data_2NY6 # _model_server_result.job_id mKVgXH7ius_59m5o_hFUjg _model_server_result.datetime_utc '2024-11-24 16:08:40' _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 2ny6 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"L","auth_seq_id":886}' # _entry.id 2NY6 # _exptl.entry_id 2NY6 _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 221.208 _entity.id 6 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description 2-acetamido-2-deoxy-beta-D-glucopyranose _entity.pdbx_number_of_molecules 8 _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 2NY6 _cell.length_a 72.31 _cell.length_b 87.018 _cell.length_c 196.078 _cell.Z_PDB 4 _cell.pdbx_unique_axis ? # _symmetry.entry_id 2NY6 _symmetry.cell_setting ? _symmetry.Int_Tables_number 17 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 2 2 21' # _pdbx_struct_assembly.method_details ? _pdbx_struct_assembly.oligomeric_details tetrameric _pdbx_struct_assembly.oligomeric_count 4 _pdbx_struct_assembly.details author_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 _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 ? 6 F N N ? 6 G N N ? 6 H N N ? 6 I N N ? 6 J N N ? 6 K N N ? 6 L N N ? 6 M N N # _pdbx_entity_branch.entity_id 5 _pdbx_entity_branch.type oligosaccharide # _pdbx_entity_branch_link.link_id 1 _pdbx_entity_branch_link.details ? _pdbx_entity_branch_link.entity_id 5 _pdbx_entity_branch_link.entity_branch_list_num_1 1 _pdbx_entity_branch_link.entity_branch_list_num_2 2 _pdbx_entity_branch_link.comp_id_1 GLC _pdbx_entity_branch_link.comp_id_2 FRU _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 O2 _pdbx_entity_branch_link.leaving_atom_id_2 HO2 _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 5 n E GLC 1 E 1 GLC ? 4000 SUC 5 n E FRU 2 E 2 FRU ? 4000 SUC # 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 14 A CYS 96 1_555 A SG CYS 129 A CYS 275 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.046 ? disulf ? disulf2 A SG CYS 27 A CYS 109 1_555 A SG CYS 253 A CYS 428 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.051 ? disulf ? disulf3 A SG CYS 37 A CYS 119 1_555 A SG CYS 59 A CYS 205 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.054 ? disulf ? disulf4 A SG CYS 41 A CYS 123 1_555 A SG CYS 256 A CYS 431 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.055 ? disulf ? disulf5 A SG CYS 44 A CYS 126 1_555 A SG CYS 50 A CYS 196 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.041 ? disulf ? disulf6 A SG CYS 72 A CYS 218 1_555 A SG CYS 101 A CYS 247 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.039 ? disulf ? disulf7 A SG CYS 82 A CYS 228 1_555 A SG CYS 93 A CYS 239 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.051 ? disulf ? disulf8 A SG CYS 150 A CYS 296 1_555 A SG CYS 156 A CYS 331 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.04 ? disulf ? disulf9 A SG CYS 203 A CYS 378 1_555 A SG CYS 270 A CYS 445 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.055 ? disulf ? disulf10 A SG CYS 210 A CYS 385 1_555 A SG CYS 243 A CYS 418 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.041 ? disulf ? disulf11 B SG CYS 17 B CYS 1016 1_555 B SG CYS 85 B CYS 1084 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.036 ? disulf ? disulf12 B SG CYS 131 B CYS 1130 1_555 B SG CYS 160 B CYS 1159 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.048 ? disulf ? disulf13 C SG CYS 23 C CYS 2023 1_555 C SG CYS 88 C CYS 2088 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.071 ? disulf ? disulf14 C SG CYS 136 C CYS 2136 1_555 C SG CYS 196 C CYS 2196 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.045 ? disulf ? disulf15 D SG CYS 22 D CYS 3022 1_555 D SG CYS 96 D CYS 3096 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.059 ? disulf ? disulf16 D SG CYS 155 D CYS 3155 1_555 D SG CYS 211 D CYS 3211 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.042 ? covale ? covale1 A ND2 ASN 88 A ASN 234 1_555 F C1 NAG . A NAG 734 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.438 ? covale ? covale2 A ND2 ASN 116 A ASN 262 1_555 G C1 NAG . A NAG 762 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.444 ? covale ? covale3 A ND2 ASN 130 A ASN 276 1_555 H C1 NAG . A NAG 776 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.453 ? covale ? covale4 A ND2 ASN 143 A ASN 289 1_555 I C1 NAG . A NAG 789 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.441 ? covale ? covale5 A ND2 ASN 149 A ASN 295 1_555 J C1 NAG . A NAG 795 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.437 ? covale ? covale6 A ND2 ASN 164 A ASN 339 1_555 K C1 NAG . A NAG 839 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.448 ? covale ? covale7 A ND2 ASN 211 A ASN 386 1_555 L C1 NAG . A NAG 886 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.426 ? covale ? covale8 A ND2 ASN 273 A ASN 448 1_555 M C1 NAG . A NAG 948 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.446 ? covale ? covale9 E C1 GLC . E GLC 1 1_555 E O2 FRU . E FRU 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.417 sing # _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 285 n n C1 O1 NAG sing 286 n n C1 O5 NAG sing 287 n n C1 H1 NAG sing 288 n n C2 C3 NAG sing 289 n n C2 N2 NAG sing 290 n n C2 H2 NAG sing 291 n n C3 C4 NAG sing 292 n n C3 O3 NAG sing 293 n n C3 H3 NAG sing 294 n n C4 C5 NAG sing 295 n n C4 O4 NAG sing 296 n n C4 H4 NAG sing 297 n n C5 C6 NAG sing 298 n n C5 O5 NAG sing 299 n n C5 H5 NAG sing 300 n n C6 O6 NAG sing 301 n n C6 H61 NAG sing 302 n n C6 H62 NAG sing 303 n n C7 C8 NAG sing 304 n n C7 N2 NAG sing 305 n n C7 O7 NAG doub 306 n n C8 H81 NAG sing 307 n n C8 H82 NAG sing 308 n n C8 H83 NAG sing 309 n n N2 HN2 NAG sing 310 n n O1 HO1 NAG sing 311 n n O3 HO3 NAG sing 312 n n O4 HO4 NAG sing 313 n n O6 HO6 NAG sing 314 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 2NY6 _atom_sites.fract_transf_matrix[1][1] 0.013829 _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] 0.011492 _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] 0.0051 _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 6 NAG A 1 734 734 NAG NAG . G 6 NAG A 1 762 762 NAG NAG . H 6 NAG A 1 776 776 NAG NAG . I 6 NAG A 1 789 789 NAG NAG . J 6 NAG A 1 795 795 NAG NAG . K 6 NAG A 1 839 839 NAG NAG . L 6 NAG A 1 886 886 NAG NAG . M 6 NAG A 1 948 948 NAG NAG . N 7 HOH A 1 949 4 HOH HOH . N 7 HOH A 2 950 6 HOH HOH . N 7 HOH A 3 951 7 HOH HOH . N 7 HOH A 4 952 9 HOH HOH . N 7 HOH A 5 953 10 HOH HOH . N 7 HOH A 6 954 15 HOH HOH . N 7 HOH A 7 955 19 HOH HOH . N 7 HOH A 8 956 20 HOH HOH . N 7 HOH A 9 957 21 HOH HOH . N 7 HOH A 10 958 22 HOH HOH . N 7 HOH A 11 959 24 HOH HOH . N 7 HOH A 12 960 26 HOH HOH . N 7 HOH A 13 961 28 HOH HOH . N 7 HOH A 14 962 30 HOH HOH . N 7 HOH A 15 963 32 HOH HOH . N 7 HOH A 16 964 34 HOH HOH . N 7 HOH A 17 965 35 HOH HOH . N 7 HOH A 18 966 37 HOH HOH . N 7 HOH A 19 967 40 HOH HOH . N 7 HOH A 20 968 44 HOH HOH . N 7 HOH A 21 969 45 HOH HOH . N 7 HOH A 22 970 49 HOH HOH . N 7 HOH A 23 971 55 HOH HOH . N 7 HOH A 24 972 60 HOH HOH . N 7 HOH A 25 973 62 HOH HOH . N 7 HOH A 26 974 64 HOH HOH . N 7 HOH A 27 975 74 HOH HOH . N 7 HOH A 28 976 81 HOH HOH . N 7 HOH A 29 977 83 HOH HOH . N 7 HOH A 30 978 87 HOH HOH . N 7 HOH A 31 979 89 HOH HOH . N 7 HOH A 32 980 91 HOH HOH . N 7 HOH A 33 981 94 HOH HOH . N 7 HOH A 34 982 106 HOH HOH . N 7 HOH A 35 983 111 HOH HOH . N 7 HOH A 36 984 112 HOH HOH . N 7 HOH A 37 985 114 HOH HOH . N 7 HOH A 38 986 116 HOH HOH . N 7 HOH A 39 987 118 HOH HOH . N 7 HOH A 40 988 119 HOH HOH . N 7 HOH A 41 989 124 HOH HOH . N 7 HOH A 42 990 128 HOH HOH . O 7 HOH B 1 5 5 HOH HOH . O 7 HOH B 2 8 8 HOH HOH . O 7 HOH B 3 13 13 HOH HOH . O 7 HOH B 4 17 17 HOH HOH . O 7 HOH B 5 29 29 HOH HOH . O 7 HOH B 6 31 31 HOH HOH . O 7 HOH B 7 54 54 HOH HOH . O 7 HOH B 8 57 57 HOH HOH . O 7 HOH B 9 63 63 HOH HOH . O 7 HOH B 10 66 66 HOH HOH . O 7 HOH B 11 70 70 HOH HOH . O 7 HOH B 12 76 76 HOH HOH . O 7 HOH B 13 108 108 HOH HOH . O 7 HOH B 14 109 109 HOH HOH . O 7 HOH B 15 131 131 HOH HOH . O 7 HOH B 16 132 132 HOH HOH . O 7 HOH B 17 133 133 HOH HOH . P 7 HOH C 1 16 16 HOH HOH . P 7 HOH C 2 18 18 HOH HOH . P 7 HOH C 3 23 23 HOH HOH . P 7 HOH C 4 36 36 HOH HOH . P 7 HOH C 5 41 41 HOH HOH . P 7 HOH C 6 46 46 HOH HOH . P 7 HOH C 7 50 50 HOH HOH . P 7 HOH C 8 51 51 HOH HOH . P 7 HOH C 9 53 53 HOH HOH . P 7 HOH C 10 58 58 HOH HOH . P 7 HOH C 11 67 67 HOH HOH . P 7 HOH C 12 73 73 HOH HOH . P 7 HOH C 13 82 82 HOH HOH . P 7 HOH C 14 84 84 HOH HOH . P 7 HOH C 15 85 85 HOH HOH . P 7 HOH C 16 86 86 HOH HOH . P 7 HOH C 17 97 97 HOH HOH . P 7 HOH C 18 113 113 HOH HOH . P 7 HOH C 19 122 122 HOH HOH . P 7 HOH C 20 129 129 HOH HOH . P 7 HOH C 21 134 134 HOH HOH . P 7 HOH C 22 135 135 HOH HOH . P 7 HOH C 23 136 136 HOH HOH . P 7 HOH C 24 137 137 HOH HOH . P 7 HOH C 25 138 138 HOH HOH . P 7 HOH C 26 139 139 HOH HOH . P 7 HOH C 27 140 140 HOH HOH . P 7 HOH C 28 141 141 HOH HOH . Q 7 HOH D 1 1 1 HOH HOH . Q 7 HOH D 2 2 2 HOH HOH . Q 7 HOH D 3 3 3 HOH HOH . Q 7 HOH D 4 11 11 HOH HOH . Q 7 HOH D 5 12 12 HOH HOH . Q 7 HOH D 6 14 14 HOH HOH . Q 7 HOH D 7 25 25 HOH HOH . Q 7 HOH D 8 27 27 HOH HOH . Q 7 HOH D 9 38 38 HOH HOH . Q 7 HOH D 10 39 39 HOH HOH . Q 7 HOH D 11 43 43 HOH HOH . Q 7 HOH D 12 47 47 HOH HOH . Q 7 HOH D 13 48 48 HOH HOH . Q 7 HOH D 14 52 52 HOH HOH . Q 7 HOH D 15 56 56 HOH HOH . Q 7 HOH D 16 65 65 HOH HOH . Q 7 HOH D 17 77 77 HOH HOH . Q 7 HOH D 18 80 80 HOH HOH . Q 7 HOH D 19 95 95 HOH HOH . Q 7 HOH D 20 96 96 HOH HOH . Q 7 HOH D 21 98 98 HOH HOH . Q 7 HOH D 22 101 101 HOH HOH . Q 7 HOH D 23 102 102 HOH HOH . Q 7 HOH D 24 103 103 HOH HOH . Q 7 HOH D 25 105 105 HOH HOH . Q 7 HOH D 26 107 107 HOH HOH . Q 7 HOH D 27 120 120 HOH HOH . Q 7 HOH D 28 130 130 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 . . . L 6 39.524 -2.121 92.296 1 58.04 ? C1 NAG 886 A 1 HETATM 2 C C2 NAG . . . L 6 40.365 -1.317 91.305 1 60.58 ? C2 NAG 886 A 1 HETATM 3 C C3 NAG . . . L 6 41.836 -1.576 91.59 1 60.14 ? C3 NAG 886 A 1 HETATM 4 C C4 NAG . . . L 6 42.04 -1.157 93.029 1 59.06 ? C4 NAG 886 A 1 HETATM 5 C C5 NAG . . . L 6 41.27 -2.172 93.85 1 59.16 ? C5 NAG 886 A 1 HETATM 6 C C6 NAG . . . L 6 41.542 -2.046 95.339 1 60.97 ? C6 NAG 886 A 1 HETATM 7 C C7 NAG . . . L 6 38.724 -1.486 89.515 1 60.11 ? C7 NAG 886 A 1 HETATM 8 C C8 NAG . . . L 6 38.083 -0.129 89.685 1 58.97 ? C8 NAG 886 A 1 HETATM 9 N N2 NAG . . . L 6 39.99 -1.624 89.928 1 60.32 ? N2 NAG 886 A 1 HETATM 10 O O3 NAG . . . L 6 42.67 -0.841 90.728 1 61.48 ? O3 NAG 886 A 1 HETATM 11 O O4 NAG . . . L 6 43.401 -1.161 93.356 1 58.74 ? O4 NAG 886 A 1 HETATM 12 O O5 NAG . . . L 6 39.907 -1.918 93.634 1 58.03 ? O5 NAG 886 A 1 HETATM 13 O O6 NAG . . . L 6 40.645 -2.906 96.008 1 61.52 ? O6 NAG 886 A 1 HETATM 14 O O7 NAG . . . L 6 38.08 -2.426 89.044 1 58.36 ? O7 NAG 886 A 1 # _model_server_stats.io_time_ms 25 _model_server_stats.parse_time_ms 16 _model_server_stats.create_model_time_ms 13 _model_server_stats.query_time_ms 693 _model_server_stats.encode_time_ms 28 _model_server_stats.element_count 14 #