data_8GF2 # _model_server_result.job_id TzVqrKQ5cG81gjHQwhotqA _model_server_result.datetime_utc '2024-11-09 02:20:35' _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 8gf2 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"L","auth_seq_id":601}' # _entry.id 8GF2 # _exptl.entry_id 8GF2 _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 221.208 _entity.id 7 _entity.src_method syn _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 90 _cell.angle_gamma 90 _cell.entry_id 8GF2 _cell.length_a 157.57 _cell.length_b 161.22 _cell.length_c 230.117 _cell.Z_PDB 16 _cell.pdbx_unique_axis ? # _symmetry.entry_id 8GF2 _symmetry.cell_setting ? _symmetry.Int_Tables_number 20 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'C 2 2 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 pentameric 5 author_and_software_defined_assembly 1 PISA pentameric 5 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,D,E,L 1 1 F,G,H,I,J,K 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 # _struct_asym.details ? _struct_asym.entity_id 7 _struct_asym.id L _struct_asym.pdbx_modified N _struct_asym.pdbx_blank_PDB_chainid_flag N # _pdbx_entity_branch.entity_id 6 _pdbx_entity_branch.type oligosaccharide # _pdbx_entity_branch_link.link_id 1 _pdbx_entity_branch_link.details ? _pdbx_entity_branch_link.entity_id 6 _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 6 n K NAG 1 G 1 NAG B 529 NAG 6 n K NAG 2 G 2 NAG B 530 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 A SG CYS 18 A CYS 336 1_555 A SG CYS 43 A CYS 361 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.028 ? disulf ? disulf2 A SG CYS 61 A CYS 379 1_555 A SG CYS 114 A CYS 432 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.049 ? disulf ? disulf3 A SG CYS 73 A CYS 391 1_555 A SG CYS 207 A CYS 525 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.03 ? disulf ? disulf4 A SG CYS 162 A CYS 480 1_555 A SG CYS 170 A CYS 488 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.035 ? disulf ? disulf5 B SG CYS 22 C CYS 22 1_555 B SG CYS 95 C CYS 92 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.035 ? disulf ? disulf6 B SG CYS 144 C CYS 140 1_555 B SG CYS 200 C CYS 196 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.03 ? disulf ? disulf7 C SG CYS 23 D CYS 23 1_555 C SG CYS 88 D CYS 88 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.024 ? disulf ? disulf8 C SG CYS 134 D CYS 134 1_555 C SG CYS 194 D CYS 194 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.014 ? disulf ? disulf9 D SG CYS 22 H CYS 22 1_555 D SG CYS 96 H CYS 92 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.033 ? disulf ? disulf10 D SG CYS 146 H CYS 140 1_555 D SG CYS 202 H CYS 196 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.041 ? disulf ? disulf11 E SG CYS 23 L CYS 23 1_555 E SG CYS 94 L CYS 88 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.043 ? disulf ? disulf12 E SG CYS 140 L CYS 134 1_555 E SG CYS 200 L CYS 194 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.042 ? disulf ? disulf13 F SG CYS 18 B CYS 336 1_555 F SG CYS 43 B CYS 361 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.022 ? disulf ? disulf14 F SG CYS 61 B CYS 379 1_555 F SG CYS 114 B CYS 432 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.041 ? disulf ? disulf15 F SG CYS 73 B CYS 391 1_555 F SG CYS 207 B CYS 525 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.039 ? disulf ? disulf16 F SG CYS 162 B CYS 480 1_555 F SG CYS 170 B CYS 488 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.045 ? disulf ? disulf17 G SG CYS 22 E CYS 22 1_555 G SG CYS 95 E CYS 92 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.023 ? disulf ? disulf18 G SG CYS 144 E CYS 140 1_555 G SG CYS 200 E CYS 196 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.033 ? disulf ? disulf19 H SG CYS 23 F CYS 23 1_555 H SG CYS 88 F CYS 88 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.037 ? disulf ? disulf20 H SG CYS 134 F CYS 134 1_555 H SG CYS 194 F CYS 194 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.03 ? disulf ? disulf21 I SG CYS 22 X CYS 22 1_555 I SG CYS 96 X CYS 92 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.032 ? disulf ? disulf22 I SG CYS 146 X CYS 140 1_555 I SG CYS 202 X CYS 196 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.009 ? disulf ? disulf23 I SG CYS 222 X CYS 216 1_555 J SG CYS 220 Y CYS 214 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.032 ? disulf ? disulf24 J SG CYS 23 Y CYS 23 1_555 J SG CYS 94 Y CYS 88 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.006 ? disulf ? disulf25 J SG CYS 140 Y CYS 134 1_555 J SG CYS 200 Y CYS 194 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.022 ? covale ? covale1 A ND2 ASN 25 A ASN 343 1_555 L C1 NAG . A NAG 601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.446 ? covale ? covale2 F ND2 ASN 25 B ASN 343 1_555 K C1 NAG . G NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.435 ? covale ? covale3 K O4 NAG . G NAG 1 1_555 K C1 NAG . G NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.375 ? # _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 235 n n C1 O1 NAG sing 236 n n C1 O5 NAG sing 237 n n C1 H1 NAG sing 238 n n C2 C3 NAG sing 239 n n C2 N2 NAG sing 240 n n C2 H2 NAG sing 241 n n C3 C4 NAG sing 242 n n C3 O3 NAG sing 243 n n C3 H3 NAG sing 244 n n C4 C5 NAG sing 245 n n C4 O4 NAG sing 246 n n C4 H4 NAG sing 247 n n C5 C6 NAG sing 248 n n C5 O5 NAG sing 249 n n C5 H5 NAG sing 250 n n C6 O6 NAG sing 251 n n C6 H61 NAG sing 252 n n C6 H62 NAG sing 253 n n C7 C8 NAG sing 254 n n C7 N2 NAG sing 255 n n C7 O7 NAG doub 256 n n C8 H81 NAG sing 257 n n C8 H82 NAG sing 258 n n C8 H83 NAG sing 259 n n N2 HN2 NAG sing 260 n n O1 HO1 NAG sing 261 n n O3 HO3 NAG sing 262 n n O4 HO4 NAG sing 263 n n O6 HO6 NAG sing 264 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 8GF2 _atom_sites.fract_transf_matrix[1][1] 0.006346 _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] 0.006203 _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] 0.004346 _atom_sites.fract_transf_vector[1] 0 _atom_sites.fract_transf_vector[2] 0 _atom_sites.fract_transf_vector[3] 0 # _pdbx_nonpoly_scheme.asym_id L _pdbx_nonpoly_scheme.entity_id 7 _pdbx_nonpoly_scheme.mon_id NAG _pdbx_nonpoly_scheme.pdb_strand_id A _pdbx_nonpoly_scheme.ndb_seq_num 1 _pdbx_nonpoly_scheme.pdb_seq_num 601 _pdbx_nonpoly_scheme.auth_seq_num 529 _pdbx_nonpoly_scheme.pdb_mon_id NAG _pdbx_nonpoly_scheme.auth_mon_id NAG _pdbx_nonpoly_scheme.pdb_ins_code . # 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 . . . L 7 7.154 12.607 -12.943 1 113.2 ? C1 NAG 601 A 1 HETATM 2 C C2 NAG . . . L 7 8.248 13.664 -13.143 1 116.67 ? C2 NAG 601 A 1 HETATM 3 C C3 NAG . . . L 7 9.622 13 -13.235 1 118.39 ? C3 NAG 601 A 1 HETATM 4 C C4 NAG . . . L 7 9.858 12.087 -12.04 1 121.51 ? C4 NAG 601 A 1 HETATM 5 C C5 NAG . . . L 7 8.713 11.087 -11.918 1 122.09 ? C5 NAG 601 A 1 HETATM 6 C C6 NAG . . . L 7 8.828 10.198 -10.701 1 119.36 ? C6 NAG 601 A 1 HETATM 7 C C7 NAG . . . L 7 7.8 15.793 -14.278 1 120.14 ? C7 NAG 601 A 1 HETATM 8 C C8 NAG . . . L 7 7.564 16.469 -15.595 1 116.94 ? C8 NAG 601 A 1 HETATM 9 N N2 NAG . . . L 7 7.994 14.471 -14.325 1 118.52 ? N2 NAG 601 A 1 HETATM 10 O O3 NAG . . . L 7 10.635 13.998 -13.292 1 117.73 ? O3 NAG 601 A 1 HETATM 11 O O4 NAG . . . L 7 11.086 11.386 -12.202 1 120.93 ? O4 NAG 601 A 1 HETATM 12 O O5 NAG . . . L 7 7.47 11.794 -11.799 1 120.2 ? O5 NAG 601 A 1 HETATM 13 O O6 NAG . . . L 7 8.864 10.959 -9.502 1 115.52 ? O6 NAG 601 A 1 HETATM 14 O O7 NAG . . . L 7 7.812 16.415 -13.221 1 122.91 ? O7 NAG 601 A 1 # _model_server_stats.io_time_ms 107 _model_server_stats.parse_time_ms 15 _model_server_stats.create_model_time_ms 29 _model_server_stats.query_time_ms 307 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 14 #