data_5L2K # _model_server_result.job_id qr-SJmYsNw99OIehk463vA _model_server_result.datetime_utc '2024-11-01 11:31:59' _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 5l2k # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"F","auth_seq_id":402}' # _entry.id 5L2K # _exptl.entry_id 5L2K _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 120 _cell.entry_id 5L2K _cell.length_a 174.998 _cell.length_b 174.998 _cell.length_c 170.869 _cell.Z_PDB 12 _cell.pdbx_unique_axis ? # _symmetry.entry_id 5L2K _symmetry.cell_setting ? _symmetry.Int_Tables_number 181 _symmetry.space_group_name_Hall . _symmetry.space_group_name_H-M 'P 64 2 2' # loop_ _pdbx_struct_assembly.method_details _pdbx_struct_assembly.oligomeric_details _pdbx_struct_assembly.oligomeric_count _pdbx_struct_assembly.details _pdbx_struct_assembly.id ? tetrameric 4 author_defined_assembly 1 PISA hexadecameric 16 software_defined_assembly 2 # loop_ _pdbx_struct_assembly_gen.asym_id_list _pdbx_struct_assembly_gen.assembly_id _pdbx_struct_assembly_gen.oper_expression A,B,C,D,E,F,G,H,I,J,K,L,M,N,O,P,Q,R,S,T,U,V,W,X 1 1 A,B,D,E,F,G,H,I,J,K,L,M,N,O,P,S,T,U,V,W 2 1,3,6,8 C,Q,R,X 2 2,4,5,7 # 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' 3_544 -x+y,-x-1,z-1/3 -0.5 0.866025 0 -0.866025 -0.5 0 0 0 1 87.499 -151.552714 -56.956333 3 'crystal symmetry operation' 4_545 -x,-y-1,z -1 0 0 0 -1 0 0 0 1 87.499 -151.552714 0 4 'crystal symmetry operation' 6_554 x-y,x,z-1/3 0.5 -0.866025 0 0.866025 0.5 0 0 0 1 0 0 -56.956333 5 'crystal symmetry operation' 8_545 x-y,-y-1,-z 1 0 0 0 -1 0 0 0 -1 87.499 -151.552714 0 6 'crystal symmetry operation' 9_554 -x,-x+y,-z-1/3 -0.5 -0.866025 0 -0.866025 0.5 0 0 0 -1 0 0 -56.956333 7 'crystal symmetry operation' 11_555 -x+y,y,-z -1 0 0 0 1 0 0 0 -1 0 0 0 8 'crystal symmetry operation' 12_544 x,x-y-1,-z-1/3 0.5 0.866025 0 0.866025 -0.5 0 0 0 -1 87.499 -151.552714 -56.956333 # 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 # 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 101 A CYS 102 1_555 A SG CYS 165 A CYS 166 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.051 ? disulf ? disulf2 A SG CYS 130 A CYS 131 1_555 A SG CYS 144 A CYS 145 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.043 ? disulf ? disulf3 A SG CYS 205 A CYS 206 1_555 A SG CYS 260 A CYS 261 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.032 ? disulf ? disulf4 B SG CYS 25 B CYS 27 1_555 B SG CYS 80 B CYS 82 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.035 ? disulf ? disulf5 C SG CYS 22 D CYS 23 1_555 C SG CYS 88 D CYS 104 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.035 ? disulf ? disulf6 C SG CYS 133 D CYS 150 1_555 C SG CYS 183 D CYS 200 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.037 ? disulf ? disulf7 C SG CYS 158 D CYS 175 1_555 D SG CYS 170 E CYS 183 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.037 ? disulf ? disulf8 D SG CYS 23 E CYS 23 1_555 D SG CYS 91 E CYS 104 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.033 ? disulf ? disulf9 D SG CYS 144 E CYS 157 1_555 D SG CYS 209 E CYS 222 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.035 ? covale ? covale1 A ND2 ASN 19 A ASN 20 1_555 F C1 NAG . A NAG 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.431 ? covale ? covale2 A ND2 ASN 56 A ASN 57 1_555 E C1 NAG . A NAG 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.433 ? covale ? covale3 A ND2 ASN 127 A ASN 128 1_555 G C1 NAG . A NAG 403 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.435 ? # _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 490 n n C1 O1 NAG sing 491 n n C1 O5 NAG sing 492 n n C1 H1 NAG sing 493 n n C2 C3 NAG sing 494 n n C2 N2 NAG sing 495 n n C2 H2 NAG sing 496 n n C3 C4 NAG sing 497 n n C3 O3 NAG sing 498 n n C3 H3 NAG sing 499 n n C4 C5 NAG sing 500 n n C4 O4 NAG sing 501 n n C4 H4 NAG sing 502 n n C5 C6 NAG sing 503 n n C5 O5 NAG sing 504 n n C5 H5 NAG sing 505 n n C6 O6 NAG sing 506 n n C6 H61 NAG sing 507 n n C6 H62 NAG sing 508 n n C7 C8 NAG sing 509 n n C7 N2 NAG sing 510 n n C7 O7 NAG doub 511 n n C8 H81 NAG sing 512 n n C8 H82 NAG sing 513 n n C8 H83 NAG sing 514 n n N2 HN2 NAG sing 515 n n O1 HO1 NAG sing 516 n n O3 HO3 NAG sing 517 n n O4 HO4 NAG sing 518 n n O6 HO6 NAG sing 519 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 5L2K _atom_sites.fract_transf_matrix[1][1] 0.005714 _atom_sites.fract_transf_matrix[1][2] 0.003299 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.006598 _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] 0.005852 _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 1011 NAG NAG . F 5 NAG A 1 402 1001 NAG NAG . G 5 NAG A 1 403 1002 NAG NAG . H 6 SO4 A 1 404 2 SO4 SO4 . I 6 SO4 A 1 405 4 SO4 SO4 . J 6 SO4 A 1 406 1 SO4 SO4 . K 7 CL A 1 407 1 CL CL . L 7 CL A 1 408 2 CL CL . M 7 CL A 1 409 4 CL CL . N 8 NA A 1 410 2 NA NA . O 9 6UL A 1 411 1 6UL 6UL . P 7 CL B 1 201 3 CL CL . Q 6 SO4 D 1 301 3 SO4 SO4 . R 10 CS D 1 302 1 CS CS . S 6 SO4 E 1 301 2 SO4 SO4 . T 8 NA E 1 302 1 NA NA . U 11 70E E 1 303 1 70E GMM . V 12 HOH A 1 501 7 HOH HOH . V 12 HOH A 2 502 1 HOH HOH . W 12 HOH B 1 301 11 HOH HOH . W 12 HOH B 2 302 12 HOH HOH . W 12 HOH B 3 303 13 HOH HOH . X 12 HOH D 1 401 9 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 . . . F 5 31.022 -47.691 13.817 1 108.39 ? C1 NAG 402 A 1 HETATM 2 C C2 NAG . . . F 5 30.108 -47.188 14.887 1 109.5 ? C2 NAG 402 A 1 HETATM 3 C C3 NAG . . . F 5 29.286 -46.071 14.383 1 110.05 ? C3 NAG 402 A 1 HETATM 4 C C4 NAG . . . F 5 30.058 -44.985 13.776 1 110.23 ? C4 NAG 402 A 1 HETATM 5 C C5 NAG . . . F 5 31.235 -45.438 12.864 1 109.45 ? C5 NAG 402 A 1 HETATM 6 C C6 NAG . . . F 5 32.188 -44.267 12.563 1 109.17 ? C6 NAG 402 A 1 HETATM 7 C C7 NAG . . . F 5 29.29 -48.79 16.697 1 108.89 ? C7 NAG 402 A 1 HETATM 8 C C8 NAG . . . F 5 28.359 -49.935 17.112 1 108.87 ? C8 NAG 402 A 1 HETATM 9 N N2 NAG . . . F 5 29.233 -48.286 15.342 1 109.39 ? N2 NAG 402 A 1 HETATM 10 O O3 NAG . . . F 5 28.488 -45.568 15.434 1 109.84 ? O3 NAG 402 A 1 HETATM 11 O O4 NAG . . . F 5 29.14 -44.181 13.053 1 110.56 ? O4 NAG 402 A 1 HETATM 12 O O5 NAG . . . F 5 31.922 -46.601 13.306 1 108.79 ? O5 NAG 402 A 1 HETATM 13 O O6 NAG . . . F 5 33.255 -44.521 11.722 1 108.94 ? O6 NAG 402 A 1 HETATM 14 O O7 NAG . . . F 5 30.058 -48.327 17.508 1 108.43 ? O7 NAG 402 A 1 # _model_server_stats.io_time_ms 10 _model_server_stats.parse_time_ms 10 _model_server_stats.create_model_time_ms 12 _model_server_stats.query_time_ms 320 _model_server_stats.encode_time_ms 18 _model_server_stats.element_count 14 #