data_6JXK # _model_server_result.job_id nyoeeR4ivvXeLG5smOA_ng _model_server_result.datetime_utc '2024-11-24 03:53:36' _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 6jxk # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"M","auth_seq_id":301}' # _entry.id 6JXK # _exptl.entry_id 6JXK _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 221.208 _entity.id 7 _entity.src_method man _entity.type non-polymer _entity.pdbx_description 2-acetamido-2-deoxy-beta-D-glucopyranose _entity.pdbx_number_of_molecules 8 _entity.pdbx_parent_entity_id . _entity.pdbx_mutation ? _entity.pdbx_fragment ? _entity.pdbx_ec ? # _cell.angle_alpha 90 _cell.angle_beta 107.79 _cell.angle_gamma 90 _cell.entry_id 6JXK _cell.length_a 191.51 _cell.length_b 106.43 _cell.length_c 250.96 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 6JXK _symmetry.cell_setting ? _symmetry.Int_Tables_number 5 _symmetry.space_group_name_Hall 'C 2y' _symmetry.space_group_name_H-M 'C 1 2 1' # 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 dimeric 2 author_and_software_defined_assembly 1 PISA dimeric 2 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,E,F,G,H,I,J,K,L 1 1 C,D,M,N,O,P,Q,R,S,T,U,V,W,X 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 ? 7 K N N ? 7 L N N ? 7 M N N ? 7 N N N ? 7 O N N ? 7 P N N ? 7 Q N N ? 7 R 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 B SG CYS 130 B CYS 131 1_555 B SG CYS 151 B CYS 152 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.033 ? disulf ? disulf2 B SG CYS 161 B CYS 162 1_555 B SG CYS 177 B CYS 178 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.03 ? disulf ? disulf3 B SG CYS 200 B CYS 201 1_555 B SG CYS 261 B CYS 262 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.033 ? disulf ? disulf4 C SG CYS 130 F CYS 131 1_555 C SG CYS 151 F CYS 152 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.031 ? disulf ? disulf5 C SG CYS 161 F CYS 162 1_555 C SG CYS 177 F CYS 178 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.033 ? disulf ? disulf6 C SG CYS 200 F CYS 201 1_555 C SG CYS 261 F CYS 262 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.035 ? covale ? covale1 B ND2 ASN 145 B ASN 146 1_555 L C1 NAG . B NAG 302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.438 ? covale ? covale2 B ND2 ASN 192 B ASN 193 1_555 K C1 NAG . B NAG 301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.425 ? covale ? covale3 C ND2 ASN 98 F ASN 99 1_555 M C1 NAG . F NAG 301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.455 ? covale ? covale4 C ND2 ASN 129 F ASN 130 1_555 N C1 NAG . F NAG 302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.476 ? covale ? covale5 C ND2 ASN 145 F ASN 146 1_555 R C1 NAG . F NAG 306 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.469 ? covale ? covale6 C ND2 ASN 160 F ASN 161 1_555 O C1 NAG . F NAG 303 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.433 ? covale ? covale7 C ND2 ASN 192 F ASN 193 1_555 Q C1 NAG . F NAG 305 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.425 ? covale ? covale8 C ND2 ASN 220 F ASN 221 1_555 P C1 NAG . F NAG 304 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.439 ? metalc ? metalc1 A O VAL 292 A VAL 338 1_555 J K K . A K 1106 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.659 ? metalc ? metalc2 A O ALA 293 A ALA 339 1_555 J K K . A K 1106 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 3.225 ? metalc ? metalc3 A O VAL 295 A VAL 341 1_555 J K K . A K 1106 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.663 ? metalc ? metalc4 A OE1 GLU 297 A GLU 343 1_555 J K K . A K 1106 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.747 ? metalc ? metalc5 A OD1 ASP 339 A ASP 385 1_555 E MG MF4 . A MF4 1101 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.687 ? metalc ? metalc6 A O THR 341 A THR 387 1_555 F MG MG . A MG 1102 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.417 ? metalc ? metalc7 A OD1 ASP 680 A ASP 726 1_555 F MG MG . A MG 1102 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.537 ? metalc ? metalc8 A OD2 ASP 680 A ASP 726 1_555 F MG MG . A MG 1102 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.11 ? metalc ? metalc9 A O LYS 689 A LYS 735 1_555 I K K . A K 1105 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.688 ? metalc ? metalc10 A O ALA 691 A ALA 737 1_555 I K K . A K 1105 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.911 ? metalc ? metalc11 A OD1 ASP 710 A ASP 756 1_555 I K K . A K 1105 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.853 ? metalc ? metalc12 A OD2 ASP 710 A ASP 756 1_555 I K K . A K 1105 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.748 ? metalc ? metalc13 A OE2 GLU 749 A GLU 795 1_555 J K K . A K 1106 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.59 ? metalc ? metalc14 D O VAL 292 E VAL 338 1_555 X K K . E K 1105 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.635 ? metalc ? metalc15 D O ALA 293 E ALA 339 1_555 X K K . E K 1105 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.739 ? metalc ? metalc16 D O VAL 295 E VAL 341 1_555 X K K . E K 1105 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.649 ? metalc ? metalc17 D OE1 GLU 297 E GLU 343 1_555 X K K . E K 1105 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.671 ? metalc ? metalc18 D OE2 GLU 297 E GLU 343 1_555 X K K . E K 1105 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 3.473 ? metalc ? metalc19 D OD1 ASP 339 E ASP 385 1_555 T MG MF4 . E MF4 1101 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.962 ? metalc ? metalc20 D OD2 ASP 339 E ASP 385 1_555 U MG MG . E MG 1102 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.942 ? metalc ? metalc21 D O THR 341 E THR 387 1_555 U MG MG . E MG 1102 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.485 ? metalc ? metalc22 D OG1 THR 341 E THR 387 1_555 U MG MG . E MG 1102 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.992 ? metalc ? metalc23 D OD1 ASP 680 E ASP 726 1_555 U MG MG . E MG 1102 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.969 ? metalc ? metalc24 D OD2 ASP 680 E ASP 726 1_555 U MG MG . E MG 1102 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.626 ? metalc ? metalc25 D O LEU 688 E LEU 734 1_555 W K K . E K 1104 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 3.423 ? metalc ? metalc26 D O LYS 689 E LYS 735 1_555 W K K . E K 1104 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.722 ? metalc ? metalc27 D O ALA 691 E ALA 737 1_555 W K K . E K 1104 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.926 ? metalc ? metalc28 D OD1 ASP 710 E ASP 756 1_555 W K K . E K 1104 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 3.019 ? metalc ? metalc29 D OD2 ASP 710 E ASP 756 1_555 W K K . E K 1104 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.697 ? metalc ? metalc30 D OE2 GLU 749 E GLU 795 1_555 X K K . E K 1105 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.574 ? metalc ? metalc31 D OE1 GLU 774 E GLU 820 1_555 X K K . E K 1105 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 3.298 ? # _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 316 n n C1 O1 NAG sing 317 n n C1 O5 NAG sing 318 n n C1 H1 NAG sing 319 n n C2 C3 NAG sing 320 n n C2 N2 NAG sing 321 n n C2 H2 NAG sing 322 n n C3 C4 NAG sing 323 n n C3 O3 NAG sing 324 n n C3 H3 NAG sing 325 n n C4 C5 NAG sing 326 n n C4 O4 NAG sing 327 n n C4 H4 NAG sing 328 n n C5 C6 NAG sing 329 n n C5 O5 NAG sing 330 n n C5 H5 NAG sing 331 n n C6 O6 NAG sing 332 n n C6 H61 NAG sing 333 n n C6 H62 NAG sing 334 n n C7 C8 NAG sing 335 n n C7 N2 NAG sing 336 n n C7 O7 NAG doub 337 n n C8 H81 NAG sing 338 n n C8 H82 NAG sing 339 n n C8 H83 NAG sing 340 n n N2 HN2 NAG sing 341 n n O1 HO1 NAG sing 342 n n O3 HO3 NAG sing 343 n n O4 HO4 NAG sing 344 n n O6 HO6 NAG sing 345 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 6JXK _atom_sites.fract_transf_matrix[1][1] 0.005222 _atom_sites.fract_transf_matrix[1][2] 0 _atom_sites.fract_transf_matrix[1][3] 0.001675 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.009396 _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] 0.004185 _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 E 3 MF4 A 1 1101 1101 MF4 MF4 . F 4 MG A 1 1102 1102 MG MG . G 5 CLR A 1 1103 1205 CLR CLR . H 6 K A 1 1104 1 K K . I 6 K A 1 1105 3 K K . J 6 K A 1 1106 6 K K . K 7 NAG B 1 301 305 NAG NAG . L 7 NAG B 1 302 306 NAG NAG . M 7 NAG F 1 301 301 NAG NAG . N 7 NAG F 1 302 302 NAG NAG . O 7 NAG F 1 303 303 NAG NAG . P 7 NAG F 1 304 304 NAG NAG . Q 7 NAG F 1 305 305 NAG NAG . R 7 NAG F 1 306 306 NAG NAG . S 5 CLR F 1 307 1205 CLR CLR . T 3 MF4 E 1 1101 1101 MF4 MF4 . U 4 MG E 1 1102 1102 MG MG . V 6 K E 1 1103 2 K K . W 6 K E 1 1104 3 K K . X 6 K E 1 1105 6 K K . # 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 . . . M 7 278.736 -35.757 92.255 1 270.69 ? C1 NAG 301 F 1 HETATM 2 C C2 NAG . . . M 7 279.474 -35.831 90.898 1 282.19 ? C2 NAG 301 F 1 HETATM 3 C C3 NAG . . . M 7 280.955 -36.15 91.107 1 281.75 ? C3 NAG 301 F 1 HETATM 4 C C4 NAG . . . M 7 281.576 -35.157 92.077 1 275.35 ? C4 NAG 301 F 1 HETATM 5 C C5 NAG . . . M 7 280.782 -35.13 93.381 1 265.09 ? C5 NAG 301 F 1 HETATM 6 C C6 NAG . . . M 7 281.27 -34.071 94.336 1 261.4 ? C6 NAG 301 F 1 HETATM 7 C C7 NAG . . . M 7 278.972 -36.784 88.682 1 289.11 ? C7 NAG 301 F 1 HETATM 8 C C8 NAG . . . M 7 278.277 -37.89 87.94 1 288.07 ? C8 NAG 301 F 1 HETATM 9 N N2 NAG . . . M 7 278.861 -36.813 90.016 1 287.16 ? N2 NAG 301 F 1 HETATM 10 O O3 NAG . . . M 7 281.645 -36.103 89.862 1 287.44 ? O3 NAG 301 F 1 HETATM 11 O O4 NAG . . . M 7 282.924 -35.528 92.347 1 276.36 ? O4 NAG 301 F 1 HETATM 12 O O5 NAG . . . M 7 279.405 -34.823 93.119 1 262.97 ? O5 NAG 301 F 1 HETATM 13 O O6 NAG . . . M 7 280.222 -33.19 94.72 1 255.87 ? O6 NAG 301 F 1 HETATM 14 O O7 NAG . . . M 7 279.6 -35.901 88.099 1 289.67 ? O7 NAG 301 F 1 # _model_server_stats.io_time_ms 51 _model_server_stats.parse_time_ms 17 _model_server_stats.create_model_time_ms 21 _model_server_stats.query_time_ms 339 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 14 #