data_5EDK # _model_server_result.job_id fOGKu_of81MnUCIeqnYs1w _model_server_result.datetime_utc '2024-11-19 09:36:17' _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 5edk # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"C","auth_seq_id":601}' # _entry.id 5EDK # _exptl.entry_id 5EDK _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 221.208 _entity.id 3 _entity.src_method man _entity.type non-polymer _entity.pdbx_description 2-acetamido-2-deoxy-beta-D-glucopyranose _entity.pdbx_number_of_molecules 2 _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 5EDK _cell.length_a 84.192 _cell.length_b 84.192 _cell.length_c 346.427 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 5EDK _symmetry.cell_setting ? _symmetry.Int_Tables_number 92 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 41 21 2' # _pdbx_struct_assembly.method_details PISA _pdbx_struct_assembly.oligomeric_details monomeric _pdbx_struct_assembly.oligomeric_count 1 _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 _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 # loop_ _struct_asym.details _struct_asym.entity_id _struct_asym.id _struct_asym.pdbx_modified _struct_asym.pdbx_blank_PDB_chainid_flag ? 3 C N N ? 3 D N N # _pdbx_entity_branch.entity_id 2 _pdbx_entity_branch.type oligosaccharide # _pdbx_entity_branch_link.link_id 1 _pdbx_entity_branch_link.details ? _pdbx_entity_branch_link.entity_id 2 _pdbx_entity_branch_link.entity_branch_list_num_1 2 _pdbx_entity_branch_link.entity_branch_list_num_2 1 _pdbx_entity_branch_link.comp_id_1 NAG _pdbx_entity_branch_link.comp_id_2 NAG _pdbx_entity_branch_link.atom_id_1 C1 _pdbx_entity_branch_link.leaving_atom_id_1 O1 _pdbx_entity_branch_link.atom_stereo_config_1 . _pdbx_entity_branch_link.atom_id_2 O4 _pdbx_entity_branch_link.leaving_atom_id_2 HO4 _pdbx_entity_branch_link.atom_stereo_config_2 . _pdbx_entity_branch_link.value_order 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 B NAG 1 B 1 NAG A 602 NAG 2 n B NAG 2 B 2 NAG A 603 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 17 A CYS 17 1_555 A SG CYS 22 A CYS 22 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.053 ? disulf ? disulf2 A SG CYS 47 A CYS 47 1_555 A SG CYS 60 A CYS 60 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.041 ? disulf ? disulf3 A SG CYS 65 A CYS 65 1_555 A SG CYS 143 A CYS 143 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.032 ? disulf ? disulf4 A SG CYS 86 A CYS 86 1_555 A SG CYS 126 A CYS 126 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.023 ? disulf ? disulf5 A SG CYS 114 A CYS 114 1_555 A SG CYS 138 A CYS 138 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.026 ? disulf ? disulf6 A SG CYS 148 A CYS 148 1_555 A SG CYS 226 A CYS 226 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.038 ? disulf ? disulf7 A SG CYS 169 A CYS 169 1_555 A SG CYS 209 A CYS 209 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.031 ? disulf ? disulf8 A SG CYS 197 A CYS 197 1_555 A SG CYS 221 A CYS 221 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.029 ? disulf ? disulf9 A SG CYS 271 A CYS 271 1_555 A SG CYS 417 A CYS 417 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.034 ? disulf ? disulf10 A SG CYS 326 A CYS 326 1_555 A SG CYS 342 A CYS 342 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.03 ? disulf ? disulf11 A SG CYS 471 A CYS 471 1_555 A SG CYS 485 A CYS 485 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.044 ? disulf ? disulf12 A SG CYS 499 A CYS 499 1_555 A SG CYS 529 A CYS 529 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.029 ? covale ? covale1 A C CGU 6 A CGU 6 1_555 A N CGU 7 A CGU 7 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.326 ? covale ? covale2 A C CGU 7 A CGU 7 1_555 A N VAL 8 A VAL 8 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.334 ? covale ? covale3 A C LEU 13 A LEU 13 1_555 A N CGU 14 A CGU 14 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.333 ? covale ? covale4 A C CGU 14 A CGU 14 1_555 A N ARG 15 A ARG 15 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.335 ? covale ? covale5 A C ARG 15 A ARG 15 1_555 A N CGU 16 A CGU 16 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.331 ? covale ? covale6 A C CGU 16 A CGU 16 1_555 A N CYS 17 A CYS 17 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.333 ? covale ? covale7 A C VAL 18 A VAL 18 1_555 A N CGU 19 A CGU 19 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.341 ? covale ? covale8 A C CGU 19 A CGU 19 1_555 A N CGU 20 A CGU 20 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.329 ? covale ? covale9 A C CGU 20 A CGU 20 1_555 A N THR 21 A THR 21 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.332 ? covale ? covale10 A C TYR 24 A TYR 24 1_555 A N CGU 25 A CGU 25 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.336 ? covale ? covale11 A C CGU 25 A CGU 25 1_555 A N CGU 26 A CGU 26 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.338 ? covale ? covale12 A C CGU 26 A CGU 26 1_555 A N ALA 27 A ALA 27 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.331 ? covale ? covale13 A C PHE 28 A PHE 28 1_555 A N CGU 29 A CGU 29 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.335 ? covale ? covale14 A C CGU 29 A CGU 29 1_555 A N ALA 30 A ALA 30 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.333 ? covale ? covale15 A C LEU 31 A LEU 31 1_555 A N CGU 32 A CGU 32 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.335 ? covale ? covale16 A C CGU 32 A CGU 32 1_555 A N SER 33 A SER 33 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.339 ? covale ? covale17 A ND2 ASN 78 A ASN 78 1_555 B C1 NAG . B NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.433 ? covale ? covale18 A ND2 ASN 100 A ASN 100 1_555 D C1 NAG . A NAG 604 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.448 ? covale ? covale19 A ND2 ASN 351 A ASN 351 1_555 C C1 NAG . A NAG 601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.444 ? covale ? covale20 B O4 NAG . B NAG 1 1_555 B C1 NAG . B NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.443 ? metalc ? metalc1 A OE11 CGU 16 A CGU 16 1_555 F MG MG . A MG 606 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.48 ? metalc ? metalc2 A OE11 CGU 19 A CGU 19 1_555 E MG MG . A MG 605 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.132 ? metalc ? metalc3 A OE21 CGU 19 A CGU 19 1_555 E MG MG . A MG 605 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.266 ? metalc ? metalc4 A OE22 CGU 20 A CGU 20 1_555 H MG MG . A MG 608 8_665 ? ? ? ? ? ? ? ? ? ? ? ? 1.925 ? metalc ? metalc5 A OE22 CGU 25 A CGU 25 1_555 G MG MG . A MG 607 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.512 ? metalc ? metalc6 A OE22 CGU 26 A CGU 26 1_555 F MG MG . A MG 606 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.292 ? metalc ? metalc7 A OE11 CGU 26 A CGU 26 1_555 H MG MG . A MG 608 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.633 ? metalc ? metalc8 A OE12 CGU 26 A CGU 26 1_555 H MG MG . A MG 608 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.984 ? metalc ? metalc9 A OE22 CGU 29 A CGU 29 1_555 G MG MG . A MG 607 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.103 ? # _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 256 n n C1 O1 NAG sing 257 n n C1 O5 NAG sing 258 n n C1 H1 NAG sing 259 n n C2 C3 NAG sing 260 n n C2 N2 NAG sing 261 n n C2 H2 NAG sing 262 n n C3 C4 NAG sing 263 n n C3 O3 NAG sing 264 n n C3 H3 NAG sing 265 n n C4 C5 NAG sing 266 n n C4 O4 NAG sing 267 n n C4 H4 NAG sing 268 n n C5 C6 NAG sing 269 n n C5 O5 NAG sing 270 n n C5 H5 NAG sing 271 n n C6 O6 NAG sing 272 n n C6 H61 NAG sing 273 n n C6 H62 NAG sing 274 n n C7 C8 NAG sing 275 n n C7 N2 NAG sing 276 n n C7 O7 NAG doub 277 n n C8 H81 NAG sing 278 n n C8 H82 NAG sing 279 n n C8 H83 NAG sing 280 n n N2 HN2 NAG sing 281 n n O1 HO1 NAG sing 282 n n O3 HO3 NAG sing 283 n n O4 HO4 NAG sing 284 n n O6 HO6 NAG sing 285 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 5EDK _atom_sites.fract_transf_matrix[1][1] 0.011878 _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] 0.011878 _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] 0.002887 _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 3 NAG A 1 601 601 NAG NAG . D 3 NAG A 1 604 604 NAG NAG . E 4 MG A 1 605 701 MG MG . F 4 MG A 1 606 702 MG MG . G 4 MG A 1 607 703 MG MG . H 4 MG A 1 608 704 MG MG . # 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 . . . C 3 -1.158 38.024 24.706 1 82.4 ? C1 NAG 601 A 1 HETATM 2 C C2 NAG . . . C 3 -0.945 38.174 26.211 1 83.79 ? C2 NAG 601 A 1 HETATM 3 C C3 NAG . . . C 3 -2.115 37.644 27.054 1 83.75 ? C3 NAG 601 A 1 HETATM 4 C C4 NAG . . . C 3 -3.179 36.831 26.295 1 82.04 ? C4 NAG 601 A 1 HETATM 5 C C5 NAG . . . C 3 -3.386 37.22 24.824 1 81.24 ? C5 NAG 601 A 1 HETATM 6 C C6 NAG . . . C 3 -4.839 37.61 24.536 1 79.22 ? C6 NAG 601 A 1 HETATM 7 C C7 NAG . . . C 3 1.115 37.992 27.544 1 87.06 ? C7 NAG 601 A 1 HETATM 8 C C8 NAG . . . C 3 2.319 37.143 27.835 1 86.69 ? C8 NAG 601 A 1 HETATM 9 N N2 NAG . . . C 3 0.279 37.502 26.624 1 85.82 ? N2 NAG 601 A 1 HETATM 10 O O3 NAG . . . C 3 -2.724 38.72 27.744 1 84.36 ? O3 NAG 601 A 1 HETATM 11 O O4 NAG . . . C 3 -2.833 35.459 26.332 1 80.15 ? O4 NAG 601 A 1 HETATM 12 O O5 NAG . . . C 3 -2.522 38.265 24.422 1 82.16 ? O5 NAG 601 A 1 HETATM 13 O O6 NAG . . . C 3 -5.136 37.381 23.175 1 75.29 ? O6 NAG 601 A 1 HETATM 14 O O7 NAG . . . C 3 0.949 39.062 28.135 1 87.8 ? O7 NAG 601 A 1 # _model_server_stats.io_time_ms 10 _model_server_stats.parse_time_ms 26 _model_server_stats.create_model_time_ms 6 _model_server_stats.query_time_ms 267 _model_server_stats.encode_time_ms 9 _model_server_stats.element_count 14 #