 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 C 1 NAG E 2 NAG 4 n D NAG 2 C 2 NAG E 3 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 4 A CYS 14 1_555 B SG CYS 137 B CYS 137 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.941 ? disulf ? disulf2 A SG CYS 42 A CYS 52 1_555 A SG CYS 274 A CYS 277 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.044 ? disulf ? disulf3 A SG CYS 90 A CYS 97 1_555 A SG CYS 135 A CYS 139 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.039 ? disulf ? disulf4 A SG CYS 278 A CYS 281 1_555 A SG CYS 302 A CYS 305 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.023 ? disulf ? disulf5 B SG CYS 144 B CYS 144 1_555 B SG CYS 148 B CYS 148 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.038 ? covale ? covale1 A ND2 ASN 11 A ASN 21 1_555 F C1 NAG . A NAG 404 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.471 ? covale ? covale2 A ND2 ASN 23 A ASN 33 1_555 D C1 NAG . C NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.5 ? covale ? covale3 A ND2 ASN 286 A ASN 289 1_555 E C1 NAG . A NAG 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.458 ? covale ? covale4 B ND2 ASN 154 B ASN 154 1_555 G C1 NAG . B NAG 201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.446 ? covale ? covale5 C C ACE 1 D ACE 1 1_555 C N ARG 2 D ARG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.307 ? covale ? covale6 C C ARG 2 D ARG 2 1_555 C N ORN 3 D ORN 3 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.319 ? covale ? covale7 C C ORN 3 D ORN 3 1_555 C N LEU 4 D LEU 4 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.385 ? covale ? covale8 C NE ORN 3 D ORN 3 1_555 C C BAL 12 D BAL 12 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.397 ? covale ? covale9 C C SER 11 D SER 11 1_555 C N BAL 12 D BAL 12 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.376 ? covale ? covale10 D O4 NAG . C NAG 1 1_555 D C1 NAG . C NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.43 ? # _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 255 n n C1 O1 NAG sing 256 n n C1 O5 NAG sing 257 n n C1 H1 NAG sing 258 n n C2 C3 NAG sing 259 n n C2 N2 NAG sing 260 n n C2 H2 NAG sing 261 n n C3 C4 NAG sing 262 n n C3 O3 NAG sing 263 n n C3 H3 NAG sing 264 n n C4 C5 NAG sing 265 n n C4 O4 NAG sing 266 n n C4 H4 NAG sing 267 n n C5 C6 NAG sing 268 n n C5 O5 NAG sing 269 n n C5 H5 NAG sing 270 n n C6 O6 NAG sing 271 n n C6 H61 NAG sing 272 n n C6 H62 NAG sing 273 n n C7 C8 NAG sing 274 n n C7 N2 NAG sing 275 n n C7 O7 NAG doub 276 n n C8 H81 NAG sing 277 n n C8 H82 NAG sing 278 n n C8 H83 NAG sing 279 n n N2 HN2 NAG sing 280 n n O1 HO1 NAG sing 281 n n O3 HO3 NAG sing 282 n n O4 HO4 NAG sing 283 n n O6 HO6 NAG sing 284 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 5W6U _atom_sites.fract_transf_matrix[1][1] 0.006021 _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] 0.006021 _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] 0.006021 _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 5 NAG A 1 401 1 NAG NAG . F 5 NAG A 1 404 4 NAG NAG . G 5 NAG B 1 201 5 NAG NAG . H 6 HOH A 1 501 1 HOH HOH . H 6 HOH A 2 502 18 HOH HOH . H 6 HOH A 3 503 3 HOH HOH . H 6 HOH A 4 504 15 HOH HOH . H 6 HOH A 5 505 4 HOH HOH . H 6 HOH A 6 506 2 HOH HOH . H 6 HOH A 7 507 35 HOH HOH . H 6 HOH A 8 508 11 HOH HOH . H 6 HOH A 9 509 13 HOH HOH . H 6 HOH A 10 510 29 HOH HOH . H 6 HOH A 11 511 9 HOH HOH . H 6 HOH A 12 512 5 HOH HOH . H 6 HOH A 13 513 24 HOH HOH . H 6 HOH A 14 514 17 HOH HOH . H 6 HOH A 15 515 6 HOH HOH . H 6 HOH A 16 516 21 HOH HOH . H 6 HOH A 17 517 23 HOH HOH . H 6 HOH A 18 518 7 HOH HOH . H 6 HOH A 19 519 30 HOH HOH . H 6 HOH A 20 520 33 HOH HOH . H 6 HOH A 21 521 34 HOH HOH . H 6 HOH A 22 522 14 HOH HOH . H 6 HOH A 23 523 31 HOH HOH . I 6 HOH B 1 301 26 HOH HOH . I 6 HOH B 2 302 8 HOH HOH . I 6 HOH B 3 303 20 HOH HOH . I 6 HOH B 4 304 32 HOH HOH . I 6 HOH B 5 307 27 HOH HOH . J 6 HOH D 1 101 28 HOH HOH . J 6 HOH D 2 102 19 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 . . . E 5 -22.208 -51.851 -9.021 1 110.9 ? C1 NAG 401 A 1 HETATM 2 C C2 NAG . . . E 5 -21.188 -52.784 -8.35 1 120 ? C2 NAG 401 A 1 HETATM 3 C C3 NAG . . . E 5 -21.041 -54.069 -9.166 1 126.3 ? C3 NAG 401 A 1 HETATM 4 C C4 NAG . . . E 5 -22.397 -54.708 -9.454 1 125 ? C4 NAG 401 A 1 HETATM 5 C C5 NAG . . . E 5 -23.408 -53.694 -9.992 1 123.5 ? C5 NAG 401 A 1 HETATM 6 C C6 NAG . . . E 5 -24.818 -54.237 -10.027 1 127.1 ? C6 NAG 401 A 1 HETATM 7 C C7 NAG . . . E 5 -19.554 -51.406 -7.122 1 115 ? C7 NAG 401 A 1 HETATM 8 C C8 NAG . . . E 5 -18.165 -50.843 -7.137 1 101.8 ? C8 NAG 401 A 1 HETATM 9 N N2 NAG . . . E 5 -19.889 -52.151 -8.177 1 121.8 ? N2 NAG 401 A 1 HETATM 10 O O3 NAG . . . E 5 -20.213 -54.992 -8.461 1 138.1 ? O3 NAG 401 A 1 HETATM 11 O O4 NAG . . . E 5 -22.231 -55.738 -10.423 1 123.5 ? O4 NAG 401 A 1 HETATM 12 O O5 NAG . . . E 5 -23.449 -52.528 -9.152 1 115.6 ? O5 NAG 401 A 1 HETATM 13 O O6 NAG . . . E 5 -24.997 -55.241 -9.035 1 130.8 ? O6 NAG 401 A 1 HETATM 14 O O7 NAG . . . E 5 -20.348 -51.172 -6.216 1 113.1 ? O7 NAG 401 A 1 # _model_server_stats.io_time_ms 103 _model_server_stats.parse_time_ms 18 _model_server_stats.create_model_time_ms 17 _model_server_stats.query_time_ms 328 _model_server_stats.encode_time_ms 9 _model_server_stats.element_count 14 #