data_6L6N # _model_server_result.job_id DLPNx-PbOCMlfdGDJx8iKA _model_server_result.datetime_utc '2025-03-26 05:22:00' _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 6l6n # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"D","auth_seq_id":501}' # _entry.id 6L6N # _exptl.entry_id 6L6N _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 221.208 _entity.id 2 _entity.src_method man _entity.type non-polymer _entity.pdbx_description 2-acetamido-2-deoxy-alpha-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 6L6N _cell.length_a 83.65 _cell.length_b 142.71 _cell.length_c 221.96 _cell.Z_PDB 12 _cell.pdbx_unique_axis ? # _symmetry.entry_id 6L6N _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 # _pdbx_struct_assembly_gen.asym_id_list A,B,C,D,E,F,G,H,I,J,K,L,M,N _pdbx_struct_assembly_gen.assembly_id 1 _pdbx_struct_assembly_gen.oper_expression 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 2 _struct_asym.id D _struct_asym.pdbx_modified N _struct_asym.pdbx_blank_PDB_chainid_flag 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 83 A CYS 93 1_555 A SG CYS 184 A CYS 194 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.081 ? disulf ? disulf2 A SG CYS 280 A CYS 290 1_555 A SG CYS 357 A CYS 367 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.089 ? disulf ? disulf3 A SG CYS 300 A CYS 310 1_555 A SG CYS 353 A CYS 363 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.069 ? disulf ? disulf4 A SG CYS 304 A CYS 314 1_555 A SG CYS 351 A CYS 361 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.066 ? disulf ? disulf5 A SG CYS 313 A CYS 323 1_555 A SG CYS 335 A CYS 345 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.065 ? disulf ? disulf6 A SG CYS 315 A CYS 325 1_555 A SG CYS 327 A CYS 337 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.082 ? disulf ? disulf7 B SG CYS 83 B CYS 93 1_555 B SG CYS 184 B CYS 194 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.051 ? disulf ? disulf8 B SG CYS 280 B CYS 290 1_555 B SG CYS 357 B CYS 367 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.077 ? disulf ? disulf9 B SG CYS 300 B CYS 310 1_555 B SG CYS 353 B CYS 363 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.091 ? disulf ? disulf10 B SG CYS 304 B CYS 314 1_555 B SG CYS 351 B CYS 361 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.079 ? disulf ? disulf11 B SG CYS 313 B CYS 323 1_555 B SG CYS 335 B CYS 345 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.095 ? disulf ? disulf12 B SG CYS 315 B CYS 325 1_555 B SG CYS 327 B CYS 337 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.091 ? disulf ? disulf13 C SG CYS 83 C CYS 93 1_555 C SG CYS 184 C CYS 194 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.061 ? disulf ? disulf14 C SG CYS 280 C CYS 290 1_555 C SG CYS 357 C CYS 367 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.752 ? disulf ? disulf15 C SG CYS 300 C CYS 310 1_555 C SG CYS 353 C CYS 363 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.084 ? disulf ? disulf16 C SG CYS 304 C CYS 314 1_555 C SG CYS 351 C CYS 361 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.092 ? disulf ? disulf17 C SG CYS 313 C CYS 323 1_555 C SG CYS 335 C CYS 345 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.071 ? disulf ? disulf18 C SG CYS 315 C CYS 325 1_555 C SG CYS 327 C CYS 337 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.095 ? covale ? covale1 A ND2 ASN 385 A ASN 395 1_555 E C1 NAG . A NAG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.477 ? covale ? covale2 B ND2 ASN 358 B ASN 368 1_555 F C1 NAG . B NAG 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.421 ? covale ? covale3 C ND2 ASN 358 C ASN 368 1_555 I C1 NAG . C NAG 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.427 ? covale ? covale4 C ND2 ASN 385 C ASN 395 1_555 J C1 NAG . C NAG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.453 ? # _chem_comp.formula 'C8 H15 N O6' _chem_comp.formula_weight 221.208 _chem_comp.id NDG _chem_comp.mon_nstd_flag . _chem_comp.name 2-acetamido-2-deoxy-alpha-D-glucopyranose _chem_comp.type 'd-saccharide, alpha linking' _chem_comp.pdbx_synonyms N-acetyl-alpha-D-glucosamine;2-acetamido-2-deoxy-alpha-D-glucose;2-acetamido-2-deoxy-D-glucose;2-acetamido-2-deoxy-glucose;2-(ACETYLAMINO)-2-DEOXY-A-D-GLUCOPYRANOSE # 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 NDG sing 276 n n C1 O5 NDG sing 277 n n C1 O1 NDG sing 278 n n C1 H1 NDG sing 279 n n C2 C3 NDG sing 280 n n C2 N2 NDG sing 281 n n C2 H2 NDG sing 282 n n C3 C4 NDG sing 283 n n C3 O3 NDG sing 284 n n C3 H3 NDG sing 285 n n C4 C5 NDG sing 286 n n C4 O4 NDG sing 287 n n C4 H4 NDG sing 288 n n C5 C6 NDG sing 289 n n C5 O5 NDG sing 290 n n C5 H5 NDG sing 291 n n C6 O6 NDG sing 292 n n C6 H61 NDG sing 293 n n C6 H62 NDG sing 294 n n C7 C8 NDG sing 295 n n C7 O7 NDG doub 296 n n C7 N2 NDG sing 297 n n C8 H81 NDG sing 298 n n C8 H82 NDG sing 299 n n C8 H83 NDG sing 300 n n O3 HO3 NDG sing 301 n n O4 HO4 NDG sing 302 n n O6 HO6 NDG sing 303 n n N2 HN2 NDG sing 304 n n O1 HO1 NDG sing 305 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 NDG DGlcpNAca 'CONDENSED IUPAC CARBOHYDRATE SYMBOL' GMML 1 NDG N-acetyl-a-D-glucopyranosamine 'COMMON NAME' GMML 1 NDG a-D-GlcpNAc 'IUPAC CARBOHYDRATE SYMBOL' PDB-CARE 1 NDG GlcNAc 'SNFG CARBOHYDRATE SYMBOL' GMML 1 # _atom_sites.entry_id 6L6N _atom_sites.fract_transf_matrix[1][1] 0.011955 _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] 0.007007 _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] 0.004505 _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 2 NDG A 1 501 450 NDG NAG . E 3 NAG A 1 502 451 NAG NAG . F 3 NAG B 1 501 450 NAG NAG . G 4 CL B 1 502 2 CL CL . H 5 EDO B 1 503 1 EDO EDO . I 3 NAG C 1 501 450 NAG NAG . J 3 NAG C 1 502 451 NAG NAG . K 4 CL C 1 503 1 CL CL . L 6 HOH A 1 601 39 HOH HOH . L 6 HOH A 2 602 31 HOH HOH . L 6 HOH A 3 603 20 HOH HOH . L 6 HOH A 4 604 17 HOH HOH . L 6 HOH A 5 605 1 HOH HOH . L 6 HOH A 6 606 40 HOH HOH . M 6 HOH B 1 601 15 HOH HOH . M 6 HOH B 2 602 16 HOH HOH . M 6 HOH B 3 603 13 HOH HOH . M 6 HOH B 4 604 29 HOH HOH . M 6 HOH B 5 605 23 HOH HOH . M 6 HOH B 6 606 26 HOH HOH . M 6 HOH B 7 607 21 HOH HOH . M 6 HOH B 8 608 2 HOH HOH . M 6 HOH B 9 609 33 HOH HOH . M 6 HOH B 10 610 41 HOH HOH . M 6 HOH B 11 611 25 HOH HOH . M 6 HOH B 12 612 28 HOH HOH . M 6 HOH B 13 613 14 HOH HOH . M 6 HOH B 14 614 18 HOH HOH . M 6 HOH B 15 615 10 HOH HOH . M 6 HOH B 16 616 36 HOH HOH . M 6 HOH B 17 617 35 HOH HOH . M 6 HOH B 18 618 3 HOH HOH . M 6 HOH B 19 619 12 HOH HOH . M 6 HOH B 20 620 42 HOH HOH . M 6 HOH B 21 621 11 HOH HOH . N 6 HOH C 1 601 19 HOH HOH . N 6 HOH C 2 602 9 HOH HOH . N 6 HOH C 3 603 30 HOH HOH . N 6 HOH C 4 604 24 HOH HOH . N 6 HOH C 5 605 27 HOH HOH . N 6 HOH C 6 606 34 HOH HOH . N 6 HOH C 7 607 22 HOH HOH . N 6 HOH C 8 608 5 HOH HOH . N 6 HOH C 9 609 7 HOH HOH . N 6 HOH C 10 610 43 HOH HOH . N 6 HOH C 11 611 6 HOH HOH . N 6 HOH C 12 612 32 HOH HOH . N 6 HOH C 13 613 4 HOH HOH . N 6 HOH C 14 614 8 HOH HOH . N 6 HOH C 15 615 38 HOH HOH . N 6 HOH C 16 616 37 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 NDG . . . D 2 -19.9 1.304 14.466 1 144.34 ? C1 NDG 501 A 1 HETATM 2 C C2 NDG . . . D 2 -20.595 2.617 14.076 1 148.37 ? C2 NDG 501 A 1 HETATM 3 C C3 NDG . . . D 2 -20.937 2.62 12.578 1 162.72 ? C3 NDG 501 A 1 HETATM 4 C C4 NDG . . . D 2 -19.748 2.201 11.678 1 163.05 ? C4 NDG 501 A 1 HETATM 5 C C5 NDG . . . D 2 -19.047 0.952 12.203 1 151.87 ? C5 NDG 501 A 1 HETATM 6 C C6 NDG . . . D 2 -17.753 0.663 11.427 1 145.4 ? C6 NDG 501 A 1 HETATM 7 C C7 NDG . . . D 2 -22.822 2.453 15.279 1 132.23 ? C7 NDG 501 A 1 HETATM 8 C C8 NDG . . . D 2 -23.864 3.271 16.009 1 117.68 ? C8 NDG 501 A 1 HETATM 9 O O5 NDG . . . D 2 -18.762 1.191 13.586 1 150.65 ? O5 NDG 501 A 1 HETATM 10 O O3 NDG . . . D 2 -21.336 3.967 12.273 1 166.6 ? O3 NDG 501 A 1 HETATM 11 O O4 NDG . . . D 2 -20.127 1.967 10.308 1 152.14 ? O4 NDG 501 A 1 HETATM 12 O O6 NDG . . . D 2 -17.515 -0.75 11.331 1 139.48 ? O6 NDG 501 A 1 HETATM 13 O O7 NDG . . . D 2 -23.023 1.286 15.005 1 132.46 ? O7 NDG 501 A 1 HETATM 14 N N2 NDG . . . D 2 -21.702 3.101 14.925 1 143.66 ? N2 NDG 501 A 1 # _model_server_stats.io_time_ms 0 _model_server_stats.parse_time_ms 11 _model_server_stats.create_model_time_ms 10 _model_server_stats.query_time_ms 280 _model_server_stats.encode_time_ms 4 _model_server_stats.element_count 14 #