data_6CKB # _model_server_result.job_id b1OnFqvS2c0aLcXOlTx-4A _model_server_result.datetime_utc '2024-11-04 20:15:47' _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 6ckb # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"D","auth_seq_id":502}' # _entry.id 6CKB # _exptl.entry_id 6CKB _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 221.208 _entity.id 3 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description 2-acetamido-2-deoxy-beta-D-glucopyranose _entity.pdbx_number_of_molecules 5 _entity.pdbx_parent_entity_id . _entity.pdbx_mutation ? _entity.pdbx_fragment ? _entity.pdbx_ec ? # _cell.angle_alpha 90 _cell.angle_beta 96.36 _cell.angle_gamma 90 _cell.entry_id 6CKB _cell.length_a 59.08 _cell.length_b 80.91 _cell.length_c 126.72 _cell.Z_PDB 4 _cell.pdbx_unique_axis ? # _symmetry.entry_id 6CKB _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 monomeric 1 author_and_software_defined_assembly 1 PISA monomeric 1 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,C,D,E,J 1 1 B,F,G,H,I 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 ? 3 D N N ? 3 E N N ? 3 F N N ? 3 G N N ? 3 H 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 5 1_555 A SG CYS 23 A CYS 23 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.026 ? disulf ? disulf2 A SG CYS 13 A CYS 13 1_555 A SG CYS 372 A CYS 372 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.028 ? disulf ? disulf3 A SG CYS 16 A CYS 16 1_555 A SG CYS 38 A CYS 38 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.014 ? disulf ? disulf4 A SG CYS 26 A CYS 26 1_555 A SG CYS 49 A CYS 49 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.022 ? disulf ? disulf5 A SG CYS 311 A CYS 311 1_555 A SG CYS 323 A CYS 323 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.029 ? disulf ? disulf6 A SG CYS 343 A CYS 343 1_555 A SG CYS 370 A CYS 370 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.018 ? disulf ? disulf7 A SG CYS 374 A CYS 374 1_555 A SG CYS 394 A CYS 394 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.023 ? disulf ? disulf8 A SG CYS 385 A CYS 385 1_555 A SG CYS 397 A CYS 397 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.019 ? disulf ? disulf9 A SG CYS 399 A CYS 399 1_555 A SG CYS 408 A CYS 408 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.021 ? disulf ? disulf10 A SG CYS 410 A CYS 410 1_555 A SG CYS 440 A CYS 440 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.03 ? disulf ? disulf11 A SG CYS 423 A CYS 423 1_555 A SG CYS 438 A CYS 438 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.038 ? disulf ? disulf12 A SG CYS 432 A CYS 432 1_555 A SG CYS 443 A CYS 443 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.995 ? disulf ? disulf13 A SG CYS 445 A CYS 445 1_555 A SG CYS 458 A CYS 458 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.045 ? disulf ? disulf14 B SG CYS 5 B CYS 5 1_555 B SG CYS 23 B CYS 23 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.03 ? disulf ? disulf15 B SG CYS 13 B CYS 13 1_555 B SG CYS 372 B CYS 372 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.022 ? disulf ? disulf16 B SG CYS 16 B CYS 16 1_555 B SG CYS 38 B CYS 38 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.013 ? disulf ? disulf17 B SG CYS 26 B CYS 26 1_555 B SG CYS 49 B CYS 49 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.031 ? disulf ? disulf18 B SG CYS 311 B CYS 311 1_555 B SG CYS 323 B CYS 323 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.022 ? disulf ? disulf19 B SG CYS 343 B CYS 343 1_555 B SG CYS 370 B CYS 370 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.024 ? disulf ? disulf20 B SG CYS 374 B CYS 374 1_555 B SG CYS 394 B CYS 394 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.034 ? disulf ? disulf21 B SG CYS 385 B CYS 385 1_555 B SG CYS 397 B CYS 397 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.021 ? disulf ? disulf22 B SG CYS 399 B CYS 399 1_555 B SG CYS 408 B CYS 408 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.025 ? disulf ? disulf23 B SG CYS 410 B CYS 410 1_555 B SG CYS 440 B CYS 440 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.023 ? disulf ? disulf24 B SG CYS 423 B CYS 423 1_555 B SG CYS 438 B CYS 438 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.027 ? disulf ? disulf25 B SG CYS 432 B CYS 432 1_555 B SG CYS 443 B CYS 443 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.022 ? disulf ? disulf26 B SG CYS 445 B CYS 445 1_555 B SG CYS 458 B CYS 458 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.035 ? covale ? covale1 A ND2 ASN 145 A ASN 145 1_555 D C1 NAG . A NAG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.424 ? covale ? covale2 A ND2 ASN 308 A ASN 308 1_555 E C1 NAG . A NAG 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.424 ? covale ? covale3 B ND2 ASN 99 B ASN 99 1_555 G C1 NAG . B NAG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.449 ? covale ? covale4 B ND2 ASN 308 B ASN 308 1_555 F C1 NAG . B NAG 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.438 ? covale ? covale5 B ND2 ASN 389 B ASN 389 1_555 H C1 NAG . B NAG 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.467 ? metalc ? metalc1 A OG SER 121 A SER 121 1_555 C MG MG . A MG 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.29 ? metalc ? metalc2 A OG SER 123 A SER 123 1_555 C MG MG . A MG 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.998 ? metalc ? metalc3 A O ASP 221 A ASP 221 1_555 C MG MG . A MG 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.218 ? metalc ? metalc4 A OD1 ASP 221 A ASP 221 1_555 C MG MG . A MG 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.334 ? metalc ? metalc5 A OD2 ASP 221 A ASP 221 1_555 C MG MG . A MG 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.841 ? metalc ? metalc6 C MG MG . A MG 501 1_555 J O HOH . A HOH 601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.828 ? metalc ? metalc7 C MG MG . A MG 501 1_555 J O HOH . A HOH 602 1_655 ? ? ? ? ? ? ? ? ? ? ? ? 1.903 ? metalc ? metalc8 B OD2 ASP 66 B ASP 66 1_555 I CA CA . B CA 504 1_655 ? ? ? ? ? ? ? ? ? ? ? ? 2.273 ? metalc ? metalc9 B OG SER 121 B SER 121 1_555 I CA CA . B CA 504 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.233 ? metalc ? metalc10 B OG SER 123 B SER 123 1_555 I CA CA . B CA 504 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.487 ? metalc ? metalc11 B OD1 ASP 221 B ASP 221 1_555 I CA CA . B CA 504 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.256 ? metalc ? metalc12 B OD2 ASP 221 B ASP 221 1_555 I CA CA . B CA 504 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.571 ? # _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 6CKB _atom_sites.fract_transf_matrix[1][1] 0.016926 _atom_sites.fract_transf_matrix[1][2] 0 _atom_sites.fract_transf_matrix[1][3] 0.001887 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.012359 _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] 0.00794 _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 C 2 MG A 1 501 1 MG MG . D 3 NAG A 1 502 2 NAG NAG . E 3 NAG A 1 503 3 NAG NAG . F 3 NAG B 1 501 1 NAG NAG . G 3 NAG B 1 502 4 NAG NAG . H 3 NAG B 1 503 5 NAG NAG . I 4 CA B 1 504 1 CA CA . J 5 HOH A 1 601 4 HOH HOH . J 5 HOH A 2 602 3 HOH HOH . J 5 HOH A 3 603 1 HOH HOH . J 5 HOH A 4 604 2 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 . . . D 3 -58.131 -51.612 164.359 1 171.28 ? C1 NAG 502 A 1 HETATM 2 C C2 NAG . . . D 3 -57.642 -50.274 164.903 1 207.59 ? C2 NAG 502 A 1 HETATM 3 C C3 NAG . . . D 3 -58.689 -49.676 165.844 1 210.27 ? C3 NAG 502 A 1 HETATM 4 C C4 NAG . . . D 3 -60.06 -49.63 165.177 1 192.76 ? C4 NAG 502 A 1 HETATM 5 C C5 NAG . . . D 3 -60.416 -50.987 164.573 1 182.94 ? C5 NAG 502 A 1 HETATM 6 C C6 NAG . . . D 3 -61.667 -50.955 163.726 1 169.99 ? C6 NAG 502 A 1 HETATM 7 C C7 NAG . . . D 3 -55.209 -50.66 164.955 1 255.75 ? C7 NAG 502 A 1 HETATM 8 C C8 NAG . . . D 3 -53.996 -50.753 165.828 1 258.94 ? C8 NAG 502 A 1 HETATM 9 N N2 NAG . . . D 3 -56.364 -50.414 165.585 1 237.2 ? N2 NAG 502 A 1 HETATM 10 O O3 NAG . . . D 3 -58.293 -48.362 166.218 1 222.23 ? O3 NAG 502 A 1 HETATM 11 O O4 NAG . . . D 3 -61.05 -49.28 166.138 1 193.75 ? O4 NAG 502 A 1 HETATM 12 O O5 NAG . . . D 3 -59.364 -51.434 163.709 1 173.92 ? O5 NAG 502 A 1 HETATM 13 O O6 NAG . . . D 3 -61.475 -51.644 162.497 1 142.71 ? O6 NAG 502 A 1 HETATM 14 O O7 NAG . . . D 3 -55.147 -50.815 163.736 1 263.16 ? O7 NAG 502 A 1 # _model_server_stats.io_time_ms 21 _model_server_stats.parse_time_ms 17 _model_server_stats.create_model_time_ms 6 _model_server_stats.query_time_ms 296 _model_server_stats.encode_time_ms 20 _model_server_stats.element_count 14 #