data_6QFY # _model_server_result.job_id ELSxg79nWKHmlwsbYZxv2A _model_server_result.datetime_utc '2024-11-29 14:09:32' _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 6qfy # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"H","auth_seq_id":501}' # _entry.id 6QFY # _exptl.entry_id 6QFY _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 221.208 _entity.id 4 _entity.src_method man _entity.type non-polymer _entity.pdbx_description 2-acetamido-2-deoxy-beta-D-glucopyranose _entity.pdbx_number_of_molecules 3 _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 120 _cell.entry_id 6QFY _cell.length_a 112.572 _cell.length_b 112.572 _cell.length_c 141.441 _cell.Z_PDB 12 _cell.pdbx_unique_axis ? # _symmetry.entry_id 6QFY _symmetry.cell_setting ? _symmetry.Int_Tables_number 152 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 31 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 ? monomeric 1 author_defined_assembly 1 ? monomeric 1 author_defined_assembly 2 # loop_ _pdbx_struct_assembly_gen.asym_id_list _pdbx_struct_assembly_gen.assembly_id _pdbx_struct_assembly_gen.oper_expression A,C,D,H,I,K 1 1 B,E,F,G,J,L 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 ? 4 H N N ? 4 I N N ? 4 J N N # loop_ _pdbx_entity_branch.entity_id _pdbx_entity_branch.type 2 oligosaccharide 3 oligosaccharide # loop_ _pdbx_entity_branch_link.link_id _pdbx_entity_branch_link.details _pdbx_entity_branch_link.entity_id _pdbx_entity_branch_link.entity_branch_list_num_1 _pdbx_entity_branch_link.entity_branch_list_num_2 _pdbx_entity_branch_link.comp_id_1 _pdbx_entity_branch_link.comp_id_2 _pdbx_entity_branch_link.atom_id_1 _pdbx_entity_branch_link.leaving_atom_id_1 _pdbx_entity_branch_link.atom_stereo_config_1 _pdbx_entity_branch_link.atom_id_2 _pdbx_entity_branch_link.leaving_atom_id_2 _pdbx_entity_branch_link.atom_stereo_config_2 _pdbx_entity_branch_link.value_order 1 ? 2 2 1 NAG NAG C1 O1 . O4 HO4 . sing 2 ? 3 2 1 NAG NAG C1 O1 . O4 HO4 . sing 3 ? 3 3 2 BMA NAG C1 O1 . O4 HO4 . 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 2 n C NAG 1 C 1 NAG A 511 NAG 2 n C NAG 2 C 2 NAG A 512 NAG 2 n D NAG 1 D 1 NAG A 521 NAG 2 n D NAG 2 D 2 NAG A 522 NAG 3 n E NAG 1 E 1 NAG B 501 NAG 3 n E NAG 2 E 2 NAG B 502 NAG 3 n E BMA 3 E 3 BMA B 533 BMA 2 n F NAG 1 F 1 NAG B 521 NAG 2 n F NAG 2 F 2 NAG B 524 NAG 2 n G NAG 1 G 1 NAG B 531 NAG 2 n G NAG 2 G 2 NAG B 532 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 7 A CYS 21 1_555 A SG CYS 151 A CYS 165 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.055 ? disulf ? disulf2 A SG CYS 146 A CYS 160 1_555 A SG CYS 179 A CYS 193 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.059 ? disulf ? disulf3 A SG CYS 158 A CYS 172 1_555 A SG CYS 238 A CYS 252 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.061 ? disulf ? disulf4 A SG CYS 272 A CYS 286 1_555 A SG CYS 282 A CYS 296 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.019 ? disulf ? disulf5 B SG CYS 7 B CYS 21 1_555 B SG CYS 151 B CYS 165 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.072 ? disulf ? disulf6 B SG CYS 146 B CYS 160 1_555 B SG CYS 179 B CYS 193 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.059 ? disulf ? disulf7 B SG CYS 158 B CYS 172 1_555 B SG CYS 238 B CYS 252 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.064 ? disulf ? disulf8 B SG CYS 272 B CYS 286 1_555 B SG CYS 282 B CYS 296 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.054 ? covale ? covale1 A ND2 ASN 8 A ASN 22 1_555 H C1 NAG . A NAG 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.454 ? covale ? covale2 A ND2 ASN 45 A ASN 59 1_555 I C1 NAG . A NAG 506 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.438 ? covale ? covale3 A ND2 ASN 119 A ASN 133 1_555 C C1 NAG . C NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.454 ? covale ? covale4 A ND2 ASN 184 A ASN 198 1_555 D C1 NAG . D NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.44 ? covale ? covale5 B ND2 ASN 8 B ASN 22 1_555 E C1 NAG . E NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.444 ? covale ? covale6 B ND2 ASN 45 B ASN 59 1_555 J C1 NAG . B NAG 504 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.451 ? covale ? covale7 B ND2 ASN 119 B ASN 133 1_555 F C1 NAG . F NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.452 ? covale ? covale8 B ND2 ASN 184 B ASN 198 1_555 G C1 NAG . G NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.452 ? covale ? covale9 C O4 NAG . C NAG 1 1_555 C C1 NAG . C NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.454 ? covale ? covale10 D O4 NAG . D NAG 1 1_555 D C1 NAG . D NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.446 ? covale ? covale11 E O4 NAG . E NAG 1 1_555 E C1 NAG . E NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.45 ? covale ? covale12 E O4 NAG . E NAG 2 1_555 E C1 BMA . E BMA 3 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.451 ? covale ? covale13 F O4 NAG . F NAG 1 1_555 F C1 NAG . F NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.453 ? covale ? covale14 G O4 NAG . G NAG 1 1_555 G C1 NAG . G NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.443 ? # _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 261 n n C1 O1 NAG sing 262 n n C1 O5 NAG sing 263 n n C1 H1 NAG sing 264 n n C2 C3 NAG sing 265 n n C2 N2 NAG sing 266 n n C2 H2 NAG sing 267 n n C3 C4 NAG sing 268 n n C3 O3 NAG sing 269 n n C3 H3 NAG sing 270 n n C4 C5 NAG sing 271 n n C4 O4 NAG sing 272 n n C4 H4 NAG sing 273 n n C5 C6 NAG sing 274 n n C5 O5 NAG sing 275 n n C5 H5 NAG sing 276 n n C6 O6 NAG sing 277 n n C6 H61 NAG sing 278 n n C6 H62 NAG sing 279 n n C7 C8 NAG sing 280 n n C7 N2 NAG sing 281 n n C7 O7 NAG doub 282 n n C8 H81 NAG sing 283 n n C8 H82 NAG sing 284 n n C8 H83 NAG sing 285 n n N2 HN2 NAG sing 286 n n O1 HO1 NAG sing 287 n n O3 HO3 NAG sing 288 n n O4 HO4 NAG sing 289 n n O6 HO6 NAG sing 290 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 6QFY _atom_sites.fract_transf_matrix[1][1] 0.008883 _atom_sites.fract_transf_matrix[1][2] 0.005129 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.010257 _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] 0.00707 _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 4 NAG A 1 501 501 NAG NAG . I 4 NAG A 1 506 523 NAG NAG . J 4 NAG B 1 504 511 NAG NAG . K 5 HOH A 1 601 9 HOH HOH . K 5 HOH A 2 602 11 HOH HOH . K 5 HOH A 3 603 12 HOH HOH . K 5 HOH A 4 604 16 HOH HOH . K 5 HOH A 5 605 1 HOH HOH . K 5 HOH A 6 606 10 HOH HOH . K 5 HOH A 7 607 14 HOH HOH . K 5 HOH A 8 608 7 HOH HOH . K 5 HOH A 9 609 6 HOH HOH . K 5 HOH A 10 610 4 HOH HOH . K 5 HOH A 11 611 5 HOH HOH . K 5 HOH A 12 612 8 HOH HOH . K 5 HOH A 13 613 2 HOH HOH . K 5 HOH A 14 614 15 HOH HOH . K 5 HOH A 15 615 3 HOH HOH . K 5 HOH A 16 616 13 HOH HOH . L 5 HOH B 1 601 5 HOH HOH . L 5 HOH B 2 602 7 HOH HOH . L 5 HOH B 3 603 13 HOH HOH . L 5 HOH B 4 604 1 HOH HOH . L 5 HOH B 5 605 12 HOH HOH . L 5 HOH B 6 606 3 HOH HOH . L 5 HOH B 7 607 9 HOH HOH . L 5 HOH B 8 608 14 HOH HOH . L 5 HOH B 9 609 2 HOH HOH . L 5 HOH B 10 610 11 HOH HOH . L 5 HOH B 11 611 10 HOH HOH . L 5 HOH B 12 612 4 HOH HOH . L 5 HOH B 13 613 6 HOH HOH . L 5 HOH B 14 614 8 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 . . . H 4 -28.203 82.57 48.161 1 130.67 ? C1 NAG 501 A 1 HETATM 2 C C2 NAG . . . H 4 -28.745 81.145 48.403 1 140.16 ? C2 NAG 501 A 1 HETATM 3 C C3 NAG . . . H 4 -28.83 80.856 49.915 1 140.91 ? C3 NAG 501 A 1 HETATM 4 C C4 NAG . . . H 4 -27.492 81.072 50.613 1 143.49 ? C4 NAG 501 A 1 HETATM 5 C C5 NAG . . . H 4 -26.904 82.436 50.242 1 145.49 ? C5 NAG 501 A 1 HETATM 6 C C6 NAG . . . H 4 -25.458 82.588 50.726 1 147.32 ? C6 NAG 501 A 1 HETATM 7 C C7 NAG . . . H 4 -30.314 80.766 46.511 1 149.52 ? C7 NAG 501 A 1 HETATM 8 C C8 NAG . . . H 4 -31.695 80.289 46.153 1 141.88 ? C8 NAG 501 A 1 HETATM 9 N N2 NAG . . . H 4 -30.057 80.862 47.822 1 150.27 ? N2 NAG 501 A 1 HETATM 10 O O3 NAG . . . H 4 -29.269 79.514 50.19 1 131.98 ? O3 NAG 501 A 1 HETATM 11 O O4 NAG . . . H 4 -27.688 80.964 52.032 1 138.09 ? O4 NAG 501 A 1 HETATM 12 O O5 NAG . . . H 4 -26.929 82.621 48.822 1 139.23 ? O5 NAG 501 A 1 HETATM 13 O O6 NAG . . . H 4 -24.532 82.405 49.643 1 146.8 ? O6 NAG 501 A 1 HETATM 14 O O7 NAG . . . H 4 -29.484 81.018 45.65 1 153.16 ? O7 NAG 501 A 1 # _model_server_stats.io_time_ms 81 _model_server_stats.parse_time_ms 32 _model_server_stats.create_model_time_ms 8 _model_server_stats.query_time_ms 275 _model_server_stats.encode_time_ms 5 _model_server_stats.element_count 14 #