data_5K1V # _model_server_result.job_id XhGNU-t54dSZPjNtpEm9rg _model_server_result.datetime_utc '2024-12-25 19:18:26' _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 5k1v # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"T","auth_seq_id":1011}' # _entry.id 5K1V # _exptl.entry_id 5K1V _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 221.208 _entity.id 6 _entity.src_method man _entity.type non-polymer _entity.pdbx_description 2-acetamido-2-deoxy-beta-D-glucopyranose _entity.pdbx_number_of_molecules 12 _entity.pdbx_parent_entity_id . _entity.pdbx_mutation ? _entity.pdbx_fragment ? _entity.pdbx_ec ? # _cell.angle_alpha 90 _cell.angle_beta 90.15 _cell.angle_gamma 90 _cell.entry_id 5K1V _cell.length_a 74.403 _cell.length_b 135.171 _cell.length_c 127.489 _cell.Z_PDB 4 _cell.pdbx_unique_axis ? # _symmetry.entry_id 5K1V _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 ? monomeric 1 author_defined_assembly 1 ? monomeric 1 author_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,F,G,H,I,J,K,L,M,U 1 1 B,E,N,O,P,Q,R,S,T,V 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 ? 6 H N N ? 6 I N N ? 6 J N N ? 6 K N N ? 6 L N N ? 6 M N N ? 6 O N N ? 6 P N N ? 6 Q N N ? 6 R N N ? 6 S N N ? 6 T 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 NAG NAG C1 O1 . O4 HO4 . sing 2 ? 3 2 1 NAG NAG C1 O1 . O4 HO4 . sing 3 ? 3 3 2 MAN NAG C1 O1 . O4 HO4 . sing 4 ? 3 4 3 MAN MAN C1 O1 . O4 HO4 . 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 1003 NAG 2 n C NAG 2 C 2 NAG A 1004 NAG 2 n D NAG 1 D 1 NAG A 1005 NAG 2 n D NAG 2 D 2 NAG A 1006 NAG 3 n E NAG 1 E 1 NAG B 1003 NAG 3 n E NAG 2 E 2 NAG B 1004 NAG 3 n E MAN 3 E 3 MAN B 1005 MAN 3 n E MAN 4 E 4 MAN B 1006 MAN # 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 421 A CYS 421 1_555 A SG CYS 460 A CYS 460 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.024 ? disulf ? disulf2 A SG CYS 503 A CYS 503 1_555 A SG CYS 514 A CYS 514 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.038 ? disulf ? disulf3 B SG CYS 421 B CYS 421 1_555 B SG CYS 460 B CYS 460 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.038 ? disulf ? disulf4 B SG CYS 759 B CYS 759 1_555 B SG CYS 766 B CYS 766 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.028 ? covale ? covale1 A ND2 ASN 85 A ASN 85 1_555 C C1 NAG . C NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.435 ? covale ? covale2 A ND2 ASN 103 A ASN 103 1_555 K C1 NAG . A NAG 1010 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.449 ? covale ? covale3 A ND2 ASN 219 A ASN 219 1_555 D C1 NAG . D NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.438 ? covale ? covale4 A ND2 ASN 294 A ASN 294 1_555 J C1 NAG . A NAG 1009 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.459 ? covale ? covale5 A ND2 ASN 405 A ASN 405 1_555 H C1 NAG . A NAG 1007 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.442 ? covale ? covale6 A ND2 ASN 431 A ASN 431 1_555 L C1 NAG . A NAG 1011 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.443 ? covale ? covale7 A ND2 ASN 650 A ASN 650 1_555 I C1 NAG . A NAG 1008 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.454 ? covale ? covale8 A ND2 ASN 714 A ASN 714 1_555 M C1 NAG . A NAG 1012 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.447 ? covale ? covale9 B ND2 ASN 85 B ASN 85 1_555 E C1 NAG . E NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.406 ? covale ? covale10 B ND2 ASN 103 B ASN 103 1_555 O C1 NAG . B NAG 1002 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.444 ? covale ? covale11 B ND2 ASN 219 B ASN 219 1_555 P C1 NAG . B NAG 1007 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.457 ? covale ? covale12 B ND2 ASN 294 B ASN 294 1_555 T C1 NAG . B NAG 1011 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.454 ? covale ? covale13 B ND2 ASN 405 B ASN 405 1_555 R C1 NAG . B NAG 1009 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.444 ? covale ? covale14 B ND2 ASN 431 B ASN 431 1_555 S C1 NAG . B NAG 1010 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.436 ? covale ? covale15 B ND2 ASN 650 B ASN 650 1_555 Q C1 NAG . B NAG 1008 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.449 ? covale ? covale16 C O4 NAG . C NAG 1 1_555 C C1 NAG . C NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.445 ? covale ? covale17 D O4 NAG . D NAG 1 1_555 D C1 NAG . D NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.416 ? covale ? covale18 E O4 NAG . E NAG 1 1_555 E C1 NAG . E NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.442 ? covale ? covale19 E O4 NAG . E NAG 2 1_555 E C1 MAN . E MAN 3 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.461 ? covale ? covale20 E O4 MAN . E MAN 3 1_555 E C1 MAN . E MAN 4 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.444 ? metalc ? metalc1 A NE2 HIS 370 A HIS 370 1_555 F ZN ZN . A ZN 1001 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.01 ? metalc ? metalc2 A NE2 HIS 374 A HIS 374 1_555 F ZN ZN . A ZN 1001 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.073 ? metalc ? metalc3 A OE1 GLU 393 A GLU 393 1_555 F ZN ZN . A ZN 1001 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.91 ? metalc ? metalc4 A OE2 GLU 393 A GLU 393 1_555 F ZN ZN . A ZN 1001 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.47 ? metalc ? metalc5 F ZN ZN . A ZN 1001 1_555 G O1 6PX . A 6PX 1002 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.999 ? metalc ? metalc6 B NE2 HIS 370 B HIS 370 1_555 N ZN ZN . B ZN 1001 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.1 ? metalc ? metalc7 B NE2 HIS 374 B HIS 374 1_555 N ZN ZN . B ZN 1001 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.072 ? metalc ? metalc8 B OE1 GLU 393 B GLU 393 1_555 N ZN ZN . B ZN 1001 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.956 ? metalc ? metalc9 N ZN ZN . B ZN 1001 1_555 V O HOH . B HOH 1114 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.162 ? # _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 328 n n C1 O1 NAG sing 329 n n C1 O5 NAG sing 330 n n C1 H1 NAG sing 331 n n C2 C3 NAG sing 332 n n C2 N2 NAG sing 333 n n C2 H2 NAG sing 334 n n C3 C4 NAG sing 335 n n C3 O3 NAG sing 336 n n C3 H3 NAG sing 337 n n C4 C5 NAG sing 338 n n C4 O4 NAG sing 339 n n C4 H4 NAG sing 340 n n C5 C6 NAG sing 341 n n C5 O5 NAG sing 342 n n C5 H5 NAG sing 343 n n C6 O6 NAG sing 344 n n C6 H61 NAG sing 345 n n C6 H62 NAG sing 346 n n C7 C8 NAG sing 347 n n C7 N2 NAG sing 348 n n C7 O7 NAG doub 349 n n C8 H81 NAG sing 350 n n C8 H82 NAG sing 351 n n C8 H83 NAG sing 352 n n N2 HN2 NAG sing 353 n n O1 HO1 NAG sing 354 n n O3 HO3 NAG sing 355 n n O4 HO4 NAG sing 356 n n O6 HO6 NAG sing 357 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 5K1V _atom_sites.fract_transf_matrix[1][1] 0.01344 _atom_sites.fract_transf_matrix[1][2] 0 _atom_sites.fract_transf_matrix[1][3] 0.000035 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.007398 _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] 0.007844 _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 F 4 ZN A 1 1001 1001 ZN ZN . G 5 6PX A 1 1002 1002 6PX P53 . H 6 NAG A 1 1007 1007 NAG NAG . I 6 NAG A 1 1008 1008 NAG NAG . J 6 NAG A 1 1009 1009 NAG NAG . K 6 NAG A 1 1010 1010 NAG NAG . L 6 NAG A 1 1011 1011 NAG NAG . M 6 NAG A 1 1012 1012 NAG NAG . N 4 ZN B 1 1001 1001 ZN ZN . O 6 NAG B 1 1002 1002 NAG NAG . P 6 NAG B 1 1007 1007 NAG NAG . Q 6 NAG B 1 1008 1008 NAG NAG . R 6 NAG B 1 1009 1009 NAG NAG . S 6 NAG B 1 1010 1010 NAG NAG . T 6 NAG B 1 1011 1011 NAG NAG . U 7 HOH A 1 1101 1 HOH HOH . U 7 HOH A 2 1102 2 HOH HOH . U 7 HOH A 3 1103 8 HOH HOH . U 7 HOH A 4 1104 3 HOH HOH . U 7 HOH A 5 1105 4 HOH HOH . U 7 HOH A 6 1106 5 HOH HOH . U 7 HOH A 7 1107 11 HOH HOH . U 7 HOH A 8 1108 10 HOH HOH . U 7 HOH A 9 1109 6 HOH HOH . U 7 HOH A 10 1110 9 HOH HOH . U 7 HOH A 11 1111 7 HOH HOH . U 7 HOH A 12 1112 15 HOH HOH . U 7 HOH A 13 1113 13 HOH HOH . U 7 HOH A 14 1114 12 HOH HOH . U 7 HOH A 15 1115 14 HOH HOH . U 7 HOH A 16 1116 17 HOH HOH . U 7 HOH A 17 1117 19 HOH HOH . U 7 HOH A 18 1118 18 HOH HOH . U 7 HOH A 19 1119 45 HOH HOH . U 7 HOH A 20 1120 42 HOH HOH . U 7 HOH A 21 1121 22 HOH HOH . U 7 HOH A 22 1122 21 HOH HOH . U 7 HOH A 23 1123 44 HOH HOH . U 7 HOH A 24 1124 24 HOH HOH . U 7 HOH A 25 1125 16 HOH HOH . U 7 HOH A 26 1126 20 HOH HOH . U 7 HOH A 27 1127 23 HOH HOH . U 7 HOH A 28 1128 43 HOH HOH . U 7 HOH A 29 1129 25 HOH HOH . U 7 HOH A 30 1130 26 HOH HOH . V 7 HOH B 1 1101 27 HOH HOH . V 7 HOH B 2 1102 41 HOH HOH . V 7 HOH B 3 1103 28 HOH HOH . V 7 HOH B 4 1104 30 HOH HOH . V 7 HOH B 5 1105 29 HOH HOH . V 7 HOH B 6 1106 31 HOH HOH . V 7 HOH B 7 1107 32 HOH HOH . V 7 HOH B 8 1108 40 HOH HOH . V 7 HOH B 9 1109 33 HOH HOH . V 7 HOH B 10 1110 35 HOH HOH . V 7 HOH B 11 1111 34 HOH HOH . V 7 HOH B 12 1112 37 HOH HOH . V 7 HOH B 13 1113 38 HOH HOH . V 7 HOH B 14 1114 39 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 . . . T 6 -1.537 18.951 37.117 1 117.29 ? C1 NAG 1011 B 1 HETATM 2 C C2 NAG . . . T 6 -2.785 18.134 36.691 1 126.23 ? C2 NAG 1011 B 1 HETATM 3 C C3 NAG . . . T 6 -3.987 19.04 36.433 1 123.87 ? C3 NAG 1011 B 1 HETATM 4 C C4 NAG . . . T 6 -4.058 20.141 37.478 1 118.82 ? C4 NAG 1011 B 1 HETATM 5 C C5 NAG . . . T 6 -2.909 21.111 37.246 1 118.11 ? C5 NAG 1011 B 1 HETATM 6 C C6 NAG . . . T 6 -2.524 21.9 38.477 1 119.95 ? C6 NAG 1011 B 1 HETATM 7 C C7 NAG . . . T 6 -1.793 16.177 35.576 1 132.05 ? C7 NAG 1011 B 1 HETATM 8 C C8 NAG . . . T 6 -1.581 15.475 34.264 1 124.62 ? C8 NAG 1011 B 1 HETATM 9 N N2 NAG . . . T 6 -2.491 17.318 35.523 1 137.25 ? N2 NAG 1011 B 1 HETATM 10 O O3 NAG . . . T 6 -5.18 18.263 36.474 1 134 ? O3 NAG 1011 B 1 HETATM 11 O O4 NAG . . . T 6 -5.296 20.839 37.382 1 103.64 ? O4 NAG 1011 B 1 HETATM 12 O O5 NAG . . . T 6 -1.734 20.421 36.78 1 116.1 ? O5 NAG 1011 B 1 HETATM 13 O O6 NAG . . . T 6 -2.891 23.267 38.346 1 112.3 ? O6 NAG 1011 B 1 HETATM 14 O O7 NAG . . . T 6 -1.354 15.729 36.636 1 120.36 ? O7 NAG 1011 B 1 # _model_server_stats.io_time_ms 17 _model_server_stats.parse_time_ms 29 _model_server_stats.create_model_time_ms 26 _model_server_stats.query_time_ms 464 _model_server_stats.encode_time_ms 3 _model_server_stats.element_count 14 #