data_3QNF # _model_server_result.job_id joLECpgYfxEAq7URkl_cfA _model_server_result.datetime_utc '2024-12-23 19:12:19' _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 3qnf # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"G","auth_seq_id":1154}' # _entry.id 3QNF # _exptl.entry_id 3QNF _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 4 _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 3QNF _cell.length_a 97.246 _cell.length_b 132.816 _cell.length_c 233.687 _cell.Z_PDB 12 _cell.pdbx_unique_axis ? # _symmetry.entry_id 3QNF _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 monomeric 1 author_and_software_defined_assembly 1 PISA monomeric 1 author_and_software_defined_assembly 2 PISA monomeric 1 author_and_software_defined_assembly 3 # loop_ _pdbx_struct_assembly_gen.asym_id_list _pdbx_struct_assembly_gen.assembly_id _pdbx_struct_assembly_gen.oper_expression A,D,E,L 1 1 B,F,G,H,M 2 1 C,I,J,K,N 3 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 G N N ? 4 H N N ? 4 J N N ? 4 K N N # _pdbx_entity_branch.entity_id 2 _pdbx_entity_branch.type 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 ? 2 3 2 MAN NAG C1 O1 . O4 HO4 . sing 3 ? 2 4 3 MAN MAN C1 O1 . O6 HO6 . 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 D NAG 1 D 1 NAG D 1001 NAG 2 n D NAG 2 D 2 NAG D 1002 NAG 2 n D MAN 3 D 3 MAN D 1004 MAN 2 n D MAN 4 D 4 MAN D 1005 MAN # 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 410 A CYS 404 1_555 A SG CYS 449 A CYS 443 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.049 ? disulf ? disulf2 A SG CYS 742 A CYS 736 1_555 A SG CYS 749 A CYS 743 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.059 ? disulf ? disulf3 B SG CYS 410 B CYS 404 1_555 B SG CYS 449 B CYS 443 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.04 ? disulf ? disulf4 C SG CYS 410 C CYS 404 1_555 C SG CYS 449 C CYS 443 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.021 ? covale ? covale1 A ND2 ASN 76 A ASN 70 1_555 D C1 NAG . D NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.433 ? covale ? covale2 B ND2 ASN 76 B ASN 70 1_555 H C1 NAG . B NAG 1070 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.451 ? covale ? covale3 B ND2 ASN 160 B ASN 154 1_555 G C1 NAG . B NAG 1154 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.453 ? covale ? covale4 C ND2 ASN 76 C ASN 70 1_555 J C1 NAG . C NAG 1070 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.459 ? covale ? covale5 C ND2 ASN 160 C ASN 154 1_555 K C1 NAG . C NAG 1154 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.454 ? covale ? covale6 D O4 NAG . D NAG 1 1_555 D C1 NAG . D NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.452 ? covale ? covale7 D O4 NAG . D NAG 2 1_555 D C1 MAN . D MAN 3 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.438 ? covale ? covale8 D O6 MAN . D MAN 3 1_555 D C1 MAN . D MAN 4 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.437 ? metalc ? metalc1 A NE2 HIS 359 A HIS 353 1_555 E ZN ZN . A ZN 5000 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.065 ? metalc ? metalc2 A NE2 HIS 363 A HIS 357 1_555 E ZN ZN . A ZN 5000 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.065 ? metalc ? metalc3 A OE2 GLU 382 A GLU 376 1_555 E ZN ZN . A ZN 5000 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.99 ? metalc ? metalc4 A OE1 GLU 382 A GLU 376 1_555 E ZN ZN . A ZN 5000 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.287 ? metalc ? metalc5 B NE2 HIS 359 B HIS 353 1_555 F ZN ZN . B ZN 5000 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.066 ? metalc ? metalc6 B NE2 HIS 363 B HIS 357 1_555 F ZN ZN . B ZN 5000 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.087 ? metalc ? metalc7 B OE2 GLU 382 B GLU 376 1_555 F ZN ZN . B ZN 5000 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.972 ? metalc ? metalc8 B OE1 GLU 382 B GLU 376 1_555 F ZN ZN . B ZN 5000 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.347 ? metalc ? metalc9 C NE2 HIS 359 C HIS 353 1_555 I ZN ZN . C ZN 5000 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.077 ? metalc ? metalc10 C NE2 HIS 363 C HIS 357 1_555 I ZN ZN . C ZN 5000 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.081 ? metalc ? metalc11 C OE2 GLU 382 C GLU 376 1_555 I ZN ZN . C ZN 5000 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.983 ? metalc ? metalc12 C OE1 GLU 382 C GLU 376 1_555 I ZN ZN . C ZN 5000 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.229 ? # _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 3QNF _atom_sites.fract_transf_matrix[1][1] 0.010283 _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] 0.007529 _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] 0.004279 _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 ZN A 1 5000 5000 ZN ZN . F 3 ZN B 1 5000 5000 ZN ZN . G 4 NAG B 1 1154 1154 NAG NAG . H 4 NAG B 1 1070 1070 NAG NAG . I 3 ZN C 1 5000 5000 ZN ZN . J 4 NAG C 1 1070 1070 NAG NAG . K 4 NAG C 1 1154 1154 NAG NAG . L 5 HOH A 1 949 2 HOH HOH . L 5 HOH A 2 950 14 HOH HOH . L 5 HOH A 3 951 26 HOH HOH . L 5 HOH A 4 952 27 HOH HOH . L 5 HOH A 5 953 28 HOH HOH . L 5 HOH A 6 954 29 HOH HOH . L 5 HOH A 7 955 30 HOH HOH . L 5 HOH A 8 956 31 HOH HOH . M 5 HOH B 1 949 1 HOH HOH . M 5 HOH B 2 950 3 HOH HOH . M 5 HOH B 3 951 4 HOH HOH . M 5 HOH B 4 952 5 HOH HOH . M 5 HOH B 5 953 6 HOH HOH . M 5 HOH B 6 954 7 HOH HOH . M 5 HOH B 7 955 8 HOH HOH . M 5 HOH B 8 956 9 HOH HOH . M 5 HOH B 9 957 10 HOH HOH . M 5 HOH B 10 958 13 HOH HOH . M 5 HOH B 11 959 20 HOH HOH . M 5 HOH B 12 960 32 HOH HOH . M 5 HOH B 13 961 33 HOH HOH . M 5 HOH B 14 962 34 HOH HOH . M 5 HOH B 15 963 35 HOH HOH . M 5 HOH B 16 964 36 HOH HOH . M 5 HOH B 17 965 37 HOH HOH . M 5 HOH B 18 966 38 HOH HOH . M 5 HOH B 19 967 39 HOH HOH . N 5 HOH C 1 949 11 HOH HOH . N 5 HOH C 2 950 12 HOH HOH . N 5 HOH C 3 951 15 HOH HOH . N 5 HOH C 4 952 16 HOH HOH . N 5 HOH C 5 953 17 HOH HOH . N 5 HOH C 6 954 18 HOH HOH . N 5 HOH C 7 955 19 HOH HOH . N 5 HOH C 8 956 21 HOH HOH . N 5 HOH C 9 957 22 HOH HOH . N 5 HOH C 10 958 23 HOH HOH . N 5 HOH C 11 959 24 HOH HOH . N 5 HOH C 12 960 25 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 . . . G 4 85.369 -5.999 47.108 1 89.55 ? C1 NAG 1154 B 1 HETATM 2 C C2 NAG . . . G 4 85.805 -6.091 48.589 1 94.8 ? C2 NAG 1154 B 1 HETATM 3 C C3 NAG . . . G 4 87.106 -6.883 48.79 1 93.42 ? C3 NAG 1154 B 1 HETATM 4 C C4 NAG . . . G 4 87.465 -7.744 47.579 1 97.41 ? C4 NAG 1154 B 1 HETATM 5 C C5 NAG . . . G 4 87.428 -6.937 46.268 1 99.57 ? C5 NAG 1154 B 1 HETATM 6 C C6 NAG . . . G 4 87.129 -7.843 45.069 1 101.67 ? C6 NAG 1154 B 1 HETATM 7 C C7 NAG . . . G 4 86.128 -4.608 50.526 1 104.89 ? C7 NAG 1154 B 1 HETATM 8 C C8 NAG . . . G 4 86.278 -3.187 50.997 1 103.16 ? C8 NAG 1154 B 1 HETATM 9 N N2 NAG . . . G 4 85.964 -4.778 49.208 1 100.42 ? N2 NAG 1154 B 1 HETATM 10 O O3 NAG . . . G 4 87.005 -7.687 49.949 1 80.05 ? O3 NAG 1154 B 1 HETATM 11 O O4 NAG . . . G 4 88.745 -8.327 47.758 1 82.25 ? O4 NAG 1154 B 1 HETATM 12 O O5 NAG . . . G 4 86.52 -5.825 46.292 1 92.37 ? O5 NAG 1154 B 1 HETATM 13 O O6 NAG . . . G 4 87.818 -9.077 45.169 1 91.13 ? O6 NAG 1154 B 1 HETATM 14 O O7 NAG . . . G 4 86.161 -5.534 51.342 1 105.28 ? O7 NAG 1154 B 1 # _model_server_stats.io_time_ms 13 _model_server_stats.parse_time_ms 11 _model_server_stats.create_model_time_ms 52 _model_server_stats.query_time_ms 296 _model_server_stats.encode_time_ms 12 _model_server_stats.element_count 14 #