data_3DBX # _model_server_result.job_id AV4ffI09CCFxPqVrhVcE4w _model_server_result.datetime_utc '2025-07-02 04:35:42' _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 3dbx # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"E","auth_seq_id":521}' # _entry.id 3DBX # _exptl.entry_id 3DBX _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 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 90 _cell.entry_id 3DBX _cell.length_a 92.154 _cell.length_b 92.154 _cell.length_c 96.693 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 3DBX _symmetry.cell_setting ? _symmetry.Int_Tables_number 92 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 41 21 2' # _pdbx_struct_assembly.method_details PISA _pdbx_struct_assembly.oligomeric_details dimeric _pdbx_struct_assembly.oligomeric_count 2 _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 _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 C N N ? 3 D N N ? 3 E 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 209 A CYS 209 1_555 A SG CYS 267 A CYS 267 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.984 ? disulf ? disulf2 B SG CYS 25 B CYS 25 1_555 B SG CYS 80 B CYS 80 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.019 ? covale ? covale1 A ND2 ASN 23 A ASN 23 1_555 C C1 NAG . A NAG 500 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.452 ? covale ? covale2 A ND2 ASN 51 A ASN 51 1_555 D C1 NAG . A NAG 511 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.465 ? covale ? covale3 A ND2 ASN 110 A ASN 110 1_555 E C1 NAG . A NAG 521 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.451 ? # _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 3DBX _atom_sites.fract_transf_matrix[1][1] 0.010851 _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] 0.010851 _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] 0.010342 _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 C 3 NAG A 1 500 500 NAG NAG . D 3 NAG A 1 511 511 NAG NAG . E 3 NAG A 1 521 521 NAG NAG . F 4 PLM A 1 522 1 PLM PLM . G 5 HOH A 1 523 2 HOH HOH . G 5 HOH A 2 524 5 HOH HOH . G 5 HOH A 3 525 8 HOH HOH . G 5 HOH A 4 526 12 HOH HOH . G 5 HOH A 5 527 14 HOH HOH . G 5 HOH A 6 528 17 HOH HOH . G 5 HOH A 7 529 23 HOH HOH . G 5 HOH A 8 530 24 HOH HOH . G 5 HOH A 9 531 25 HOH HOH . G 5 HOH A 10 532 29 HOH HOH . G 5 HOH A 11 533 30 HOH HOH . G 5 HOH A 12 534 31 HOH HOH . G 5 HOH A 13 535 32 HOH HOH . G 5 HOH A 14 536 33 HOH HOH . G 5 HOH A 15 537 34 HOH HOH . G 5 HOH A 16 538 36 HOH HOH . G 5 HOH A 17 539 41 HOH HOH . G 5 HOH A 18 540 43 HOH HOH . G 5 HOH A 19 541 45 HOH HOH . G 5 HOH A 20 542 47 HOH HOH . G 5 HOH A 21 543 49 HOH HOH . G 5 HOH A 22 544 51 HOH HOH . G 5 HOH A 23 545 53 HOH HOH . G 5 HOH A 24 546 57 HOH HOH . G 5 HOH A 25 547 62 HOH HOH . G 5 HOH A 26 548 66 HOH HOH . G 5 HOH A 27 549 77 HOH HOH . G 5 HOH A 28 550 78 HOH HOH . G 5 HOH A 29 551 83 HOH HOH . G 5 HOH A 30 552 84 HOH HOH . G 5 HOH A 31 553 94 HOH HOH . G 5 HOH A 32 554 97 HOH HOH . G 5 HOH A 33 555 99 HOH HOH . G 5 HOH A 34 556 100 HOH HOH . G 5 HOH A 35 557 104 HOH HOH . G 5 HOH A 36 558 111 HOH HOH . G 5 HOH A 37 559 112 HOH HOH . G 5 HOH A 38 560 113 HOH HOH . G 5 HOH A 39 561 114 HOH HOH . G 5 HOH A 40 562 115 HOH HOH . G 5 HOH A 41 563 123 HOH HOH . G 5 HOH A 42 564 124 HOH HOH . G 5 HOH A 43 565 126 HOH HOH . G 5 HOH A 44 566 127 HOH HOH . G 5 HOH A 45 567 129 HOH HOH . G 5 HOH A 46 568 132 HOH HOH . G 5 HOH A 47 569 134 HOH HOH . G 5 HOH A 48 570 140 HOH HOH . G 5 HOH A 49 571 147 HOH HOH . G 5 HOH A 50 572 148 HOH HOH . G 5 HOH A 51 573 157 HOH HOH . G 5 HOH A 52 574 158 HOH HOH . G 5 HOH A 53 575 160 HOH HOH . G 5 HOH A 54 576 167 HOH HOH . G 5 HOH A 55 577 175 HOH HOH . G 5 HOH A 56 578 176 HOH HOH . G 5 HOH A 57 579 177 HOH HOH . G 5 HOH A 58 580 185 HOH HOH . G 5 HOH A 59 581 193 HOH HOH . G 5 HOH A 60 582 196 HOH HOH . G 5 HOH A 61 583 199 HOH HOH . G 5 HOH A 62 584 200 HOH HOH . G 5 HOH A 63 585 201 HOH HOH . G 5 HOH A 64 586 203 HOH HOH . G 5 HOH A 65 587 222 HOH HOH . G 5 HOH A 66 588 223 HOH HOH . G 5 HOH A 67 589 225 HOH HOH . G 5 HOH A 68 590 229 HOH HOH . G 5 HOH A 69 591 235 HOH HOH . G 5 HOH A 70 592 236 HOH HOH . G 5 HOH A 71 593 239 HOH HOH . G 5 HOH A 72 594 244 HOH HOH . G 5 HOH A 73 595 250 HOH HOH . G 5 HOH A 74 596 253 HOH HOH . G 5 HOH A 75 597 268 HOH HOH . G 5 HOH A 76 598 288 HOH HOH . G 5 HOH A 77 599 289 HOH HOH . G 5 HOH A 78 600 294 HOH HOH . G 5 HOH A 79 601 299 HOH HOH . G 5 HOH A 80 602 302 HOH HOH . H 5 HOH B 1 100 1 HOH HOH . H 5 HOH B 2 101 4 HOH HOH . H 5 HOH B 3 102 6 HOH HOH . H 5 HOH B 4 103 7 HOH HOH . H 5 HOH B 5 104 9 HOH HOH . H 5 HOH B 6 105 10 HOH HOH . H 5 HOH B 7 106 13 HOH HOH . H 5 HOH B 8 107 15 HOH HOH . H 5 HOH B 9 108 18 HOH HOH . H 5 HOH B 10 109 19 HOH HOH . H 5 HOH B 11 110 21 HOH HOH . H 5 HOH B 12 111 27 HOH HOH . H 5 HOH B 13 112 37 HOH HOH . H 5 HOH B 14 113 38 HOH HOH . H 5 HOH B 15 114 39 HOH HOH . H 5 HOH B 16 115 40 HOH HOH . H 5 HOH B 17 116 46 HOH HOH . H 5 HOH B 18 117 50 HOH HOH . H 5 HOH B 19 118 52 HOH HOH . H 5 HOH B 20 119 60 HOH HOH . H 5 HOH B 21 120 63 HOH HOH . H 5 HOH B 22 121 65 HOH HOH . H 5 HOH B 23 122 67 HOH HOH . H 5 HOH B 24 123 73 HOH HOH . H 5 HOH B 25 124 74 HOH HOH . H 5 HOH B 26 125 79 HOH HOH . H 5 HOH B 27 126 85 HOH HOH . H 5 HOH B 28 127 86 HOH HOH . H 5 HOH B 29 128 90 HOH HOH . H 5 HOH B 30 129 92 HOH HOH . H 5 HOH B 31 130 93 HOH HOH . H 5 HOH B 32 131 95 HOH HOH . H 5 HOH B 33 132 102 HOH HOH . H 5 HOH B 34 133 103 HOH HOH . H 5 HOH B 35 134 116 HOH HOH . H 5 HOH B 36 135 118 HOH HOH . H 5 HOH B 37 136 119 HOH HOH . H 5 HOH B 38 137 120 HOH HOH . H 5 HOH B 39 138 122 HOH HOH . H 5 HOH B 40 139 125 HOH HOH . H 5 HOH B 41 140 128 HOH HOH . H 5 HOH B 42 141 130 HOH HOH . H 5 HOH B 43 142 131 HOH HOH . H 5 HOH B 44 143 136 HOH HOH . H 5 HOH B 45 144 137 HOH HOH . H 5 HOH B 46 145 138 HOH HOH . H 5 HOH B 47 146 139 HOH HOH . H 5 HOH B 48 147 141 HOH HOH . H 5 HOH B 49 148 151 HOH HOH . H 5 HOH B 50 149 156 HOH HOH . H 5 HOH B 51 150 161 HOH HOH . H 5 HOH B 52 151 168 HOH HOH . H 5 HOH B 53 152 171 HOH HOH . H 5 HOH B 54 153 172 HOH HOH . H 5 HOH B 55 154 173 HOH HOH . H 5 HOH B 56 155 179 HOH HOH . H 5 HOH B 57 156 187 HOH HOH . H 5 HOH B 58 157 188 HOH HOH . H 5 HOH B 59 158 198 HOH HOH . H 5 HOH B 60 159 209 HOH HOH . H 5 HOH B 61 160 212 HOH HOH . H 5 HOH B 62 161 213 HOH HOH . H 5 HOH B 63 162 231 HOH HOH . H 5 HOH B 64 163 232 HOH HOH . H 5 HOH B 65 164 242 HOH HOH . H 5 HOH B 66 165 256 HOH HOH . H 5 HOH B 67 166 271 HOH HOH . H 5 HOH B 68 167 272 HOH HOH . H 5 HOH B 69 168 300 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 . . . E 3 4.481 34.964 38.3 1 106.6 ? C1 NAG 521 A 1 HETATM 2 C C2 NAG . . . E 3 3.157 34.839 39.063 1 112.08 ? C2 NAG 521 A 1 HETATM 3 C C3 NAG . . . E 3 2.621 36.237 39.368 1 110.77 ? C3 NAG 521 A 1 HETATM 4 C C4 NAG . . . E 3 3.662 37.053 40.145 1 103.76 ? C4 NAG 521 A 1 HETATM 5 C C5 NAG . . . E 3 5.039 36.981 39.474 1 97.34 ? C5 NAG 521 A 1 HETATM 6 C C6 NAG . . . E 3 6.107 37.592 40.373 1 90.6 ? C6 NAG 521 A 1 HETATM 7 C C7 NAG . . . E 3 1.885 32.781 38.702 1 125.84 ? C7 NAG 521 A 1 HETATM 8 C C8 NAG . . . E 3 0.438 32.467 38.961 1 134.53 ? C8 NAG 521 A 1 HETATM 9 N N2 NAG . . . E 3 2.181 34.034 38.345 1 120.51 ? N2 NAG 521 A 1 HETATM 10 O O3 NAG . . . E 3 1.435 36.135 40.121 1 116.86 ? O3 NAG 521 A 1 HETATM 11 O O4 NAG . . . E 3 3.254 38.404 40.275 1 102.68 ? O4 NAG 521 A 1 HETATM 12 O O5 NAG . . . E 3 5.399 35.645 39.145 1 99.28 ? O5 NAG 521 A 1 HETATM 13 O O6 NAG . . . E 3 6.598 36.631 41.281 1 90.53 ? O6 NAG 521 A 1 HETATM 14 O O7 NAG . . . E 3 2.733 31.896 38.82 1 124.51 ? O7 NAG 521 A 1 # _model_server_stats.io_time_ms 10 _model_server_stats.parse_time_ms 13 _model_server_stats.create_model_time_ms 14 _model_server_stats.query_time_ms 278 _model_server_stats.encode_time_ms 6 _model_server_stats.element_count 14 #