data_4I7Y # _model_server_result.job_id p8xSGLm2ZQwqZH69ZmHZag _model_server_result.datetime_utc '2024-11-08 12:59:08' _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 4i7y # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"F","auth_seq_id":301}' # _entry.id 4I7Y # _exptl.entry_id 4I7Y _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 221.208 _entity.id 6 _entity.src_method man _entity.type non-polymer _entity.pdbx_description 2-acetamido-2-deoxy-beta-D-glucopyranose _entity.pdbx_number_of_molecules 1 _entity.pdbx_parent_entity_id . _entity.pdbx_mutation ? _entity.pdbx_fragment ? _entity.pdbx_ec ? # _cell.angle_alpha 90 _cell.angle_beta 99.66 _cell.angle_gamma 90 _cell.entry_id 4I7Y _cell.length_a 48.144 _cell.length_b 81.904 _cell.length_c 53.72 _cell.Z_PDB 2 _cell.pdbx_unique_axis ? # _symmetry.entry_id 4I7Y _symmetry.cell_setting ? _symmetry.Int_Tables_number 4 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 1 21 1' # _pdbx_struct_assembly.method_details PISA _pdbx_struct_assembly.oligomeric_details trimeric _pdbx_struct_assembly.oligomeric_count 3 _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 _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 # _struct_asym.details ? _struct_asym.entity_id 6 _struct_asym.id F _struct_asym.pdbx_modified N _struct_asym.pdbx_blank_PDB_chainid_flag 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 28 H CYS 42 1_555 A SG CYS 44 H CYS 58 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.065 ? disulf ? disulf2 A SG CYS 119 H CYS 122 1_555 B SG CYS 9 L CYS 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.04 ? disulf ? disulf3 A SG CYS 173 H CYS 168 1_555 A SG CYS 187 H CYS 182 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.033 ? disulf ? disulf4 A SG CYS 201 H CYS 191 1_555 A SG CYS 231 H CYS 220 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.05 ? covale ? covale1 A NE2 HIS 43 H HIS 57 1_555 D C3 0G6 . H 0G6 302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.499 ? covale ? covale2 A ND2 ASN 53 H ASN 60 1_555 F C1 NAG . L NAG 301 1_555 G ? ? ? ? ? ? ? ? ? ? ? 1.456 ? covale ? covale3 A OG SER 205 H SER 195 1_555 D C2 0G6 . H 0G6 302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.415 ? metalc ? metalc1 A O ARG 233 H ARG 221 1_555 E NA NA . H NA 303 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.427 ? metalc ? metalc2 A O LYS 236 H LYS 224 1_555 E NA NA . H NA 303 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.273 ? metalc ? metalc3 E NA NA . H NA 303 1_555 G O HOH . H HOH 411 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.349 ? metalc ? metalc4 E NA NA . H NA 303 1_555 G O HOH . H HOH 416 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.197 ? metalc ? metalc5 E NA NA . H NA 303 1_555 G O HOH . H HOH 429 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.498 ? metalc ? metalc6 E NA NA . H NA 303 1_555 G O HOH . H HOH 453 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.255 ? hydrog WATSON-CRICK hydrog1 C N1 DG 1 D DG 1 1_555 C N3 DC 27 D DC 27 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog2 C N2 DG 1 D DG 1 1_555 C O2 DC 27 D DC 27 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog3 C O6 DG 1 D DG 1 1_555 C N4 DC 27 D DC 27 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog4 C N3 DT 2 D DT 2 1_555 C N1 DA 26 D DA 26 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog5 C O4 DT 2 D DT 2 1_555 C N6 DA 26 D DA 26 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog6 C N3 DC 3 D DC 3 1_555 C N1 DG 25 D DG 25 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog7 C N4 DC 3 D DC 3 1_555 C O6 DG 25 D DG 25 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog8 C O2 DC 3 D DC 3 1_555 C N2 DG 25 D DG 25 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog9 C N3 DC 4 D DC 4 1_555 C N1 DG 23 D DG 23 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog10 C N4 DC 4 D DC 4 1_555 C O6 DG 23 D DG 23 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog11 C O2 DC 4 D DC 4 1_555 C N2 DG 23 D DG 23 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog 'DG-DG MISPAIR' hydrog12 C N2 DG 5 D DG 5 1_555 C O6 DG 7 D DG 7 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog TYPE_7_PAIR hydrog13 C N1 DG 5 D DG 5 1_555 C N7 DG 16 D DG 16 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog TYPE_7_PAIR hydrog14 C N2 DG 5 D DG 5 1_555 C O6 DG 16 D DG 16 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog 'REVERSED HOOGSTEEN' hydrog15 C N3 DT 6 D DT 6 1_555 C N7 DA 15 D DA 15 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog 'REVERSED HOOGSTEEN' hydrog16 C O2 DT 6 D DT 6 1_555 C N6 DA 15 D DA 15 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog TYPE_6_PAIR hydrog17 C N7 DG 8 D DG 8 1_555 C N2 DG 11 D DG 11 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog TYPE_6_PAIR hydrog18 C O6 DG 8 D DG 8 1_555 C N1 DG 11 D DG 11 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog TYPE_6_PAIR hydrog19 C N1 DG 8 D DG 8 1_555 C O6 DG 20 D DG 20 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog TYPE_6_PAIR hydrog20 C N2 DG 8 D DG 8 1_555 C N7 DG 20 D DG 20 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog 'REVERSED WATSON-CRICK' hydrog21 C N1 DA 10 D DA 10 1_555 C N3 DT 19 D DT 19 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog 'REVERSED WATSON-CRICK' hydrog22 C N6 DA 10 D DA 10 1_555 C O2 DT 19 D DT 19 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog TYPE_6_PAIR hydrog23 C N7 DG 11 D DG 11 1_555 C N2 DG 17 D DG 17 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog TYPE_6_PAIR hydrog24 C O6 DG 11 D DG 11 1_555 C N1 DG 17 D DG 17 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog TYPE_6_PAIR hydrog25 C N7 DG 17 D DG 17 1_555 C N2 DG 20 D DG 20 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog TYPE_6_PAIR hydrog26 C O6 DG 17 D DG 17 1_555 C N1 DG 20 D DG 20 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? # _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 452 n n C1 O1 NAG sing 453 n n C1 O5 NAG sing 454 n n C1 H1 NAG sing 455 n n C2 C3 NAG sing 456 n n C2 N2 NAG sing 457 n n C2 H2 NAG sing 458 n n C3 C4 NAG sing 459 n n C3 O3 NAG sing 460 n n C3 H3 NAG sing 461 n n C4 C5 NAG sing 462 n n C4 O4 NAG sing 463 n n C4 H4 NAG sing 464 n n C5 C6 NAG sing 465 n n C5 O5 NAG sing 466 n n C5 H5 NAG sing 467 n n C6 O6 NAG sing 468 n n C6 H61 NAG sing 469 n n C6 H62 NAG sing 470 n n C7 C8 NAG sing 471 n n C7 N2 NAG sing 472 n n C7 O7 NAG doub 473 n n C8 H81 NAG sing 474 n n C8 H82 NAG sing 475 n n C8 H83 NAG sing 476 n n N2 HN2 NAG sing 477 n n O1 HO1 NAG sing 478 n n O3 HO3 NAG sing 479 n n O4 HO4 NAG sing 480 n n O6 HO6 NAG sing 481 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 4I7Y _atom_sites.fract_transf_matrix[1][1] 0.020771 _atom_sites.fract_transf_matrix[1][2] 0 _atom_sites.fract_transf_matrix[1][3] 0.003536 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.012209 _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] 0.018883 _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 D 4 0G6 H 1 302 301 0G6 0G6 . E 5 NA H 1 303 303 NA NA . F 6 NAG L 1 301 302 NAG NAG . G 7 HOH H 1 401 1 HOH HOH . G 7 HOH H 2 402 2 HOH HOH . G 7 HOH H 3 403 3 HOH HOH . G 7 HOH H 4 404 4 HOH HOH . G 7 HOH H 5 405 5 HOH HOH . G 7 HOH H 6 406 6 HOH HOH . G 7 HOH H 7 407 7 HOH HOH . G 7 HOH H 8 408 8 HOH HOH . G 7 HOH H 9 409 9 HOH HOH . G 7 HOH H 10 410 10 HOH HOH . G 7 HOH H 11 411 11 HOH HOH . G 7 HOH H 12 412 13 HOH HOH . G 7 HOH H 13 413 14 HOH HOH . G 7 HOH H 14 414 15 HOH HOH . G 7 HOH H 15 415 16 HOH HOH . G 7 HOH H 16 416 17 HOH HOH . G 7 HOH H 17 417 18 HOH HOH . G 7 HOH H 18 418 19 HOH HOH . G 7 HOH H 19 419 20 HOH HOH . G 7 HOH H 20 420 23 HOH HOH . G 7 HOH H 21 421 24 HOH HOH . G 7 HOH H 22 422 25 HOH HOH . G 7 HOH H 23 423 26 HOH HOH . G 7 HOH H 24 424 28 HOH HOH . G 7 HOH H 25 425 29 HOH HOH . G 7 HOH H 26 426 30 HOH HOH . G 7 HOH H 27 427 31 HOH HOH . G 7 HOH H 28 428 32 HOH HOH . G 7 HOH H 29 429 33 HOH HOH . G 7 HOH H 30 430 34 HOH HOH . G 7 HOH H 31 431 35 HOH HOH . G 7 HOH H 32 432 36 HOH HOH . G 7 HOH H 33 433 37 HOH HOH . G 7 HOH H 34 434 38 HOH HOH . G 7 HOH H 35 435 40 HOH HOH . G 7 HOH H 36 436 41 HOH HOH . G 7 HOH H 37 437 42 HOH HOH . G 7 HOH H 38 438 43 HOH HOH . G 7 HOH H 39 439 44 HOH HOH . G 7 HOH H 40 440 47 HOH HOH . G 7 HOH H 41 441 50 HOH HOH . G 7 HOH H 42 442 51 HOH HOH . G 7 HOH H 43 443 52 HOH HOH . G 7 HOH H 44 444 53 HOH HOH . G 7 HOH H 45 445 54 HOH HOH . G 7 HOH H 46 446 55 HOH HOH . G 7 HOH H 47 447 56 HOH HOH . G 7 HOH H 48 448 57 HOH HOH . G 7 HOH H 49 449 58 HOH HOH . G 7 HOH H 50 450 59 HOH HOH . G 7 HOH H 51 451 61 HOH HOH . G 7 HOH H 52 452 62 HOH HOH . G 7 HOH H 53 453 63 HOH HOH . G 7 HOH H 54 454 65 HOH HOH . G 7 HOH H 55 455 67 HOH HOH . G 7 HOH H 56 456 69 HOH HOH . G 7 HOH H 57 457 70 HOH HOH . G 7 HOH H 58 458 71 HOH HOH . G 7 HOH H 59 459 73 HOH HOH . G 7 HOH H 60 460 74 HOH HOH . G 7 HOH H 61 461 75 HOH HOH . G 7 HOH H 62 462 77 HOH HOH . G 7 HOH H 63 463 79 HOH HOH . G 7 HOH H 64 464 80 HOH HOH . G 7 HOH H 65 465 82 HOH HOH . G 7 HOH H 66 466 83 HOH HOH . G 7 HOH H 67 467 84 HOH HOH . G 7 HOH H 68 468 85 HOH HOH . G 7 HOH H 69 469 87 HOH HOH . G 7 HOH H 70 470 90 HOH HOH . G 7 HOH H 71 471 93 HOH HOH . G 7 HOH H 72 472 94 HOH HOH . G 7 HOH H 73 473 95 HOH HOH . G 7 HOH H 74 474 98 HOH HOH . G 7 HOH H 75 475 99 HOH HOH . G 7 HOH H 76 476 100 HOH HOH . G 7 HOH H 77 477 101 HOH HOH . H 7 HOH L 1 101 21 HOH HOH . H 7 HOH L 2 102 27 HOH HOH . H 7 HOH L 3 103 48 HOH HOH . H 7 HOH L 4 104 60 HOH HOH . H 7 HOH L 5 105 66 HOH HOH . H 7 HOH L 6 106 81 HOH HOH . H 7 HOH L 7 107 86 HOH HOH . H 7 HOH L 8 108 91 HOH HOH . I 7 HOH D 1 101 12 HOH HOH . I 7 HOH D 2 102 22 HOH HOH . I 7 HOH D 3 103 39 HOH HOH . I 7 HOH D 4 104 45 HOH HOH . I 7 HOH D 5 105 46 HOH HOH . I 7 HOH D 6 106 49 HOH HOH . I 7 HOH D 7 107 64 HOH HOH . I 7 HOH D 8 108 68 HOH HOH . I 7 HOH D 9 109 72 HOH HOH . I 7 HOH D 10 110 76 HOH HOH . I 7 HOH D 11 111 78 HOH HOH . I 7 HOH D 12 112 92 HOH HOH . I 7 HOH D 13 113 97 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 6 30.489 -10.75 23.097 1 66.39 ? C1 NAG 301 L 1 HETATM 2 C C2 NAG . . . F 6 31.092 -10.476 24.471 1 71.87 ? C2 NAG 301 L 1 HETATM 3 C C3 NAG . . . F 6 32.631 -10.433 24.482 1 78.26 ? C3 NAG 301 L 1 HETATM 4 C C4 NAG . . . F 6 33.177 -11.706 23.847 1 77.16 ? C4 NAG 301 L 1 HETATM 5 C C5 NAG . . . F 6 32.586 -11.678 22.439 1 78.65 ? C5 NAG 301 L 1 HETATM 6 C C6 NAG . . . F 6 33.166 -12.778 21.572 1 79.9 ? C6 NAG 301 L 1 HETATM 7 C C7 NAG . . . F 6 29.548 -9.047 25.758 1 65.11 ? C7 NAG 301 L 1 HETATM 8 C C8 NAG . . . F 6 28.678 -10.181 26.203 1 62.96 ? C8 NAG 301 L 1 HETATM 9 N N2 NAG . . . F 6 30.61 -9.219 24.977 1 65.1 ? N2 NAG 301 L 1 HETATM 10 O O3 NAG . . . F 6 33.091 -10.289 25.809 1 80.51 ? O3 NAG 301 L 1 HETATM 11 O O4 NAG . . . F 6 34.596 -11.78 23.852 1 78.44 ? O4 NAG 301 L 1 HETATM 12 O O5 NAG . . . F 6 31.176 -11.848 22.53 1 71.85 ? O5 NAG 301 L 1 HETATM 13 O O6 NAG . . . F 6 32.643 -13.975 22.095 1 83.49 ? O6 NAG 301 L 1 HETATM 14 O O7 NAG . . . F 6 29.242 -7.929 26.129 1 74.22 ? O7 NAG 301 L 1 # _model_server_stats.io_time_ms 8 _model_server_stats.parse_time_ms 10 _model_server_stats.create_model_time_ms 21 _model_server_stats.query_time_ms 380 _model_server_stats.encode_time_ms 3 _model_server_stats.element_count 14 #