data_6NYP # _model_server_result.job_id AbRe4ZooFuiHC0KdFle5Jg _model_server_result.datetime_utc '2024-11-23 05:30:04' _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 6nyp # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"P","auth_seq_id":201}' # _entry.id 6NYP # _exptl.entry_id 6NYP _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 221.208 _entity.id 6 _entity.src_method nat _entity.type non-polymer _entity.pdbx_description 2-acetamido-2-deoxy-beta-D-glucopyranose _entity.pdbx_number_of_molecules 2 _entity.pdbx_parent_entity_id . _entity.pdbx_mutation ? _entity.pdbx_fragment ? _entity.pdbx_ec ? # _cell.angle_alpha 90 _cell.angle_beta 91.67 _cell.angle_gamma 90 _cell.entry_id 6NYP _cell.length_a 66.99 _cell.length_b 77.2 _cell.length_c 101.72 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 6NYP _symmetry.cell_setting ? _symmetry.Int_Tables_number 4 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 1 21 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 PISA dimeric 2 author_and_software_defined_assembly 3 PISA dimeric 2 author_and_software_defined_assembly 4 # loop_ _pdbx_struct_assembly_gen.asym_id_list _pdbx_struct_assembly_gen.assembly_id _pdbx_struct_assembly_gen.oper_expression A,F,I,J,K,P,S,X 1 1 B,H,R,T,Z 2 1 C,G,L,Q,U,Y 3 1 D,E,M,N,O,V,W 4 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 ? 6 P N N ? 6 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 A SG CYS 4 A CYS 34 1_555 A SG CYS 33 A CYS 63 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.03 ? disulf ? disulf2 A SG CYS 28 A CYS 58 1_555 A SG CYS 85 A CYS 115 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.034 ? disulf ? disulf3 A SG CYS 42 A CYS 72 1_555 A SG CYS 49 A CYS 79 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.039 ? disulf ? disulf4 B SG CYS 28 B CYS 58 1_555 B SG CYS 85 B CYS 115 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.998 ? disulf ? disulf5 B SG CYS 42 B CYS 72 1_555 B SG CYS 49 B CYS 79 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.041 ? disulf ? disulf6 C SG CYS 4 C CYS 34 1_555 C SG CYS 33 C CYS 63 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.041 ? disulf ? disulf7 C SG CYS 28 C CYS 58 1_555 C SG CYS 85 C CYS 115 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.991 ? disulf ? disulf8 C SG CYS 42 C CYS 72 1_555 C SG CYS 49 C CYS 79 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.029 ? disulf ? disulf9 D SG CYS 4 D CYS 34 1_555 D SG CYS 33 D CYS 63 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.059 ? disulf ? disulf10 D SG CYS 28 D CYS 58 1_555 D SG CYS 85 D CYS 115 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.007 ? disulf ? disulf11 D SG CYS 42 D CYS 72 1_555 D SG CYS 49 D CYS 79 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.029 ? disulf ? disulf12 E SG CYS 3 E CYS 23 1_555 E SG CYS 14 E CYS 34 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.069 ? disulf ? disulf13 E SG CYS 15 E CYS 35 1_555 E SG CYS 28 E CYS 48 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.065 ? disulf ? disulf14 E SG CYS 18 E CYS 38 1_555 E SG CYS 36 E CYS 56 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.045 ? disulf ? disulf15 E SG CYS 39 E CYS 59 1_555 E SG CYS 51 E CYS 71 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.052 ? disulf ? disulf16 E SG CYS 54 E CYS 74 1_555 E SG CYS 67 E CYS 87 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.037 ? disulf ? disulf17 F SG CYS 3 F CYS 23 1_555 F SG CYS 14 F CYS 34 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.054 ? disulf ? disulf18 F SG CYS 15 F CYS 35 1_555 F SG CYS 28 F CYS 48 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.032 ? disulf ? disulf19 F SG CYS 18 F CYS 38 1_555 F SG CYS 36 F CYS 56 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.045 ? disulf ? disulf20 F SG CYS 39 F CYS 59 1_555 F SG CYS 51 F CYS 71 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.052 ? disulf ? disulf21 F SG CYS 54 F CYS 74 1_555 F SG CYS 67 F CYS 87 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.055 ? disulf ? disulf22 F SG CYS 57 F CYS 77 1_555 F SG CYS 75 F CYS 95 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.04 ? disulf ? disulf23 G SG CYS 3 G CYS 23 1_555 G SG CYS 14 G CYS 34 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.062 ? disulf ? disulf24 G SG CYS 15 G CYS 35 1_555 G SG CYS 28 G CYS 48 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.056 ? disulf ? disulf25 G SG CYS 18 G CYS 38 1_555 G SG CYS 36 G CYS 56 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.03 ? disulf ? disulf26 G SG CYS 39 G CYS 59 1_555 G SG CYS 51 G CYS 71 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.014 ? disulf ? disulf27 G SG CYS 54 G CYS 74 1_555 G SG CYS 67 G CYS 87 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.015 ? disulf ? disulf28 G SG CYS 57 G CYS 77 1_555 G SG CYS 75 G CYS 95 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.042 ? disulf ? disulf29 H SG CYS 3 H CYS 23 1_555 H SG CYS 14 H CYS 34 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.06 ? disulf ? disulf30 H SG CYS 15 H CYS 35 1_555 H SG CYS 28 H CYS 48 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.029 ? disulf ? disulf31 H SG CYS 18 H CYS 38 1_555 H SG CYS 36 H CYS 56 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.034 ? disulf ? disulf32 H SG CYS 39 H CYS 59 1_555 H SG CYS 51 H CYS 71 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.05 ? disulf ? disulf33 H SG CYS 54 H CYS 74 1_555 H SG CYS 67 H CYS 87 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.042 ? disulf ? disulf34 H SG CYS 57 H CYS 77 1_555 H SG CYS 75 H CYS 95 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.039 ? covale ? covale1 F ND2 ASN 66 F ASN 86 1_555 P C1 NAG . F NAG 201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.446 ? covale ? covale2 H ND2 ASN 66 H ASN 86 1_555 R C1 NAG . H NAG 201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.442 ? metalc ? metalc1 A O LEU 8 A LEU 38 1_555 K NA NA . A NA 603 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.666 ? metalc ? metalc2 A O ILE 10 A ILE 40 1_555 K NA NA . A NA 603 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.881 ? metalc ? metalc3 D O LEU 8 D LEU 38 1_555 O NA NA . D NA 203 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.91 ? metalc ? metalc4 D O ILE 10 D ILE 40 1_555 O NA NA . D NA 203 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.541 ? # _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 231 n n C1 O1 NAG sing 232 n n C1 O5 NAG sing 233 n n C1 H1 NAG sing 234 n n C2 C3 NAG sing 235 n n C2 N2 NAG sing 236 n n C2 H2 NAG sing 237 n n C3 C4 NAG sing 238 n n C3 O3 NAG sing 239 n n C3 H3 NAG sing 240 n n C4 C5 NAG sing 241 n n C4 O4 NAG sing 242 n n C4 H4 NAG sing 243 n n C5 C6 NAG sing 244 n n C5 O5 NAG sing 245 n n C5 H5 NAG sing 246 n n C6 O6 NAG sing 247 n n C6 H61 NAG sing 248 n n C6 H62 NAG sing 249 n n C7 C8 NAG sing 250 n n C7 N2 NAG sing 251 n n C7 O7 NAG doub 252 n n C8 H81 NAG sing 253 n n C8 H82 NAG sing 254 n n C8 H83 NAG sing 255 n n N2 HN2 NAG sing 256 n n O1 HO1 NAG sing 257 n n O3 HO3 NAG sing 258 n n O4 HO4 NAG sing 259 n n O6 HO6 NAG sing 260 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 6NYP _atom_sites.fract_transf_matrix[1][1] 0.014928 _atom_sites.fract_transf_matrix[1][2] 0 _atom_sites.fract_transf_matrix[1][3] 0.000435 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.012953 _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] 0.009835 _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 I 3 GOL A 1 601 601 GOL GOL . J 4 SO4 A 1 602 6 SO4 SO4 . K 5 NA A 1 603 3 NA NA . L 4 SO4 C 1 201 5 SO4 SO4 . M 4 SO4 D 1 201 1 SO4 SO4 . N 4 SO4 D 1 202 2 SO4 SO4 . O 5 NA D 1 203 2 NA NA . P 6 NAG F 1 201 99 NAG NAG . Q 4 SO4 G 1 201 9 SO4 SO4 . R 6 NAG H 1 201 99 NAG NAG . S 7 HOH A 1 701 26 HOH HOH . S 7 HOH A 2 702 137 HOH HOH . S 7 HOH A 3 703 164 HOH HOH . S 7 HOH A 4 704 11 HOH HOH . S 7 HOH A 5 705 20 HOH HOH . S 7 HOH A 6 706 89 HOH HOH . S 7 HOH A 7 707 163 HOH HOH . T 7 HOH B 1 201 83 HOH HOH . T 7 HOH B 2 202 115 HOH HOH . T 7 HOH B 3 203 116 HOH HOH . U 7 HOH C 1 301 135 HOH HOH . U 7 HOH C 2 302 15 HOH HOH . U 7 HOH C 3 303 94 HOH HOH . V 7 HOH D 1 301 159 HOH HOH . V 7 HOH D 2 302 16 HOH HOH . V 7 HOH D 3 303 134 HOH HOH . V 7 HOH D 4 304 54 HOH HOH . V 7 HOH D 5 305 8 HOH HOH . V 7 HOH D 6 306 74 HOH HOH . V 7 HOH D 7 307 29 HOH HOH . V 7 HOH D 8 308 19 HOH HOH . V 7 HOH D 9 309 122 HOH HOH . V 7 HOH D 10 310 101 HOH HOH . V 7 HOH D 11 311 130 HOH HOH . V 7 HOH D 12 312 25 HOH HOH . V 7 HOH D 13 313 133 HOH HOH . V 7 HOH D 14 314 38 HOH HOH . V 7 HOH D 15 315 127 HOH HOH . V 7 HOH D 16 316 131 HOH HOH . V 7 HOH D 17 317 162 HOH HOH . V 7 HOH D 18 318 21 HOH HOH . W 7 HOH E 1 201 112 HOH HOH . W 7 HOH E 2 202 66 HOH HOH . W 7 HOH E 3 203 117 HOH HOH . W 7 HOH E 4 204 50 HOH HOH . W 7 HOH E 5 205 32 HOH HOH . W 7 HOH E 6 206 110 HOH HOH . W 7 HOH E 7 207 24 HOH HOH . W 7 HOH E 8 208 7 HOH HOH . W 7 HOH E 9 209 142 HOH HOH . X 7 HOH F 1 301 124 HOH HOH . X 7 HOH F 2 302 3 HOH HOH . X 7 HOH F 3 303 165 HOH HOH . X 7 HOH F 4 304 161 HOH HOH . X 7 HOH F 5 305 126 HOH HOH . X 7 HOH F 6 306 125 HOH HOH . X 7 HOH F 7 307 160 HOH HOH . Y 7 HOH G 1 301 147 HOH HOH . Y 7 HOH G 2 302 27 HOH HOH . Y 7 HOH G 3 303 75 HOH HOH . Z 7 HOH H 1 301 139 HOH HOH . Z 7 HOH H 2 302 57 HOH HOH . Z 7 HOH H 3 303 5 HOH HOH . Z 7 HOH H 4 304 150 HOH HOH . Z 7 HOH H 5 305 105 HOH HOH . Z 7 HOH H 6 306 151 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 . . . P 6 15.115 42.149 107.903 1 125.65 ? C1 NAG 201 F 1 HETATM 2 C C2 NAG . . . P 6 16.417 41.826 108.648 1 126.25 ? C2 NAG 201 F 1 HETATM 3 C C3 NAG . . . P 6 16.612 42.9 109.717 1 130.25 ? C3 NAG 201 F 1 HETATM 4 C C4 NAG . . . P 6 16.66 44.286 109.064 1 132.26 ? C4 NAG 201 F 1 HETATM 5 C C5 NAG . . . P 6 15.416 44.525 108.191 1 127.44 ? C5 NAG 201 F 1 HETATM 6 C C6 NAG . . . P 6 15.52 45.839 107.417 1 123.89 ? C6 NAG 201 F 1 HETATM 7 C C7 NAG . . . P 6 16.981 39.4 108.661 1 115.05 ? C7 NAG 201 F 1 HETATM 8 C C8 NAG . . . P 6 17.01 38.133 109.473 1 106.29 ? C8 NAG 201 F 1 HETATM 9 N N2 NAG . . . P 6 16.454 40.489 109.254 1 120.88 ? N2 NAG 201 F 1 HETATM 10 O O3 NAG . . . P 6 17.809 42.637 110.463 1 132.75 ? O3 NAG 201 F 1 HETATM 11 O O4 NAG . . . P 6 16.794 45.293 110.082 1 126.21 ? O4 NAG 201 F 1 HETATM 12 O O5 NAG . . . P 6 15.245 43.436 107.267 1 127.65 ? O5 NAG 201 F 1 HETATM 13 O O6 NAG . . . P 6 14.294 46.11 106.728 1 118 ? O6 NAG 201 F 1 HETATM 14 O O7 NAG . . . P 6 17.432 39.41 107.525 1 114.49 ? O7 NAG 201 F 1 # _model_server_stats.io_time_ms 54 _model_server_stats.parse_time_ms 14 _model_server_stats.create_model_time_ms 17 _model_server_stats.query_time_ms 303 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 14 #