data_9JCX # _model_server_result.job_id 6P5uyIWGrQpl3894DhkEig _model_server_result.datetime_utc '2025-08-08 09:11:29' _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 9jcx # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"G","auth_seq_id":702}' # _entry.id 9JCX # _exptl.entry_id 9JCX _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 221.208 _entity.id 5 _entity.src_method syn _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 90 _cell.entry_id 9JCX _cell.length_a 63.35 _cell.length_b 120.72 _cell.length_c 126.13 _cell.Z_PDB 4 _cell.pdbx_unique_axis ? # _symmetry.entry_id 9JCX _symmetry.cell_setting ? _symmetry.Int_Tables_number 19 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 21 21 21' # _pdbx_struct_assembly.method_details PISA _pdbx_struct_assembly.oligomeric_details trimeric _pdbx_struct_assembly.oligomeric_count 3 _pdbx_struct_assembly.details author_and_software_defined_assembly _pdbx_struct_assembly.id 1 # loop_ _pdbx_struct_assembly_gen.asym_id_list _pdbx_struct_assembly_gen.assembly_id _pdbx_struct_assembly_gen.oper_expression A,B,D,E,H,I 1 1 C,F,G,J 1 2 # loop_ _pdbx_struct_oper_list.id _pdbx_struct_oper_list.type _pdbx_struct_oper_list.name _pdbx_struct_oper_list.symmetry_operation _pdbx_struct_oper_list.matrix[1][1] _pdbx_struct_oper_list.matrix[1][2] _pdbx_struct_oper_list.matrix[1][3] _pdbx_struct_oper_list.matrix[2][1] _pdbx_struct_oper_list.matrix[2][2] _pdbx_struct_oper_list.matrix[2][3] _pdbx_struct_oper_list.matrix[3][1] _pdbx_struct_oper_list.matrix[3][2] _pdbx_struct_oper_list.matrix[3][3] _pdbx_struct_oper_list.vector[1] _pdbx_struct_oper_list.vector[2] _pdbx_struct_oper_list.vector[3] 1 'identity operation' 1_555 x,y,z 1 0 0 0 1 0 0 0 1 0 0 0 2 'crystal symmetry operation' 4_445 x-1/2,-y-1/2,-z 1 0 0 0 -1 0 0 0 -1 -31.675 -60.36 0 # loop_ _struct_asym.details _struct_asym.entity_id _struct_asym.id _struct_asym.pdbx_modified _struct_asym.pdbx_blank_PDB_chainid_flag ? 5 E N N ? 5 F N N ? 5 G 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 5 A CYS 113 1_555 A SG CYS 18 A CYS 126 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.032 ? disulf ? disulf2 A SG CYS 12 A CYS 120 1_555 A SG CYS 31 A CYS 139 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.033 ? disulf ? disulf3 A SG CYS 25 A CYS 133 1_555 A SG CYS 40 A CYS 148 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.031 ? disulf ? disulf4 A SG CYS 64 A CYS 172 1_555 A SG CYS 123 A CYS 231 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.033 ? disulf ? disulf5 A SG CYS 77 A CYS 185 1_555 A SG CYS 133 A CYS 241 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.034 ? disulf ? disulf6 A SG CYS 136 A CYS 244 1_555 B SG CYS 110 C CYS 365 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.033 ? disulf ? disulf7 B SG CYS 26 C CYS 281 1_555 B SG CYS 42 C CYS 297 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.03 ? disulf ? disulf8 B SG CYS 155 C CYS 410 1_555 B SG CYS 171 C CYS 426 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.031 ? disulf ? disulf9 B SG CYS 182 C CYS 437 1_555 B SG CYS 210 C CYS 465 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.035 ? disulf ? disulf10 C SG CYS 5 B CYS 327 1_555 C SG CYS 30 B CYS 352 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.03 ? disulf ? disulf11 C SG CYS 48 B CYS 370 1_555 C SG CYS 101 B CYS 423 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.034 ? disulf ? disulf12 C SG CYS 60 B CYS 382 1_555 C SG CYS 283 B CYS 605 1_555 ? ? ? ? A ? ? ? ? ? ? ? 2.038 ? disulf ? disulf13 C SG CYS 144 B CYS 466 1_555 C SG CYS 224 B CYS 546 1_555 ? A ? ? ? ? ? ? ? ? ? ? 2.039 ? disulf ? disulf14 C SG CYS 152 B CYS 474 1_555 C SG CYS 173 B CYS 495 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.029 ? disulf ? disulf15 C SG CYS 154 B CYS 476 1_555 C SG CYS 245 B CYS 567 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.033 ? disulf ? disulf16 C SG CYS 163 B CYS 485 1_555 C SG CYS 194 B CYS 516 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.032 ? disulf ? disulf17 C SG CYS 182 B CYS 504 1_555 C SG CYS 196 B CYS 518 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.034 ? disulf ? disulf18 C SG CYS 198 B CYS 520 1_555 C SG CYS 211 B CYS 533 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.032 ? disulf ? disulf19 C SG CYS 234 B CYS 556 1_555 C SG CYS 247 B CYS 569 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.032 ? disulf ? disulf20 C SG CYS 260 B CYS 582 1_555 C SG CYS 266 B CYS 588 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.033 ? covale ? covale1 A ND2 ASN 105 A ASN 213 1_555 E C1 NAG . A NAG 302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.443 ? covale ? covale2 C ND2 ASN 111 B ASN 433 1_555 F C1 NAG . B NAG 701 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.441 ? covale ? covale3 C ND2 ASN 148 B ASN 470 1_555 G C1 NAG . B NAG 702 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.439 ? metalc ? metalc1 A O ASN 23 A ASN 131 1_555 D CA CA . A CA 301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.384 ? metalc ? metalc2 A OD1 ASP 26 A ASP 134 1_555 D CA CA . A CA 301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.319 ? metalc ? metalc3 A O VAL 28 A VAL 136 1_555 D CA CA . A CA 301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.228 ? metalc ? metalc4 A OD2 ASP 36 A ASP 144 1_555 D CA CA . A CA 301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.237 ? metalc ? metalc5 A OE2 GLU 37 A GLU 145 1_555 D CA CA . A CA 301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.047 ? # _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 237 n n C1 O1 NAG sing 238 n n C1 O5 NAG sing 239 n n C1 H1 NAG sing 240 n n C2 C3 NAG sing 241 n n C2 N2 NAG sing 242 n n C2 H2 NAG sing 243 n n C3 C4 NAG sing 244 n n C3 O3 NAG sing 245 n n C3 H3 NAG sing 246 n n C4 C5 NAG sing 247 n n C4 O4 NAG sing 248 n n C4 H4 NAG sing 249 n n C5 C6 NAG sing 250 n n C5 O5 NAG sing 251 n n C5 H5 NAG sing 252 n n C6 O6 NAG sing 253 n n C6 H61 NAG sing 254 n n C6 H62 NAG sing 255 n n C7 C8 NAG sing 256 n n C7 N2 NAG sing 257 n n C7 O7 NAG doub 258 n n C8 H81 NAG sing 259 n n C8 H82 NAG sing 260 n n C8 H83 NAG sing 261 n n N2 HN2 NAG sing 262 n n O1 HO1 NAG sing 263 n n O3 HO3 NAG sing 264 n n O4 HO4 NAG sing 265 n n O6 HO6 NAG sing 266 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 9JCX _atom_sites.fract_transf_matrix[1][1] 0.015785 _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] 0.008284 _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] 0.007928 _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 D 4 CA A 1 301 1 CA CA . E 5 NAG A 1 302 349 NAG NAG . F 5 NAG B 1 701 710 NAG NAG . G 5 NAG B 1 702 711 NAG NAG . H 6 HOH A 1 401 29 HOH HOH . H 6 HOH A 2 402 28 HOH HOH . H 6 HOH A 3 403 19 HOH HOH . H 6 HOH A 4 404 18 HOH HOH . I 6 HOH C 1 601 14 HOH HOH . I 6 HOH C 2 602 22 HOH HOH . I 6 HOH C 3 603 4 HOH HOH . I 6 HOH C 4 604 16 HOH HOH . I 6 HOH C 5 605 3 HOH HOH . I 6 HOH C 6 606 20 HOH HOH . I 6 HOH C 7 607 23 HOH HOH . I 6 HOH C 8 608 21 HOH HOH . J 6 HOH B 1 801 11 HOH HOH . J 6 HOH B 2 802 15 HOH HOH . J 6 HOH B 3 803 1 HOH HOH . J 6 HOH B 4 804 6 HOH HOH . J 6 HOH B 5 805 26 HOH HOH . J 6 HOH B 6 806 12 HOH HOH . J 6 HOH B 7 807 2 HOH HOH . J 6 HOH B 8 808 8 HOH HOH . J 6 HOH B 9 809 7 HOH HOH . J 6 HOH B 10 810 13 HOH HOH . J 6 HOH B 11 811 27 HOH HOH . J 6 HOH B 12 812 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 5 -3.11 -49.88 -24.135 1 100.05 ? C1 NAG 702 B 1 HETATM 2 C C2 NAG . . . G 5 -3.584 -51.097 -23.329 1 91.1 ? C2 NAG 702 B 1 HETATM 3 C C3 NAG . . . G 5 -3.597 -50.759 -21.832 1 102.82 ? C3 NAG 702 B 1 HETATM 4 C C4 NAG . . . G 5 -2.256 -50.176 -21.397 1 100.68 ? C4 NAG 702 B 1 HETATM 5 C C5 NAG . . . G 5 -1.857 -49.045 -22.359 1 105.17 ? C5 NAG 702 B 1 HETATM 6 C C6 NAG . . . G 5 -0.525 -48.394 -22.043 1 87.99 ? C6 NAG 702 B 1 HETATM 7 C C7 NAG . . . G 5 -6.015 -50.912 -23.853 1 102.35 ? C7 NAG 702 B 1 HETATM 8 C C8 NAG . . . G 5 -7.205 -51.653 -24.419 1 94.3 ? C8 NAG 702 B 1 HETATM 9 N N2 NAG . . . G 5 -4.85 -51.595 -23.823 1 101.39 ? N2 NAG 702 B 1 HETATM 10 O O3 NAG . . . G 5 -3.891 -51.926 -21.11 1 97.75 ? O3 NAG 702 B 1 HETATM 11 O O4 NAG . . . G 5 -2.413 -49.743 -20.061 1 86.1 ? O4 NAG 702 B 1 HETATM 12 O O5 NAG . . . G 5 -1.826 -49.533 -23.691 1 106.1 ? O5 NAG 702 B 1 HETATM 13 O O6 NAG . . . G 5 -0.673 -47.575 -20.904 1 82.22 ? O6 NAG 702 B 1 HETATM 14 O O7 NAG . . . G 5 -6.137 -49.772 -23.436 1 88.38 ? O7 NAG 702 B 1 # _model_server_stats.io_time_ms 11 _model_server_stats.parse_time_ms 12 _model_server_stats.create_model_time_ms 6 _model_server_stats.query_time_ms 267 _model_server_stats.encode_time_ms 6 _model_server_stats.element_count 14 #