data_4XKE # _model_server_result.job_id hh4BI0LwbE6Ub0ZCVt12bQ _model_server_result.datetime_utc '2025-01-11 17:37:59' _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 4xke # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"L","auth_seq_id":402}' # _entry.id 4XKE # _exptl.entry_id 4XKE _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 221.208 _entity.id 4 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description 2-acetamido-2-deoxy-beta-D-glucopyranose _entity.pdbx_number_of_molecules 6 _entity.pdbx_parent_entity_id . _entity.pdbx_mutation ? _entity.pdbx_fragment ? _entity.pdbx_ec ? # _cell.angle_alpha 90 _cell.angle_beta 126.3 _cell.angle_gamma 90 _cell.entry_id 4XKE _cell.length_a 185.596 _cell.length_b 99.253 _cell.length_c 133.418 _cell.Z_PDB 12 _cell.pdbx_unique_axis ? # _symmetry.entry_id 4XKE _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 _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 ? 4 H N N ? 4 I N N ? 4 J N N ? 4 K N N ? 4 L N N ? 4 M N N # _pdbx_entity_branch.entity_id 3 _pdbx_entity_branch.type 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 ? 3 2 1 GAL NAG C1 O1 . O4 HO4 . sing 2 ? 3 3 2 SIA GAL C2 O2 . O3 HO3 . 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 3 n G NAG 1 G 1 NAG L 3003 NAG 3 n G GAL 2 G 2 GAL L 3002 GAL 3 n G SIA 3 G 3 SIA L 3001 SIA # 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 14 1_555 B SG CYS 137 B CYS 137 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.072 ? disulf ? disulf2 A SG CYS 46 A CYS 52 1_555 A SG CYS 281 A CYS 277 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.795 ? disulf ? disulf3 A SG CYS 59 A CYS 64 1_555 A SG CYS 71 A CYS 76 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.089 ? disulf ? disulf4 A SG CYS 94 A CYS 97 1_555 A SG CYS 139 A CYS 139 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.071 ? disulf ? disulf5 B SG CYS 144 B CYS 144 1_555 B SG CYS 148 B CYS 148 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.085 ? disulf ? disulf6 C SG CYS 8 C CYS 14 1_555 D SG CYS 137 D CYS 137 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.064 ? disulf ? disulf7 C SG CYS 46 C CYS 52 1_555 C SG CYS 281 C CYS 277 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.049 ? disulf ? disulf8 C SG CYS 59 C CYS 64 1_555 C SG CYS 71 C CYS 76 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.063 ? disulf ? disulf9 C SG CYS 94 C CYS 97 1_555 C SG CYS 139 C CYS 139 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.009 ? disulf ? disulf10 C SG CYS 285 C CYS 281 1_555 C SG CYS 309 C CYS 305 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.044 ? disulf ? disulf11 E SG CYS 46 E CYS 52 1_555 E SG CYS 281 E CYS 277 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.7 ? disulf ? disulf12 E SG CYS 59 E CYS 64 1_555 E SG CYS 71 E CYS 76 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.947 ? disulf ? disulf13 E SG CYS 94 E CYS 97 1_555 E SG CYS 139 E CYS 139 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.614 ? disulf ? disulf14 E SG CYS 285 E CYS 281 1_555 E SG CYS 309 E CYS 305 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.05 ? disulf ? disulf15 F SG CYS 144 F CYS 144 1_555 F SG CYS 148 F CYS 148 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.074 ? covale ? covale1 A ND2 ASN 27 A ASN 33 1_555 H C1 NAG . A NAG 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.46 ? covale ? covale2 A ND2 ASN 171 A ASN 169 1_555 I C1 NAG . A NAG 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.441 ? covale ? covale3 D ND2 ASN 154 D ASN 154 1_555 J C1 NAG . D NAG 201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.427 ? covale ? covale4 E ND2 ASN 15 E ASN 21 1_555 K C1 NAG . E NAG 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.416 ? covale ? covale5 E ND2 ASN 171 E ASN 169 1_555 L C1 NAG . E NAG 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.346 ? covale ? covale6 F ND2 ASN 154 F ASN 154 1_555 M C1 NAG . F NAG 201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.459 ? covale ? covale7 G O4 NAG . G NAG 1 1_555 G C1 GAL . G GAL 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.478 ? covale ? covale8 G O3 GAL . G GAL 2 1_555 G C2 SIA . G SIA 3 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.442 ? # _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 261 n n C1 O1 NAG sing 262 n n C1 O5 NAG sing 263 n n C1 H1 NAG sing 264 n n C2 C3 NAG sing 265 n n C2 N2 NAG sing 266 n n C2 H2 NAG sing 267 n n C3 C4 NAG sing 268 n n C3 O3 NAG sing 269 n n C3 H3 NAG sing 270 n n C4 C5 NAG sing 271 n n C4 O4 NAG sing 272 n n C4 H4 NAG sing 273 n n C5 C6 NAG sing 274 n n C5 O5 NAG sing 275 n n C5 H5 NAG sing 276 n n C6 O6 NAG sing 277 n n C6 H61 NAG sing 278 n n C6 H62 NAG sing 279 n n C7 C8 NAG sing 280 n n C7 N2 NAG sing 281 n n C7 O7 NAG doub 282 n n C8 H81 NAG sing 283 n n C8 H82 NAG sing 284 n n C8 H83 NAG sing 285 n n N2 HN2 NAG sing 286 n n O1 HO1 NAG sing 287 n n O3 HO3 NAG sing 288 n n O4 HO4 NAG sing 289 n n O6 HO6 NAG sing 290 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 4XKE _atom_sites.fract_transf_matrix[1][1] 0.005388 _atom_sites.fract_transf_matrix[1][2] 0 _atom_sites.fract_transf_matrix[1][3] 0.003958 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.010075 _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] 0.0093 _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 H 4 NAG A 1 401 1025 NAG NAG . I 4 NAG A 1 402 1169 NAG NAG . J 4 NAG D 1 201 5154 NAG NAG . K 4 NAG E 1 401 3013 NAG NAG . L 4 NAG E 1 402 3169 NAG NAG . M 4 NAG F 1 201 6154 NAG NAG . N 5 HOH A 1 501 34 HOH HOH . N 5 HOH A 2 502 85 HOH HOH . N 5 HOH A 3 503 151 HOH HOH . N 5 HOH A 4 504 4 HOH HOH . N 5 HOH A 5 505 67 HOH HOH . N 5 HOH A 6 506 14 HOH HOH . N 5 HOH A 7 507 2 HOH HOH . N 5 HOH A 8 508 19 HOH HOH . N 5 HOH A 9 509 89 HOH HOH . N 5 HOH A 10 510 47 HOH HOH . N 5 HOH A 11 511 102 HOH HOH . N 5 HOH A 12 512 37 HOH HOH . N 5 HOH A 13 513 104 HOH HOH . N 5 HOH A 14 514 12 HOH HOH . N 5 HOH A 15 515 42 HOH HOH . N 5 HOH A 16 516 22 HOH HOH . N 5 HOH A 17 517 110 HOH HOH . N 5 HOH A 18 518 150 HOH HOH . N 5 HOH A 19 519 29 HOH HOH . N 5 HOH A 20 520 156 HOH HOH . N 5 HOH A 21 521 44 HOH HOH . N 5 HOH A 22 522 25 HOH HOH . N 5 HOH A 23 523 95 HOH HOH . N 5 HOH A 24 524 106 HOH HOH . N 5 HOH A 25 525 101 HOH HOH . N 5 HOH A 26 526 139 HOH HOH . N 5 HOH A 27 527 118 HOH HOH . O 5 HOH B 1 201 21 HOH HOH . O 5 HOH B 2 202 49 HOH HOH . O 5 HOH B 3 203 3 HOH HOH . O 5 HOH B 4 204 97 HOH HOH . O 5 HOH B 5 205 61 HOH HOH . O 5 HOH B 6 206 111 HOH HOH . O 5 HOH B 7 207 86 HOH HOH . O 5 HOH B 8 208 93 HOH HOH . O 5 HOH B 9 209 124 HOH HOH . O 5 HOH B 10 210 16 HOH HOH . O 5 HOH B 11 211 116 HOH HOH . O 5 HOH B 12 212 137 HOH HOH . O 5 HOH B 13 213 15 HOH HOH . O 5 HOH B 14 214 11 HOH HOH . O 5 HOH B 15 215 129 HOH HOH . O 5 HOH B 16 216 91 HOH HOH . O 5 HOH B 17 217 73 HOH HOH . O 5 HOH B 18 218 135 HOH HOH . O 5 HOH B 19 219 92 HOH HOH . O 5 HOH B 20 220 108 HOH HOH . O 5 HOH B 21 221 64 HOH HOH . P 5 HOH C 1 401 81 HOH HOH . P 5 HOH C 2 402 40 HOH HOH . P 5 HOH C 3 403 70 HOH HOH . P 5 HOH C 4 404 62 HOH HOH . P 5 HOH C 5 405 31 HOH HOH . P 5 HOH C 6 406 56 HOH HOH . P 5 HOH C 7 407 66 HOH HOH . P 5 HOH C 8 408 140 HOH HOH . P 5 HOH C 9 409 18 HOH HOH . P 5 HOH C 10 410 20 HOH HOH . P 5 HOH C 11 411 30 HOH HOH . P 5 HOH C 12 412 43 HOH HOH . P 5 HOH C 13 413 23 HOH HOH . P 5 HOH C 14 414 55 HOH HOH . P 5 HOH C 15 415 8 HOH HOH . P 5 HOH C 16 416 5 HOH HOH . P 5 HOH C 17 417 13 HOH HOH . P 5 HOH C 18 418 51 HOH HOH . P 5 HOH C 19 419 63 HOH HOH . P 5 HOH C 20 420 10 HOH HOH . P 5 HOH C 21 421 122 HOH HOH . P 5 HOH C 22 422 26 HOH HOH . P 5 HOH C 23 423 48 HOH HOH . P 5 HOH C 24 424 88 HOH HOH . P 5 HOH C 25 425 143 HOH HOH . Q 5 HOH D 1 301 75 HOH HOH . Q 5 HOH D 2 302 36 HOH HOH . Q 5 HOH D 3 303 52 HOH HOH . Q 5 HOH D 4 304 90 HOH HOH . Q 5 HOH D 5 305 148 HOH HOH . Q 5 HOH D 6 306 57 HOH HOH . Q 5 HOH D 7 307 27 HOH HOH . Q 5 HOH D 8 308 68 HOH HOH . Q 5 HOH D 9 309 78 HOH HOH . Q 5 HOH D 10 310 32 HOH HOH . Q 5 HOH D 11 311 149 HOH HOH . Q 5 HOH D 12 312 58 HOH HOH . R 5 HOH E 1 501 69 HOH HOH . R 5 HOH E 2 502 53 HOH HOH . R 5 HOH E 3 503 24 HOH HOH . R 5 HOH E 4 504 7 HOH HOH . R 5 HOH E 5 505 17 HOH HOH . R 5 HOH E 6 506 133 HOH HOH . R 5 HOH E 7 507 74 HOH HOH . R 5 HOH E 8 508 127 HOH HOH . R 5 HOH E 9 509 46 HOH HOH . R 5 HOH E 10 510 6 HOH HOH . R 5 HOH E 11 511 141 HOH HOH . R 5 HOH E 12 512 99 HOH HOH . R 5 HOH E 13 513 60 HOH HOH . R 5 HOH E 14 514 98 HOH HOH . R 5 HOH E 15 515 142 HOH HOH . R 5 HOH E 16 516 155 HOH HOH . R 5 HOH E 17 517 138 HOH HOH . R 5 HOH E 18 518 33 HOH HOH . R 5 HOH E 19 519 83 HOH HOH . S 5 HOH F 1 301 9 HOH HOH . S 5 HOH F 2 302 152 HOH HOH . S 5 HOH F 3 303 121 HOH HOH . S 5 HOH F 4 304 123 HOH HOH . S 5 HOH F 5 305 38 HOH HOH . S 5 HOH F 6 306 39 HOH HOH . S 5 HOH F 7 307 45 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 . . . L 4 131.418 29.123 106.752 1 94.23 ? C1 NAG 402 E 1 HETATM 2 C C2 NAG . . . L 4 130.838 28.876 105.35 1 97.77 ? C2 NAG 402 E 1 HETATM 3 C C3 NAG . . . L 4 131.93 28.977 104.285 1 100.8 ? C3 NAG 402 E 1 HETATM 4 C C4 NAG . . . L 4 132.685 30.292 104.418 1 103.77 ? C4 NAG 402 E 1 HETATM 5 C C5 NAG . . . L 4 133.236 30.413 105.831 1 98.06 ? C5 NAG 402 E 1 HETATM 6 C C6 NAG . . . L 4 133.651 31.859 106.008 1 98.52 ? C6 NAG 402 E 1 HETATM 7 C C7 NAG . . . L 4 129.372 27.015 105.501 1 97.09 ? C7 NAG 402 E 1 HETATM 8 C C8 NAG . . . L 4 129.266 25.551 105.239 1 91.19 ? C8 NAG 402 E 1 HETATM 9 N N2 NAG . . . L 4 130.585 27.473 105.362 1 93.93 ? N2 NAG 402 E 1 HETATM 10 O O3 NAG . . . L 4 131.449 28.777 102.945 1 99.37 ? O3 NAG 402 E 1 HETATM 11 O O4 NAG . . . L 4 133.794 30.344 103.516 1 103.43 ? O4 NAG 402 E 1 HETATM 12 O O5 NAG . . . L 4 132.151 30.346 106.764 1 96.9 ? O5 NAG 402 E 1 HETATM 13 O O6 NAG . . . L 4 135.031 32.034 105.719 1 108.88 ? O6 NAG 402 E 1 HETATM 14 O O7 NAG . . . L 4 128.434 27.728 105.811 1 95.12 ? O7 NAG 402 E 1 # _model_server_stats.io_time_ms 54 _model_server_stats.parse_time_ms 19 _model_server_stats.create_model_time_ms 24 _model_server_stats.query_time_ms 320 _model_server_stats.encode_time_ms 4 _model_server_stats.element_count 14 #