data_5K70 # _model_server_result.job_id yYKQ0hq5l-SgfvsCnRZSMg _model_server_result.datetime_utc '2024-11-28 05:30:36' _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 5k70 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"U","auth_seq_id":403}' # _entry.id 5K70 # _exptl.entry_id 5K70 _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 221.208 _entity.id 4 _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 103.69 _cell.angle_gamma 90 _cell.entry_id 5K70 _cell.length_a 110.89 _cell.length_b 113.43 _cell.length_c 185.906 _cell.Z_PDB 16 _cell.pdbx_unique_axis ? # _symmetry.entry_id 5K70 _symmetry.cell_setting ? _symmetry.Int_Tables_number 5 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'I 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 PISA monomeric 1 author_and_software_defined_assembly 1 PISA monomeric 1 author_and_software_defined_assembly 2 PISA monomeric 1 author_and_software_defined_assembly 3 PISA monomeric 1 author_and_software_defined_assembly 4 # loop_ _pdbx_struct_assembly_gen.asym_id_list _pdbx_struct_assembly_gen.assembly_id _pdbx_struct_assembly_gen.oper_expression A,E,I,J,K,L,M,N,O,Z 1 1 B,F,P,Q,R,S,T,AA 2 1 C,G,U,V,W,BA 3 1 D,H,X,Y,CA 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 ? 4 I N N ? 4 P N N ? 4 U N N # loop_ _pdbx_entity_branch.entity_id _pdbx_entity_branch.type 2 oligosaccharide 3 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 ? 2 2 1 NAG NAG C1 O1 . O4 HO4 . sing 2 ? 2 3 1 FUC NAG C1 O1 . O6 HO6 . sing 3 ? 3 2 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 2 n E NAG 1 E 1 NAG A 383 NAG 2 n E NAG 2 E 2 NAG A 386 NAG 2 n E FUC 3 E 3 FUC A 384 FUC 3 n F NAG 1 F 1 NAG B 383 NAG 3 n F FUC 2 F 2 FUC B 384 FUC 3 n G NAG 1 G 1 NAG C 383 NAG 3 n G FUC 2 G 2 FUC C 384 FUC 3 n H NAG 1 H 1 NAG D 383 NAG 3 n H FUC 2 H 2 FUC D 384 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 33 A CYS 28 1_555 A SG CYS 76 A CYS 71 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.029 ? disulf ? disulf2 A SG CYS 222 A CYS 217 1_555 A SG CYS 269 A CYS 264 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.029 ? disulf ? disulf3 A SG CYS 315 A CYS 310 1_555 A SG CYS 365 A CYS 360 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.031 ? disulf ? disulf4 B SG CYS 33 B CYS 28 1_555 B SG CYS 76 B CYS 71 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.034 ? disulf ? disulf5 B SG CYS 222 B CYS 217 1_555 B SG CYS 269 B CYS 264 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.032 ? disulf ? disulf6 B SG CYS 315 B CYS 310 1_555 B SG CYS 365 B CYS 360 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.032 ? disulf ? disulf7 C SG CYS 33 C CYS 28 1_555 C SG CYS 76 C CYS 71 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.029 ? disulf ? disulf8 C SG CYS 222 C CYS 217 1_555 C SG CYS 269 C CYS 264 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.029 ? disulf ? disulf9 C SG CYS 315 C CYS 310 1_555 C SG CYS 365 C CYS 360 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.028 ? disulf ? disulf10 D SG CYS 33 D CYS 28 1_555 D SG CYS 76 D CYS 71 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.03 ? disulf ? disulf11 D SG CYS 222 D CYS 217 1_555 D SG CYS 269 D CYS 264 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.031 ? disulf ? disulf12 D SG CYS 315 D CYS 310 1_555 D SG CYS 365 D CYS 360 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.036 ? covale ? covale1 A ND2 ASN 178 A ASN 173 1_555 I C1 NAG . A NAG 404 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.443 ? covale ? covale2 A ND2 ASN 208 A ASN 203 1_555 E C1 NAG . E NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.441 ? covale ? covale3 B ND2 ASN 178 B ASN 173 1_555 P C1 NAG . B NAG 403 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.447 ? covale ? covale4 B ND2 ASN 208 B ASN 203 1_555 F C1 NAG . F NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.452 ? covale ? covale5 C ND2 ASN 178 C ASN 173 1_555 U C1 NAG . C NAG 403 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.446 ? covale ? covale6 C ND2 ASN 208 C ASN 203 1_555 G C1 NAG . G NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.434 ? covale ? covale7 D ND2 ASN 208 D ASN 203 1_555 H C1 NAG . H NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.446 ? covale ? covale8 E O4 NAG . E NAG 1 1_555 E C1 NAG . E NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.443 ? covale ? covale9 E O6 NAG . E NAG 1 1_555 E C1 FUC . E FUC 3 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.438 ? covale ? covale10 F O6 NAG . F NAG 1 1_555 F C1 FUC . F FUC 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.435 ? covale ? covale11 G O6 NAG . G NAG 1 1_555 G C1 FUC . G FUC 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.434 ? covale ? covale12 H O6 NAG . H NAG 1 1_555 H C1 FUC . H FUC 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.441 ? # _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 5K70 _atom_sites.fract_transf_matrix[1][1] 0.009018 _atom_sites.fract_transf_matrix[1][2] 0 _atom_sites.fract_transf_matrix[1][3] 0.002197 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.008816 _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] 0.005536 _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 I 4 NAG A 1 404 385 NAG NAG . J 5 PO4 A 1 405 401 PO4 PO4 . K 5 PO4 A 1 406 402 PO4 PO4 . L 5 PO4 A 1 407 403 PO4 PO4 . M 5 PO4 A 1 408 405 PO4 PO4 . N 5 PO4 A 1 409 406 PO4 PO4 . O 5 PO4 A 1 410 407 PO4 PO4 . P 4 NAG B 1 403 395 NAG NAG . Q 5 PO4 B 1 404 401 PO4 PO4 . R 5 PO4 B 1 405 402 PO4 PO4 . S 5 PO4 B 1 406 403 PO4 PO4 . T 5 PO4 B 1 407 402 PO4 PO4 . U 4 NAG C 1 403 385 NAG NAG . V 5 PO4 C 1 404 401 PO4 PO4 . W 5 PO4 C 1 405 402 PO4 PO4 . X 5 PO4 D 1 401 404 PO4 PO4 . Y 5 PO4 D 1 404 401 PO4 PO4 . Z 6 HOH A 1 501 10 HOH HOH . Z 6 HOH A 2 502 16 HOH HOH . Z 6 HOH A 3 503 44 HOH HOH . Z 6 HOH A 4 504 13 HOH HOH . Z 6 HOH A 5 505 21 HOH HOH . Z 6 HOH A 6 506 7 HOH HOH . Z 6 HOH A 7 507 4 HOH HOH . Z 6 HOH A 8 508 11 HOH HOH . Z 6 HOH A 9 509 1 HOH HOH . Z 6 HOH A 10 510 41 HOH HOH . Z 6 HOH A 11 511 23 HOH HOH . Z 6 HOH A 12 512 43 HOH HOH . Z 6 HOH A 13 513 60 HOH HOH . Z 6 HOH A 14 514 6 HOH HOH . Z 6 HOH A 15 515 29 HOH HOH . Z 6 HOH A 16 516 12 HOH HOH . Z 6 HOH A 17 517 36 HOH HOH . Z 6 HOH A 18 518 49 HOH HOH . Z 6 HOH A 19 519 45 HOH HOH . Z 6 HOH A 20 520 42 HOH HOH . Z 6 HOH A 21 521 56 HOH HOH . Z 6 HOH A 22 522 54 HOH HOH . Z 6 HOH A 23 523 50 HOH HOH . Z 6 HOH A 24 524 55 HOH HOH . Z 6 HOH A 25 525 48 HOH HOH . Z 6 HOH A 26 526 9 HOH HOH . AA 6 HOH B 1 501 40 HOH HOH . AA 6 HOH B 2 502 17 HOH HOH . AA 6 HOH B 3 503 46 HOH HOH . AA 6 HOH B 4 504 25 HOH HOH . AA 6 HOH B 5 505 59 HOH HOH . AA 6 HOH B 6 506 26 HOH HOH . AA 6 HOH B 7 507 52 HOH HOH . AA 6 HOH B 8 508 20 HOH HOH . AA 6 HOH B 9 509 2 HOH HOH . AA 6 HOH B 10 510 8 HOH HOH . AA 6 HOH B 11 511 39 HOH HOH . AA 6 HOH B 12 512 19 HOH HOH . AA 6 HOH B 13 513 38 HOH HOH . AA 6 HOH B 14 514 57 HOH HOH . AA 6 HOH B 15 515 53 HOH HOH . AA 6 HOH B 16 516 47 HOH HOH . AA 6 HOH B 17 517 18 HOH HOH . BA 6 HOH C 1 501 5 HOH HOH . BA 6 HOH C 2 502 30 HOH HOH . BA 6 HOH C 3 503 31 HOH HOH . BA 6 HOH C 4 504 27 HOH HOH . BA 6 HOH C 5 505 51 HOH HOH . BA 6 HOH C 6 506 15 HOH HOH . BA 6 HOH C 7 507 3 HOH HOH . BA 6 HOH C 8 508 37 HOH HOH . BA 6 HOH C 9 509 34 HOH HOH . BA 6 HOH C 10 510 35 HOH HOH . BA 6 HOH C 11 511 58 HOH HOH . BA 6 HOH C 12 512 62 HOH HOH . CA 6 HOH D 1 501 24 HOH HOH . CA 6 HOH D 2 502 61 HOH HOH . CA 6 HOH D 3 503 32 HOH HOH . CA 6 HOH D 4 504 28 HOH HOH . CA 6 HOH D 5 505 14 HOH HOH . CA 6 HOH D 6 506 33 HOH HOH . CA 6 HOH D 7 507 22 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 . . . U 4 -78.422 -47.162 -37.581 1 88.46 ? C1 NAG 403 C 1 HETATM 2 C C2 NAG . . . U 4 -77.637 -45.879 -37.862 1 112.87 ? C2 NAG 403 C 1 HETATM 3 C C3 NAG . . . U 4 -76.568 -45.665 -36.796 1 102.79 ? C3 NAG 403 C 1 HETATM 4 C C4 NAG . . . U 4 -77.206 -45.657 -35.415 1 101.15 ? C4 NAG 403 C 1 HETATM 5 C C5 NAG . . . U 4 -78.029 -46.929 -35.203 1 105.77 ? C5 NAG 403 C 1 HETATM 6 C C6 NAG . . . U 4 -78.803 -46.92 -33.905 1 100.18 ? C6 NAG 403 C 1 HETATM 7 C C7 NAG . . . U 4 -76.102 -46.703 -39.624 1 120.5 ? C7 NAG 403 C 1 HETATM 8 C C8 NAG . . . U 4 -75.637 -46.497 -41.035 1 126.38 ? C8 NAG 403 C 1 HETATM 9 N N2 NAG . . . U 4 -77.054 -45.864 -39.199 1 114.83 ? N2 NAG 403 C 1 HETATM 10 O O3 NAG . . . U 4 -75.896 -44.432 -37.031 1 91.21 ? O3 NAG 403 C 1 HETATM 11 O O4 NAG . . . U 4 -76.193 -45.569 -34.419 1 71.14 ? O4 NAG 403 C 1 HETATM 12 O O5 NAG . . . U 4 -78.992 -47.095 -36.259 1 93.25 ? O5 NAG 403 C 1 HETATM 13 O O6 NAG . . . U 4 -79.994 -46.151 -34.016 1 88.53 ? O6 NAG 403 C 1 HETATM 14 O O7 NAG . . . U 4 -75.638 -47.59 -38.912 1 112.65 ? O7 NAG 403 C 1 # _model_server_stats.io_time_ms 29 _model_server_stats.parse_time_ms 13 _model_server_stats.create_model_time_ms 13 _model_server_stats.query_time_ms 302 _model_server_stats.encode_time_ms 11 _model_server_stats.element_count 14 #