data_4HYT # _model_server_result.job_id 0az-Qu2YM0ga9ylBVh7RHA _model_server_result.datetime_utc '2024-11-05 05:38:20' _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 4hyt # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"BA","auth_seq_id":2001}' # _entry.id 4HYT # _exptl.entry_id 4HYT _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 221.208 _entity.id 12 _entity.src_method man _entity.type non-polymer _entity.pdbx_description 2-acetamido-2-deoxy-beta-D-glucopyranose _entity.pdbx_number_of_molecules 5 _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 4HYT _cell.length_a 117.47 _cell.length_b 118.08 _cell.length_c 494.66 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 4HYT _symmetry.cell_setting ? _symmetry.Int_Tables_number 19 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 21 21 21' # loop_ _pdbx_struct_assembly.method_details _pdbx_struct_assembly.oligomeric_details _pdbx_struct_assembly.oligomeric_count _pdbx_struct_assembly.details _pdbx_struct_assembly.id PISA trimeric 3 author_and_software_defined_assembly 1 PISA trimeric 3 author_and_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,G,H,I,J,K,L,M,N,O,P,Q,R,S,T,U,V,HA 1 1 D,E,F,W,X,Y,Z,AA,BA,CA,DA,EA,FA,GA,IA 2 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 ? 12 R N N ? 12 S N N ? 12 BA N N ? 12 CA N N ? 12 DA N N # _pdbx_entity_branch.entity_id 4 _pdbx_entity_branch.type oligosaccharide # _pdbx_entity_branch_link.link_id 1 _pdbx_entity_branch_link.details ? _pdbx_entity_branch_link.entity_id 4 _pdbx_entity_branch_link.entity_branch_list_num_1 2 _pdbx_entity_branch_link.entity_branch_list_num_2 1 _pdbx_entity_branch_link.comp_id_1 NAG _pdbx_entity_branch_link.comp_id_2 NAG _pdbx_entity_branch_link.atom_id_1 C1 _pdbx_entity_branch_link.leaving_atom_id_1 O1 _pdbx_entity_branch_link.atom_stereo_config_1 . _pdbx_entity_branch_link.atom_id_2 O4 _pdbx_entity_branch_link.leaving_atom_id_2 HO4 _pdbx_entity_branch_link.atom_stereo_config_2 . _pdbx_entity_branch_link.value_order 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 4 n G NAG 1 F 1 NAG M 1001 NAG 4 n G NAG 2 F 2 NAG M 1002 NAG # 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 B SG CYS 126 B CYS 126 1_555 B SG CYS 149 B CYS 149 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.034 ? disulf ? disulf2 B SG CYS 159 B CYS 159 1_555 B SG CYS 175 B CYS 175 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.038 ? disulf ? disulf3 B SG CYS 213 B CYS 213 1_555 B SG CYS 276 B CYS 276 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.952 ? disulf ? disulf4 E SG CYS 126 D CYS 126 1_555 E SG CYS 149 D CYS 149 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.035 ? disulf ? disulf5 E SG CYS 159 D CYS 159 1_555 E SG CYS 175 D CYS 175 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.038 ? disulf ? disulf6 E SG CYS 213 D CYS 213 1_555 E SG CYS 276 D CYS 276 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.985 ? covale ? covale1 A C SER 373 A SER 368 1_555 A N PHD 374 A PHD 369 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.33 ? covale ? covale2 A C PHD 374 A PHD 369 1_555 A N LYS 375 A LYS 370 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.332 ? covale ? covale3 B ND2 ASN 158 B ASN 158 1_555 G C1 NAG . F NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.437 ? covale ? covale4 B ND2 ASN 193 B ASN 193 1_555 R C1 NAG . B NAG 1003 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.441 ? covale ? covale5 B ND2 ASN 265 B ASN 265 1_555 S C1 NAG . B NAG 1004 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.443 ? covale ? covale6 D C SER 373 C SER 368 1_555 D N PHD 374 C PHD 369 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.327 ? covale ? covale7 D C PHD 374 C PHD 369 1_555 D N LYS 375 C LYS 370 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.332 ? covale ? covale8 E ND2 ASN 158 D ASN 158 1_555 BA C1 NAG . D NAG 2001 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.45 ? covale ? covale9 E ND2 ASN 193 D ASN 193 1_555 CA C1 NAG . D NAG 2002 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.455 ? covale ? covale10 E ND2 ASN 265 D ASN 265 1_555 DA C1 NAG . D NAG 2003 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.432 ? covale ? covale11 G O4 NAG . F NAG 1 1_555 G C1 NAG . F NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.435 ? metalc ? metalc1 A OP1 PHD 374 A PHD 369 1_555 H MG MG . A MG 1101 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.985 ? metalc ? metalc2 A OD2 PHD 374 A PHD 369 1_555 H MG MG . A MG 1101 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.01 ? metalc ? metalc3 A OP3 PHD 374 A PHD 369 1_555 H MG MG . A MG 1101 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.078 ? metalc ? metalc4 A O THR 376 A THR 371 1_555 H MG MG . A MG 1101 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.08 ? metalc ? metalc5 A OG1 THR 376 A THR 371 1_555 H MG MG . A MG 1101 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.656 ? metalc ? metalc6 A OD2 ASP 715 A ASP 710 1_555 H MG MG . A MG 1101 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.382 ? metalc ? metalc7 A OD1 ASP 715 A ASP 710 1_555 H MG MG . A MG 1101 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.855 ? metalc ? metalc8 A OD2 ASP 745 A ASP 740 1_555 I MG MG . A MG 1102 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.129 ? metalc ? metalc9 A OD1 ASP 745 A ASP 740 1_555 I MG MG . A MG 1102 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.238 ? metalc ? metalc10 A OD1 ASN 781 A ASN 776 1_555 J MG MG . A MG 1103 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.469 ? metalc ? metalc11 A OE2 GLU 784 A GLU 779 1_555 J MG MG . A MG 1103 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.039 ? metalc ? metalc12 A OD1 ASP 809 A ASP 804 1_555 J MG MG . A MG 1103 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.28 ? metalc ? metalc13 A OD2 ASP 809 A ASP 804 1_555 J MG MG . A MG 1103 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.927 ? metalc ? metalc14 J MG MG . A MG 1103 1_555 HA O HOH . A HOH 1201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.085 ? metalc ? metalc15 J MG MG . A MG 1103 1_555 HA O HOH . A HOH 1202 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.112 ? metalc ? metalc16 J MG MG . A MG 1103 1_555 HA O HOH . A HOH 1203 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.073 ? metalc ? metalc17 D OP3 PHD 374 C PHD 369 1_555 W MG MG . C MG 2001 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.101 ? metalc ? metalc18 D OD2 PHD 374 C PHD 369 1_555 W MG MG . C MG 2001 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.183 ? metalc ? metalc19 D OP1 PHD 374 C PHD 369 1_555 W MG MG . C MG 2001 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.332 ? metalc ? metalc20 D O THR 376 C THR 371 1_555 W MG MG . C MG 2001 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.066 ? metalc ? metalc21 D OG1 THR 376 C THR 371 1_555 W MG MG . C MG 2001 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.801 ? metalc ? metalc22 D OD2 ASP 715 C ASP 710 1_555 W MG MG . C MG 2001 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.039 ? metalc ? metalc23 D OD1 ASP 715 C ASP 710 1_555 W MG MG . C MG 2001 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.547 ? metalc ? metalc24 D OD1 ASP 745 C ASP 740 1_555 X MG MG . C MG 2002 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.101 ? metalc ? metalc25 D OD2 ASP 745 C ASP 740 1_555 X MG MG . C MG 2002 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.181 ? metalc ? metalc26 D OD1 ASN 781 C ASN 776 1_555 Y MG MG . C MG 2003 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.469 ? metalc ? metalc27 D OE2 GLU 784 C GLU 779 1_555 Y MG MG . C MG 2003 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.023 ? metalc ? metalc28 D OD1 ASP 809 C ASP 804 1_555 Y MG MG . C MG 2003 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.281 ? metalc ? metalc29 D OD2 ASP 809 C ASP 804 1_555 Y MG MG . C MG 2003 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.939 ? metalc ? metalc30 Y MG MG . C MG 2003 1_555 IA O HOH . C HOH 2101 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.087 ? metalc ? metalc31 Y MG MG . C MG 2003 1_555 IA O HOH . C HOH 2102 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.11 ? metalc ? metalc32 Y MG MG . C MG 2003 1_555 IA O HOH . C HOH 2103 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.08 ? # _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 689 n n C1 O1 NAG sing 690 n n C1 O5 NAG sing 691 n n C1 H1 NAG sing 692 n n C2 C3 NAG sing 693 n n C2 N2 NAG sing 694 n n C2 H2 NAG sing 695 n n C3 C4 NAG sing 696 n n C3 O3 NAG sing 697 n n C3 H3 NAG sing 698 n n C4 C5 NAG sing 699 n n C4 O4 NAG sing 700 n n C4 H4 NAG sing 701 n n C5 C6 NAG sing 702 n n C5 O5 NAG sing 703 n n C5 H5 NAG sing 704 n n C6 O6 NAG sing 705 n n C6 H61 NAG sing 706 n n C6 H62 NAG sing 707 n n C7 C8 NAG sing 708 n n C7 N2 NAG sing 709 n n C7 O7 NAG doub 710 n n C8 H81 NAG sing 711 n n C8 H82 NAG sing 712 n n C8 H83 NAG sing 713 n n N2 HN2 NAG sing 714 n n O1 HO1 NAG sing 715 n n O3 HO3 NAG sing 716 n n O4 HO4 NAG sing 717 n n O6 HO6 NAG sing 718 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 4HYT _atom_sites.fract_transf_matrix[1][1] 0.008513 _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] 0.008469 _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] 0.002022 _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 5 MG A 1 1101 1001 MG MG . I 5 MG A 1 1102 1002 MG MG . J 5 MG A 1 1103 1003 MG MG . K 6 OBN A 1 1104 1001 OBN OBN . L 7 CLR A 1 1105 1 CLR CLR . M 8 1AT A 1 1106 3 1AT 6DS . N 9 1DS A 1 1107 4 1DS 1DS . O 10 17F A 1 1108 6 17F PS1 . P 10 17F A 1 1109 7 17F PS1 . Q 11 CE1 A 1 1110 10 CE1 CE1 . R 12 NAG B 1 1003 1003 NAG NAG . S 12 NAG B 1 1004 1004 NAG NAG . T 10 17F B 1 1005 8 17F PS1 . U 7 CLR G 1 1001 1001 CLR CLR . V 10 17F G 1 1002 5 17F PS1 . W 5 MG C 1 2001 2001 MG MG . X 5 MG C 1 2002 2002 MG MG . Y 5 MG C 1 2003 2003 MG MG . Z 6 OBN C 1 2004 2001 OBN OBN . AA 7 CLR C 1 2005 2 CLR CLR . BA 12 NAG D 1 2001 2001 NAG NAG . CA 12 NAG D 1 2002 2002 NAG NAG . DA 12 NAG D 1 2003 2003 NAG NAG . EA 10 17F D 1 2004 9 17F PS1 . FA 7 CLR E 1 2001 2001 CLR CLR . GA 11 CE1 E 1 2002 11 CE1 CE1 . HA 13 HOH A 1 1201 1001 HOH HOH . HA 13 HOH A 2 1202 1002 HOH HOH . HA 13 HOH A 3 1203 1003 HOH HOH . IA 13 HOH C 1 2101 2001 HOH HOH . IA 13 HOH C 2 2102 2002 HOH HOH . IA 13 HOH C 3 2103 2003 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 . . . BA 12 -59.04 83.563 0.196 1 152.94 ? C1 NAG 2001 D 1 HETATM 2 C C2 NAG . . . BA 12 -57.749 84.373 0.371 1 153.76 ? C2 NAG 2001 D 1 HETATM 3 C C3 NAG . . . BA 12 -57.538 84.732 1.84 1 160.54 ? C3 NAG 2001 D 1 HETATM 4 C C4 NAG . . . BA 12 -58.775 85.41 2.421 1 166.83 ? C4 NAG 2001 D 1 HETATM 5 C C5 NAG . . . BA 12 -60.013 84.549 2.168 1 165.55 ? C5 NAG 2001 D 1 HETATM 6 C C6 NAG . . . BA 12 -61.298 85.212 2.62 1 171.95 ? C6 NAG 2001 D 1 HETATM 7 C C7 NAG . . . BA 12 -56.05 83.877 -1.331 1 143.6 ? C7 NAG 2001 D 1 HETATM 8 C C8 NAG . . . BA 12 -54.877 83.009 -1.7 1 138.7 ? C8 NAG 2001 D 1 HETATM 9 N N2 NAG . . . BA 12 -56.603 83.639 -0.136 1 148.18 ? N2 NAG 2001 D 1 HETATM 10 O O3 NAG . . . BA 12 -56.405 85.589 1.928 1 161.92 ? O3 NAG 2001 D 1 HETATM 11 O O4 NAG . . . BA 12 -58.628 85.628 3.823 1 173.49 ? O4 NAG 2001 D 1 HETATM 12 O O5 NAG . . . BA 12 -60.147 84.287 0.761 1 159.21 ? O5 NAG 2001 D 1 HETATM 13 O O6 NAG . . . BA 12 -62.04 84.385 3.508 1 175.36 ? O6 NAG 2001 D 1 HETATM 14 O O7 NAG . . . BA 12 -56.48 84.75 -2.085 1 143.85 ? O7 NAG 2001 D 1 # _model_server_stats.io_time_ms 56 _model_server_stats.parse_time_ms 13 _model_server_stats.create_model_time_ms 46 _model_server_stats.query_time_ms 333 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 14 #