data_5WKV # _model_server_result.job_id GWZxX-0p781dAd14eV0jSg _model_server_result.datetime_utc '2024-11-07 16:43:56' _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 5wkv # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"F","auth_seq_id":501}' # _entry.id 5WKV # _exptl.entry_id 5WKV _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 221.208 _entity.id 3 _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 90 _cell.angle_gamma 90 _cell.entry_id 5WKV _cell.length_a 109.18 _cell.length_b 133.7 _cell.length_c 157.65 _cell.Z_PDB 12 _cell.pdbx_unique_axis ? # _symmetry.entry_id 5WKV _symmetry.cell_setting ? _symmetry.Int_Tables_number 19 _symmetry.space_group_name_Hall . _symmetry.space_group_name_H-M 'P 21 21 21' # _pdbx_struct_assembly.method_details PISA _pdbx_struct_assembly.oligomeric_details trimeric _pdbx_struct_assembly.oligomeric_count 3 _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,K,L,M,N,O,P,Q _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 ? 3 F N N ? 3 G N N ? 3 K N N ? 3 N N N # _pdbx_entity_branch.entity_id 2 _pdbx_entity_branch.type oligosaccharide # _pdbx_entity_branch_link.link_id 1 _pdbx_entity_branch_link.details ? _pdbx_entity_branch_link.entity_id 2 _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 2 n D NAG 1 D 1 NAG C 501 NAG 2 n D NAG 2 D 2 NAG C 502 NAG 2 n E NAG 1 E 1 NAG B 500 NAG 2 n E NAG 2 E 2 NAG B 502 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 70 A CYS 94 1_555 A SG CYS 171 A CYS 195 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.026 ? disulf ? disulf2 A SG CYS 149 A CYS 173 1_555 A SG CYS 156 A CYS 180 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.037 ? disulf ? disulf3 A SG CYS 267 A CYS 291 1_555 A SG CYS 342 A CYS 366 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.036 ? disulf ? disulf4 A SG CYS 285 A CYS 309 1_555 A SG CYS 338 A CYS 362 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.034 ? disulf ? disulf5 A SG CYS 289 A CYS 313 1_555 A SG CYS 336 A CYS 360 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.037 ? disulf ? disulf6 A SG CYS 298 A CYS 322 1_555 A SG CYS 320 A CYS 344 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.037 ? disulf ? disulf7 A SG CYS 300 A CYS 324 1_555 A SG CYS 312 A CYS 336 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.039 ? disulf ? disulf8 B SG CYS 70 C CYS 94 1_555 B SG CYS 171 C CYS 195 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.027 ? disulf ? disulf9 B SG CYS 149 C CYS 173 1_555 B SG CYS 156 C CYS 180 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.035 ? disulf ? disulf10 B SG CYS 267 C CYS 291 1_555 B SG CYS 342 C CYS 366 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.035 ? disulf ? disulf11 B SG CYS 285 C CYS 309 1_555 B SG CYS 338 C CYS 362 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.031 ? disulf ? disulf12 B SG CYS 289 C CYS 313 1_555 B SG CYS 336 C CYS 360 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.032 ? disulf ? disulf13 B SG CYS 298 C CYS 322 1_555 B SG CYS 320 C CYS 344 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.032 ? disulf ? disulf14 B SG CYS 300 C CYS 324 1_555 B SG CYS 312 C CYS 336 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.029 ? disulf ? disulf15 C SG CYS 70 B CYS 94 1_555 C SG CYS 171 B CYS 195 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.03 ? disulf ? disulf16 C SG CYS 149 B CYS 173 1_555 C SG CYS 156 B CYS 180 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.043 ? disulf ? disulf17 C SG CYS 267 B CYS 291 1_555 C SG CYS 342 B CYS 366 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.038 ? disulf ? disulf18 C SG CYS 285 B CYS 309 1_555 C SG CYS 338 B CYS 362 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.03 ? disulf ? disulf19 C SG CYS 289 B CYS 313 1_555 C SG CYS 336 B CYS 360 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.028 ? disulf ? disulf20 C SG CYS 298 B CYS 322 1_555 C SG CYS 320 B CYS 344 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.034 ? disulf ? disulf21 C SG CYS 300 B CYS 324 1_555 C SG CYS 312 B CYS 336 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.033 ? covale ? covale1 A ND2 ASN 343 A ASN 367 1_555 G C1 NAG . A NAG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.442 ? covale ? covale2 A ND2 ASN 370 A ASN 394 1_555 F C1 NAG . A NAG 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.437 ? covale ? covale3 B ND2 ASN 343 C ASN 367 1_555 K C1 NAG . C NAG 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.438 ? covale ? covale4 B ND2 ASN 370 C ASN 394 1_555 D C1 NAG . D NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.446 ? covale ? covale5 C ND2 ASN 343 B ASN 367 1_555 E C1 NAG . E NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.435 ? covale ? covale6 C ND2 ASN 370 B ASN 394 1_555 N C1 NAG . B NAG 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.441 ? covale ? covale7 D O4 NAG . D NAG 1 1_555 D C1 NAG . D NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.452 ? covale ? covale8 E O4 NAG . E NAG 1 1_555 E C1 NAG . E NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.444 ? metalc ? metalc1 A OE2 GLU 196 A GLU 220 1_555 J CA CA . A CA 505 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.987 ? metalc ? metalc2 B OE1 GLN 253 C GLN 277 1_555 L CA CA . C CA 504 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.485 ? metalc ? metalc3 C OE1 GLN 253 B GLN 277 1_555 P CA CA . B CA 505 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.944 ? # _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 5WKV _atom_sites.fract_transf_matrix[1][1] 0.009159 _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] 0.007479 _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] 0.006343 _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 3 NAG A 1 501 500 NAG NAG . G 3 NAG A 1 502 501 NAG NAG . H 4 CL A 1 503 2 CL CL . I 5 CA A 1 504 1 CA CA . J 5 CA A 1 505 5 CA CA . K 3 NAG C 1 501 500 NAG NAG . L 5 CA C 1 504 2 CA CA . M 5 CA C 1 505 6 CA CA . N 3 NAG B 1 503 501 NAG NAG . O 4 CL B 1 504 1 CL CL . P 5 CA B 1 505 3 CA CA . Q 5 CA B 1 506 4 CA CA . # 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 . . . F 3 -33.402 20.32 -33.001 1 147.98 ? C1 NAG 501 A 1 HETATM 2 C C2 NAG . . . F 3 -32.956 21.398 -33.989 1 166.1 ? C2 NAG 501 A 1 HETATM 3 C C3 NAG . . . F 3 -33.652 21.208 -35.334 1 173.95 ? C3 NAG 501 A 1 HETATM 4 C C4 NAG . . . F 3 -33.461 19.784 -35.842 1 180.68 ? C4 NAG 501 A 1 HETATM 5 C C5 NAG . . . F 3 -33.89 18.781 -34.776 1 184.26 ? C5 NAG 501 A 1 HETATM 6 C C6 NAG . . . F 3 -33.616 17.347 -35.166 1 172.88 ? C6 NAG 501 A 1 HETATM 7 C C7 NAG . . . F 3 -32.256 23.556 -33.052 1 169.24 ? C7 NAG 501 A 1 HETATM 8 C C8 NAG . . . F 3 -32.709 24.887 -32.533 1 156.43 ? C8 NAG 501 A 1 HETATM 9 N N2 NAG . . . F 3 -33.221 22.726 -33.459 1 167.2 ? N2 NAG 501 A 1 HETATM 10 O O3 NAG . . . F 3 -33.117 22.133 -36.274 1 171.7 ? O3 NAG 501 A 1 HETATM 11 O O4 NAG . . . F 3 -34.236 19.58 -37.018 1 165.62 ? O4 NAG 501 A 1 HETATM 12 O O5 NAG . . . F 3 -33.166 19.025 -33.561 1 170.82 ? O5 NAG 501 A 1 HETATM 13 O O6 NAG . . . F 3 -33.674 16.482 -34.04 1 142.94 ? O6 NAG 501 A 1 HETATM 14 O O7 NAG . . . F 3 -31.07 23.248 -33.101 1 166.24 ? O7 NAG 501 A 1 # _model_server_stats.io_time_ms 21 _model_server_stats.parse_time_ms 14 _model_server_stats.create_model_time_ms 27 _model_server_stats.query_time_ms 235 _model_server_stats.encode_time_ms 5 _model_server_stats.element_count 14 #