data_4DJ8 # _model_server_result.job_id p7nml0mRVRJJESHjwsuAjQ _model_server_result.datetime_utc '2024-11-27 17:58:21' _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 4dj8 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"I","auth_seq_id":403}' # _entry.id 4DJ8 # _exptl.entry_id 4DJ8 _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 12 _entity.pdbx_parent_entity_id . _entity.pdbx_mutation ? _entity.pdbx_fragment ? _entity.pdbx_ec ? # _cell.angle_alpha 90 _cell.angle_beta 124.15 _cell.angle_gamma 90 _cell.entry_id 4DJ8 _cell.length_a 203.774 _cell.length_b 117.603 _cell.length_c 120.456 _cell.Z_PDB 12 _cell.pdbx_unique_axis ? # _symmetry.entry_id 4DJ8 _symmetry.cell_setting ? _symmetry.Int_Tables_number 5 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'C 1 2 1' # _pdbx_struct_assembly.method_details PISA _pdbx_struct_assembly.oligomeric_details hexameric _pdbx_struct_assembly.oligomeric_count 6 _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,R,S,T,U,V,W,X,Y,Z,AA _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 G N N ? 3 H N N ? 3 I N N ? 3 K N N ? 3 L N N ? 3 M N N ? 3 N N N ? 3 P N N ? 3 Q N N ? 3 R N N ? 3 S N N ? 3 U 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 8 A CYS 4 1_555 B SG CYS 137 B CYS 137 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.042 ? disulf ? disulf2 A SG CYS 46 A CYS 42 1_555 A SG CYS 272 A CYS 268 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.108 ? disulf ? disulf3 A SG CYS 58 A CYS 54 1_555 A SG CYS 70 A CYS 66 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.145 ? disulf ? disulf4 A SG CYS 91 A CYS 87 1_555 A SG CYS 133 A CYS 129 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.057 ? disulf ? disulf5 A SG CYS 276 A CYS 272 1_555 A SG CYS 300 A CYS 296 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.162 ? disulf ? disulf6 B SG CYS 144 B CYS 144 1_555 B SG CYS 148 B CYS 148 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.05 ? disulf ? disulf7 C SG CYS 8 C CYS 4 1_555 D SG CYS 137 D CYS 137 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.03 ? disulf ? disulf8 C SG CYS 46 C CYS 42 1_555 C SG CYS 272 C CYS 268 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.126 ? disulf ? disulf9 C SG CYS 58 C CYS 54 1_555 C SG CYS 70 C CYS 66 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.147 ? disulf ? disulf10 C SG CYS 91 C CYS 87 1_555 C SG CYS 133 C CYS 129 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.069 ? disulf ? disulf11 C SG CYS 276 C CYS 272 1_555 C SG CYS 300 C CYS 296 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.155 ? disulf ? disulf12 D SG CYS 144 D CYS 144 1_555 D SG CYS 148 D CYS 148 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.06 ? disulf ? disulf13 E SG CYS 8 E CYS 4 1_555 F SG CYS 137 F CYS 137 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.039 ? disulf ? disulf14 E SG CYS 46 E CYS 42 1_555 E SG CYS 272 E CYS 268 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.109 ? disulf ? disulf15 E SG CYS 58 E CYS 54 1_555 E SG CYS 70 E CYS 66 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.14 ? disulf ? disulf16 E SG CYS 91 E CYS 87 1_555 E SG CYS 133 E CYS 129 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.064 ? disulf ? disulf17 E SG CYS 276 E CYS 272 1_555 E SG CYS 300 E CYS 296 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.177 ? disulf ? disulf18 F SG CYS 144 F CYS 144 1_555 F SG CYS 148 F CYS 148 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.046 ? covale ? covale1 A ND2 ASN 32 A ASN 28 1_555 H C1 NAG . A NAG 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.468 ? covale ? covale2 A ND2 ASN 127 A ASN 123 1_555 G C1 NAG . A NAG 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.458 ? covale ? covale3 A ND2 ASN 235 A ASN 231 1_555 I C1 NAG . A NAG 403 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.472 ? covale ? covale4 B ND2 ASN 82 B ASN 82 1_555 K C1 NAG . B NAG 201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.451 ? covale ? covale5 C ND2 ASN 32 C ASN 28 1_555 M C1 NAG . C NAG 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.456 ? covale ? covale6 C ND2 ASN 127 C ASN 123 1_555 L C1 NAG . C NAG 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.459 ? covale ? covale7 C ND2 ASN 235 C ASN 231 1_555 N C1 NAG . C NAG 403 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.46 ? covale ? covale8 D ND2 ASN 82 D ASN 82 1_555 P C1 NAG . D NAG 201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.446 ? covale ? covale9 E ND2 ASN 32 E ASN 28 1_555 R C1 NAG . E NAG 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.464 ? covale ? covale10 E ND2 ASN 127 E ASN 123 1_555 Q C1 NAG . E NAG 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.444 ? covale ? covale11 E ND2 ASN 235 E ASN 231 1_555 S C1 NAG . E NAG 403 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.462 ? covale ? covale12 F ND2 ASN 82 F ASN 82 1_555 U C1 NAG . F NAG 201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.449 ? # _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 237 n n C1 O1 NAG sing 238 n n C1 O5 NAG sing 239 n n C1 H1 NAG sing 240 n n C2 C3 NAG sing 241 n n C2 N2 NAG sing 242 n n C2 H2 NAG sing 243 n n C3 C4 NAG sing 244 n n C3 O3 NAG sing 245 n n C3 H3 NAG sing 246 n n C4 C5 NAG sing 247 n n C4 O4 NAG sing 248 n n C4 H4 NAG sing 249 n n C5 C6 NAG sing 250 n n C5 O5 NAG sing 251 n n C5 H5 NAG sing 252 n n C6 O6 NAG sing 253 n n C6 H61 NAG sing 254 n n C6 H62 NAG sing 255 n n C7 C8 NAG sing 256 n n C7 N2 NAG sing 257 n n C7 O7 NAG doub 258 n n C8 H81 NAG sing 259 n n C8 H82 NAG sing 260 n n C8 H83 NAG sing 261 n n N2 HN2 NAG sing 262 n n O1 HO1 NAG sing 263 n n O3 HO3 NAG sing 264 n n O4 HO4 NAG sing 265 n n O6 HO6 NAG sing 266 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 4DJ8 _atom_sites.fract_transf_matrix[1][1] 0.004907 _atom_sites.fract_transf_matrix[1][2] 0 _atom_sites.fract_transf_matrix[1][3] 0.003329 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.008503 _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] 0.010032 _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 G 3 NAG A 1 401 1 NAG NAG . H 3 NAG A 1 402 1 NAG NAG . I 3 NAG A 1 403 1 NAG NAG . J 4 SIA A 1 404 1 SIA SIA . K 3 NAG B 1 201 1 NAG NAG . L 3 NAG C 1 401 1 NAG NAG . M 3 NAG C 1 402 1 NAG NAG . N 3 NAG C 1 403 1 NAG NAG . O 4 SIA C 1 404 1 SIA SIA . P 3 NAG D 1 201 1 NAG NAG . Q 3 NAG E 1 401 1 NAG NAG . R 3 NAG E 1 402 1 NAG NAG . S 3 NAG E 1 403 1 NAG NAG . T 4 SIA E 1 404 1 SIA SIA . U 3 NAG F 1 201 1 NAG NAG . V 5 HOH A 1 501 2 HOH HOH . V 5 HOH A 2 502 8 HOH HOH . V 5 HOH A 3 503 13 HOH HOH . V 5 HOH A 4 504 16 HOH HOH . V 5 HOH A 5 505 25 HOH HOH . V 5 HOH A 6 506 30 HOH HOH . V 5 HOH A 7 507 34 HOH HOH . V 5 HOH A 8 508 36 HOH HOH . V 5 HOH A 9 509 42 HOH HOH . V 5 HOH A 10 510 46 HOH HOH . V 5 HOH A 11 511 54 HOH HOH . V 5 HOH A 12 512 56 HOH HOH . V 5 HOH A 13 513 61 HOH HOH . V 5 HOH A 14 514 66 HOH HOH . V 5 HOH A 15 515 68 HOH HOH . V 5 HOH A 16 516 69 HOH HOH . V 5 HOH A 17 517 72 HOH HOH . V 5 HOH A 18 518 77 HOH HOH . V 5 HOH A 19 519 85 HOH HOH . V 5 HOH A 20 520 89 HOH HOH . V 5 HOH A 21 521 100 HOH HOH . V 5 HOH A 22 522 108 HOH HOH . W 5 HOH B 1 301 6 HOH HOH . W 5 HOH B 2 302 17 HOH HOH . W 5 HOH B 3 303 22 HOH HOH . W 5 HOH B 4 304 23 HOH HOH . W 5 HOH B 5 305 26 HOH HOH . W 5 HOH B 6 306 27 HOH HOH . W 5 HOH B 7 307 31 HOH HOH . W 5 HOH B 8 308 52 HOH HOH . W 5 HOH B 9 309 59 HOH HOH . W 5 HOH B 10 310 65 HOH HOH . W 5 HOH B 11 311 87 HOH HOH . W 5 HOH B 12 312 94 HOH HOH . W 5 HOH B 13 313 95 HOH HOH . W 5 HOH B 14 314 114 HOH HOH . X 5 HOH C 1 501 3 HOH HOH . X 5 HOH C 2 502 18 HOH HOH . X 5 HOH C 3 503 19 HOH HOH . X 5 HOH C 4 504 20 HOH HOH . X 5 HOH C 5 505 21 HOH HOH . X 5 HOH C 6 506 24 HOH HOH . X 5 HOH C 7 507 28 HOH HOH . X 5 HOH C 8 508 44 HOH HOH . X 5 HOH C 9 509 47 HOH HOH . X 5 HOH C 10 510 55 HOH HOH . X 5 HOH C 11 511 62 HOH HOH . X 5 HOH C 12 512 63 HOH HOH . X 5 HOH C 13 513 67 HOH HOH . X 5 HOH C 14 514 71 HOH HOH . X 5 HOH C 15 515 76 HOH HOH . X 5 HOH C 16 516 80 HOH HOH . X 5 HOH C 17 517 81 HOH HOH . X 5 HOH C 18 518 83 HOH HOH . X 5 HOH C 19 519 91 HOH HOH . X 5 HOH C 20 520 92 HOH HOH . X 5 HOH C 21 521 102 HOH HOH . X 5 HOH C 22 522 103 HOH HOH . X 5 HOH C 23 523 110 HOH HOH . X 5 HOH C 24 524 113 HOH HOH . X 5 HOH C 25 525 116 HOH HOH . Y 5 HOH D 1 301 9 HOH HOH . Y 5 HOH D 2 302 11 HOH HOH . Y 5 HOH D 3 303 15 HOH HOH . Y 5 HOH D 4 304 32 HOH HOH . Y 5 HOH D 5 305 43 HOH HOH . Y 5 HOH D 6 306 51 HOH HOH . Y 5 HOH D 7 307 64 HOH HOH . Y 5 HOH D 8 308 70 HOH HOH . Y 5 HOH D 9 309 84 HOH HOH . Y 5 HOH D 10 310 99 HOH HOH . Y 5 HOH D 11 311 104 HOH HOH . Z 5 HOH E 1 501 4 HOH HOH . Z 5 HOH E 2 502 33 HOH HOH . Z 5 HOH E 3 503 35 HOH HOH . Z 5 HOH E 4 504 39 HOH HOH . Z 5 HOH E 5 505 45 HOH HOH . Z 5 HOH E 6 506 48 HOH HOH . Z 5 HOH E 7 507 49 HOH HOH . Z 5 HOH E 8 508 50 HOH HOH . Z 5 HOH E 9 509 57 HOH HOH . Z 5 HOH E 10 510 58 HOH HOH . Z 5 HOH E 11 511 60 HOH HOH . Z 5 HOH E 12 512 73 HOH HOH . Z 5 HOH E 13 513 75 HOH HOH . Z 5 HOH E 14 514 90 HOH HOH . Z 5 HOH E 15 515 96 HOH HOH . Z 5 HOH E 16 516 97 HOH HOH . Z 5 HOH E 17 517 98 HOH HOH . Z 5 HOH E 18 518 107 HOH HOH . AA 5 HOH F 1 301 7 HOH HOH . AA 5 HOH F 2 302 10 HOH HOH . AA 5 HOH F 3 303 14 HOH HOH . AA 5 HOH F 4 304 29 HOH HOH . AA 5 HOH F 5 305 37 HOH HOH . AA 5 HOH F 6 306 38 HOH HOH . AA 5 HOH F 7 307 40 HOH HOH . AA 5 HOH F 8 308 41 HOH HOH . AA 5 HOH F 9 309 79 HOH HOH . AA 5 HOH F 10 310 82 HOH HOH . AA 5 HOH F 11 311 86 HOH HOH . AA 5 HOH F 12 312 106 HOH HOH . AA 5 HOH F 13 313 112 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 . . . I 3 54.436 16.669 68.361 1 136.33 ? C1 NAG 403 A 1 HETATM 2 C C2 NAG . . . I 3 54.373 17.452 67.036 1 152.7 ? C2 NAG 403 A 1 HETATM 3 C C3 NAG . . . I 3 55.707 18.159 66.751 1 129.93 ? C3 NAG 403 A 1 HETATM 4 C C4 NAG . . . I 3 56.058 19.131 67.886 1 142.41 ? C4 NAG 403 A 1 HETATM 5 C C5 NAG . . . I 3 55.976 18.407 69.242 1 143.66 ? C5 NAG 403 A 1 HETATM 6 C C6 NAG . . . I 3 56.112 19.404 70.407 1 129.84 ? C6 NAG 403 A 1 HETATM 7 C C7 NAG . . . I 3 52.667 16.165 65.751 1 151.33 ? C7 NAG 403 A 1 HETATM 8 C C8 NAG . . . I 3 52.315 15.483 64.447 1 106.6 ? C8 NAG 403 A 1 HETATM 9 N N2 NAG . . . I 3 53.886 16.724 65.855 1 157.78 ? N2 NAG 403 A 1 HETATM 10 O O3 NAG . . . I 3 55.573 18.882 65.551 1 95.86 ? O3 NAG 403 A 1 HETATM 11 O O4 NAG . . . I 3 57.326 19.758 67.685 1 107.31 ? O4 NAG 403 A 1 HETATM 12 O O5 NAG . . . I 3 54.771 17.63 69.378 1 166.91 ? O5 NAG 403 A 1 HETATM 13 O O6 NAG . . . I 3 57.303 19.167 71.143 1 92.92 ? O6 NAG 403 A 1 HETATM 14 O O7 NAG . . . I 3 51.849 16.178 66.679 1 128.2 ? O7 NAG 403 A 1 # _model_server_stats.io_time_ms 27 _model_server_stats.parse_time_ms 11 _model_server_stats.create_model_time_ms 45 _model_server_stats.query_time_ms 265 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 14 #