data_5K6X # _model_server_result.job_id -lU2oXiRMjyQDTTKl5GuiQ _model_server_result.datetime_utc '2024-11-15 00:21:26' _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 5k6x # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"O","auth_seq_id":501}' # _entry.id 5K6X # _exptl.entry_id 5K6X _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 2 _entity.pdbx_parent_entity_id . _entity.pdbx_mutation ? _entity.pdbx_fragment ? _entity.pdbx_ec ? # _cell.angle_alpha 90 _cell.angle_beta 100.67 _cell.angle_gamma 90 _cell.entry_id 5K6X _cell.length_a 55.11 _cell.length_b 130.01 _cell.length_c 78.39 _cell.Z_PDB 4 _cell.pdbx_unique_axis ? # _symmetry.entry_id 5K6X _symmetry.cell_setting ? _symmetry.Int_Tables_number 4 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 1 21 1' # _pdbx_struct_assembly.method_details PISA _pdbx_struct_assembly.oligomeric_details dimeric _pdbx_struct_assembly.oligomeric_count 2 _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,O,P,Q,R,S,T,U _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 ? 4 E N N ? 4 O N N # loop_ _pdbx_entity_branch.entity_id _pdbx_entity_branch.type 2 oligosaccharide 3 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 FUC NAG C1 O1 . O6 HO6 . sing 2 ? 3 2 1 NAG NAG C1 O1 . O4 HO4 . sing 3 ? 3 3 1 FUC NAG 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 C NAG 1 C 1 NAG A 502 NAG 2 n C FUC 2 C 2 FUC A 503 FUC 3 n D NAG 1 D 1 NAG B 502 NAG 3 n D NAG 2 D 2 NAG B 504 NAG 3 n D FUC 3 D 3 FUC B 503 FUC # 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 33 A CYS 28 1_555 A SG CYS 76 A CYS 71 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.03 ? disulf ? disulf2 A SG CYS 222 A CYS 217 1_555 A SG CYS 269 A CYS 264 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.032 ? disulf ? disulf3 A SG CYS 315 A CYS 310 1_555 A SG CYS 365 A CYS 360 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.032 ? disulf ? disulf4 B SG CYS 33 B CYS 28 1_555 B SG CYS 76 B CYS 71 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.032 ? disulf ? disulf5 B SG CYS 222 B CYS 217 1_555 B SG CYS 269 B CYS 264 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.032 ? disulf ? disulf6 B SG CYS 315 B CYS 310 1_555 B SG CYS 365 B CYS 360 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.031 ? covale ? covale1 A ND2 ASN 178 A ASN 173 1_555 E C1 NAG . A NAG 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.438 ? covale ? covale2 A ND2 ASN 208 A ASN 203 1_555 C C1 NAG . C NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.437 ? covale ? covale3 B ND2 ASN 178 B ASN 173 1_555 O C1 NAG . B NAG 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.442 ? covale ? covale4 B ND2 ASN 208 B ASN 203 1_555 D C1 NAG . D NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.439 ? covale ? covale5 C O6 NAG . C NAG 1 1_555 C C1 FUC . C FUC 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.441 ? covale ? covale6 D O4 NAG . D NAG 1 1_555 D C1 NAG . D NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.441 ? covale ? covale7 D O6 NAG . D NAG 1 1_555 D C1 FUC . D FUC 3 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.44 ? # _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 273 n n C1 O1 NAG sing 274 n n C1 O5 NAG sing 275 n n C1 H1 NAG sing 276 n n C2 C3 NAG sing 277 n n C2 N2 NAG sing 278 n n C2 H2 NAG sing 279 n n C3 C4 NAG sing 280 n n C3 O3 NAG sing 281 n n C3 H3 NAG sing 282 n n C4 C5 NAG sing 283 n n C4 O4 NAG sing 284 n n C4 H4 NAG sing 285 n n C5 C6 NAG sing 286 n n C5 O5 NAG sing 287 n n C5 H5 NAG sing 288 n n C6 O6 NAG sing 289 n n C6 H61 NAG sing 290 n n C6 H62 NAG sing 291 n n C7 C8 NAG sing 292 n n C7 N2 NAG sing 293 n n C7 O7 NAG doub 294 n n C8 H81 NAG sing 295 n n C8 H82 NAG sing 296 n n C8 H83 NAG sing 297 n n N2 HN2 NAG sing 298 n n O1 HO1 NAG sing 299 n n O3 HO3 NAG sing 300 n n O4 HO4 NAG sing 301 n n O6 HO6 NAG sing 302 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 5K6X _atom_sites.fract_transf_matrix[1][1] 0.018146 _atom_sites.fract_transf_matrix[1][2] 0 _atom_sites.fract_transf_matrix[1][3] 0.003419 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.007692 _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] 0.012981 _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 4 NAG A 1 501 501 NAG NAG . F 5 SO4 A 1 504 1 SO4 SO4 . G 5 SO4 A 1 505 2 SO4 SO4 . H 5 SO4 A 1 506 3 SO4 SO4 . I 5 SO4 A 1 507 4 SO4 SO4 . J 5 SO4 A 1 508 5 SO4 SO4 . K 5 SO4 A 1 509 6 SO4 SO4 . L 5 SO4 A 1 510 9 SO4 SO4 . M 5 SO4 A 1 511 10 SO4 SO4 . N 6 GOL A 1 512 1 GOL GOL . O 4 NAG B 1 501 501 NAG NAG . P 5 SO4 B 1 505 7 SO4 SO4 . Q 5 SO4 B 1 506 8 SO4 SO4 . R 5 SO4 B 1 507 11 SO4 SO4 . S 5 SO4 B 1 508 12 SO4 SO4 . T 7 HOH A 1 601 36 HOH HOH . T 7 HOH A 2 602 10 HOH HOH . T 7 HOH A 3 603 21 HOH HOH . T 7 HOH A 4 604 25 HOH HOH . T 7 HOH A 5 605 16 HOH HOH . T 7 HOH A 6 606 26 HOH HOH . T 7 HOH A 7 607 19 HOH HOH . T 7 HOH A 8 608 34 HOH HOH . T 7 HOH A 9 609 27 HOH HOH . T 7 HOH A 10 610 18 HOH HOH . T 7 HOH A 11 611 9 HOH HOH . T 7 HOH A 12 612 15 HOH HOH . U 7 HOH B 1 601 37 HOH HOH . U 7 HOH B 2 602 30 HOH HOH . U 7 HOH B 3 603 14 HOH HOH . U 7 HOH B 4 604 24 HOH HOH . U 7 HOH B 5 605 1 HOH HOH . U 7 HOH B 6 606 22 HOH HOH . U 7 HOH B 7 607 3 HOH HOH . U 7 HOH B 8 608 2 HOH HOH . U 7 HOH B 9 609 17 HOH HOH . U 7 HOH B 10 610 12 HOH HOH . U 7 HOH B 11 611 23 HOH HOH . U 7 HOH B 12 612 11 HOH HOH . U 7 HOH B 13 613 32 HOH HOH . U 7 HOH B 14 614 29 HOH HOH . U 7 HOH B 15 615 5 HOH HOH . U 7 HOH B 16 616 8 HOH HOH . U 7 HOH B 17 617 4 HOH HOH . U 7 HOH B 18 618 6 HOH HOH . U 7 HOH B 19 619 28 HOH HOH . U 7 HOH B 20 620 33 HOH HOH . U 7 HOH B 21 621 20 HOH HOH . U 7 HOH B 22 622 35 HOH HOH . U 7 HOH B 23 623 31 HOH HOH . U 7 HOH B 24 624 7 HOH HOH . U 7 HOH B 25 625 13 HOH HOH . U 7 HOH B 26 626 38 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 . . . O 4 -7.716 21.141 26.842 1 84.19 ? C1 NAG 501 B 1 HETATM 2 C C2 NAG . . . O 4 -7.655 22.627 27.193 1 88.73 ? C2 NAG 501 B 1 HETATM 3 C C3 NAG . . . O 4 -7.102 22.806 28.608 1 88.74 ? C3 NAG 501 B 1 HETATM 4 C C4 NAG . . . O 4 -7.895 21.974 29.604 1 93.28 ? C4 NAG 501 B 1 HETATM 5 C C5 NAG . . . O 4 -7.928 20.517 29.153 1 91.25 ? C5 NAG 501 B 1 HETATM 6 C C6 NAG . . . O 4 -8.795 19.645 30.031 1 68.83 ? C6 NAG 501 B 1 HETATM 7 C C7 NAG . . . O 4 -7.229 24.538 25.708 1 93.26 ? C7 NAG 501 B 1 HETATM 8 C C8 NAG . . . O 4 -8.556 25.073 26.162 1 91.23 ? C8 NAG 501 B 1 HETATM 9 N N2 NAG . . . O 4 -6.858 23.364 26.236 1 80.17 ? N2 NAG 501 B 1 HETATM 10 O O3 NAG . . . O 4 -7.162 24.184 28.966 1 83.89 ? O3 NAG 501 B 1 HETATM 11 O O4 NAG . . . O 4 -7.302 22.056 30.895 1 96.1 ? O4 NAG 501 B 1 HETATM 12 O O5 NAG . . . O 4 -8.473 20.433 27.827 1 84.31 ? O5 NAG 501 B 1 HETATM 13 O O6 NAG . . . O 4 -8.275 18.327 30.133 1 89.86 ? O6 NAG 501 B 1 HETATM 14 O O7 NAG . . . O 4 -6.529 25.138 24.9 1 107.09 ? O7 NAG 501 B 1 # _model_server_stats.io_time_ms 23 _model_server_stats.parse_time_ms 18 _model_server_stats.create_model_time_ms 33 _model_server_stats.query_time_ms 259 _model_server_stats.encode_time_ms 8 _model_server_stats.element_count 14 #