data_5Y3M # _model_server_result.job_id 1XsKqE9uBUCI2VygHhWSRA _model_server_result.datetime_utc '2024-10-19 15:28:46' _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 5y3m # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"O","auth_seq_id":1003}' # _entry.id 5Y3M # _exptl.entry_id 5Y3M _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 10 _entity.pdbx_parent_entity_id . _entity.pdbx_mutation ? _entity.pdbx_fragment ? _entity.pdbx_ec ? # _cell.angle_alpha 90 _cell.angle_beta 100.64 _cell.angle_gamma 90 _cell.entry_id 5Y3M _cell.length_a 88.177 _cell.length_b 68.693 _cell.length_c 153.535 _cell.Z_PDB 4 _cell.pdbx_unique_axis ? # _symmetry.entry_id 5Y3M _symmetry.cell_setting ? _symmetry.Int_Tables_number 3 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 1 2 1' # _pdbx_struct_assembly.method_details PISA _pdbx_struct_assembly.oligomeric_details hexameric _pdbx_struct_assembly.oligomeric_count 6 _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 _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 G N N ? 4 H N N ? 4 I N N ? 4 J N N ? 4 K N N ? 4 L N N ? 4 M N N ? 4 N N N ? 4 O N N ? 4 P N 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 14 A CYS 34 1_555 A SG CYS 24 A CYS 44 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.047 ? disulf ? disulf2 A SG CYS 77 A CYS 97 1_555 A SG CYS 89 A CYS 109 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.043 ? disulf ? disulf3 A SG CYS 157 A CYS 177 1_555 A SG CYS 163 A CYS 183 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.052 ? disulf ? disulf4 A SG CYS 234 A CYS 254 1_555 A SG CYS 247 A CYS 267 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.033 ? disulf ? disulf5 A SG CYS 237 A CYS 257 1_555 A SG CYS 244 A CYS 264 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.038 ? disulf ? disulf6 A SG CYS 449 A CYS 469 1_555 A SG CYS 478 A CYS 498 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.043 ? disulf ? disulf7 A SG CYS 742 A CYS 762 1_555 A SG CYS 768 A CYS 788 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.034 ? disulf ? disulf8 F SG CYS 14 B CYS 34 1_555 F SG CYS 24 B CYS 44 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.033 ? disulf ? disulf9 F SG CYS 77 B CYS 97 1_555 F SG CYS 89 B CYS 109 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.033 ? disulf ? disulf10 F SG CYS 157 B CYS 177 1_555 F SG CYS 163 B CYS 183 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.055 ? disulf ? disulf11 F SG CYS 234 B CYS 254 1_555 F SG CYS 247 B CYS 267 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.051 ? disulf ? disulf12 F SG CYS 237 B CYS 257 1_555 F SG CYS 244 B CYS 264 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.044 ? disulf ? disulf13 F SG CYS 449 B CYS 469 1_555 F SG CYS 478 B CYS 498 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.017 ? disulf ? disulf14 F SG CYS 742 B CYS 762 1_555 F SG CYS 768 B CYS 788 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.025 ? covale ? covale1 A ND2 ASN 189 A ASN 209 1_555 G C1 NAG . A NAG 1000 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.452 ? covale ? covale2 A ND2 ASN 452 A ASN 472 1_555 I C1 NAG . A NAG 1002 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.44 ? covale ? covale3 A ND2 ASN 491 A ASN 511 1_555 J C1 NAG . A NAG 1003 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.442 ? covale ? covale4 A ND2 ASN 545 A ASN 565 1_555 H C1 NAG . A NAG 1001 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.44 ? covale ? covale5 A ND2 ASN 709 A ASN 729 1_555 K C1 NAG . A NAG 1004 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.455 ? covale ? covale6 F ND2 ASN 189 B ASN 209 1_555 L C1 NAG . B NAG 1000 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.446 ? covale ? covale7 F ND2 ASN 360 B ASN 380 1_555 M C1 NAG . B NAG 1001 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.441 ? covale ? covale8 F ND2 ASN 491 B ASN 511 1_555 P C1 NAG . B NAG 1004 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.437 ? covale ? covale9 F ND2 ASN 545 B ASN 565 1_555 O C1 NAG . B NAG 1003 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.439 ? covale ? covale10 F ND2 ASN 647 B ASN 667 1_555 N C1 NAG . B NAG 1002 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.437 ? # _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 386 n n C1 O1 NAG sing 387 n n C1 O5 NAG sing 388 n n C1 H1 NAG sing 389 n n C2 C3 NAG sing 390 n n C2 N2 NAG sing 391 n n C2 H2 NAG sing 392 n n C3 C4 NAG sing 393 n n C3 O3 NAG sing 394 n n C3 H3 NAG sing 395 n n C4 C5 NAG sing 396 n n C4 O4 NAG sing 397 n n C4 H4 NAG sing 398 n n C5 C6 NAG sing 399 n n C5 O5 NAG sing 400 n n C5 H5 NAG sing 401 n n C6 O6 NAG sing 402 n n C6 H61 NAG sing 403 n n C6 H62 NAG sing 404 n n C7 C8 NAG sing 405 n n C7 N2 NAG sing 406 n n C7 O7 NAG doub 407 n n C8 H81 NAG sing 408 n n C8 H82 NAG sing 409 n n C8 H83 NAG sing 410 n n N2 HN2 NAG sing 411 n n O1 HO1 NAG sing 412 n n O3 HO3 NAG sing 413 n n O4 HO4 NAG sing 414 n n O6 HO6 NAG sing 415 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 5Y3M _atom_sites.fract_transf_matrix[1][1] 0.011341 _atom_sites.fract_transf_matrix[1][2] 0 _atom_sites.fract_transf_matrix[1][3] 0.002131 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.014558 _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] 0.006627 _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 G 4 NAG A 1 1000 1000 NAG NAG . H 4 NAG A 1 1001 1001 NAG NAG . I 4 NAG A 1 1002 1002 NAG NAG . J 4 NAG A 1 1003 1003 NAG NAG . K 4 NAG A 1 1004 1004 NAG NAG . L 4 NAG B 1 1000 1000 NAG NAG . M 4 NAG B 1 1001 1001 NAG NAG . N 4 NAG B 1 1002 1002 NAG NAG . O 4 NAG B 1 1003 1003 NAG NAG . P 4 NAG B 1 1004 1004 NAG NAG . Q 5 HOH A 1 1101 132 HOH HOH . Q 5 HOH A 2 1102 62 HOH HOH . Q 5 HOH A 3 1103 123 HOH HOH . Q 5 HOH A 4 1104 76 HOH HOH . Q 5 HOH A 5 1105 78 HOH HOH . Q 5 HOH A 6 1106 43 HOH HOH . Q 5 HOH A 7 1107 63 HOH HOH . Q 5 HOH A 8 1108 49 HOH HOH . Q 5 HOH A 9 1109 21 HOH HOH . Q 5 HOH A 10 1110 87 HOH HOH . Q 5 HOH A 11 1111 55 HOH HOH . Q 5 HOH A 12 1112 72 HOH HOH . Q 5 HOH A 13 1113 75 HOH HOH . Q 5 HOH A 14 1114 101 HOH HOH . Q 5 HOH A 15 1115 60 HOH HOH . Q 5 HOH A 16 1116 103 HOH HOH . Q 5 HOH A 17 1117 17 HOH HOH . Q 5 HOH A 18 1118 36 HOH HOH . Q 5 HOH A 19 1119 115 HOH HOH . Q 5 HOH A 20 1120 105 HOH HOH . Q 5 HOH A 21 1121 11 HOH HOH . Q 5 HOH A 22 1122 81 HOH HOH . Q 5 HOH A 23 1123 91 HOH HOH . Q 5 HOH A 24 1124 106 HOH HOH . Q 5 HOH A 25 1125 32 HOH HOH . Q 5 HOH A 26 1126 116 HOH HOH . Q 5 HOH A 27 1127 45 HOH HOH . Q 5 HOH A 28 1128 6 HOH HOH . Q 5 HOH A 29 1129 107 HOH HOH . Q 5 HOH A 30 1130 119 HOH HOH . Q 5 HOH A 31 1131 20 HOH HOH . Q 5 HOH A 32 1132 7 HOH HOH . Q 5 HOH A 33 1133 104 HOH HOH . Q 5 HOH A 34 1134 127 HOH HOH . Q 5 HOH A 35 1135 85 HOH HOH . Q 5 HOH A 36 1136 46 HOH HOH . Q 5 HOH A 37 1137 25 HOH HOH . Q 5 HOH A 38 1138 2 HOH HOH . Q 5 HOH A 39 1139 112 HOH HOH . Q 5 HOH A 40 1140 70 HOH HOH . Q 5 HOH A 41 1141 23 HOH HOH . Q 5 HOH A 42 1142 18 HOH HOH . Q 5 HOH A 43 1143 118 HOH HOH . Q 5 HOH A 44 1144 3 HOH HOH . Q 5 HOH A 45 1145 83 HOH HOH . Q 5 HOH A 46 1146 95 HOH HOH . Q 5 HOH A 47 1147 39 HOH HOH . Q 5 HOH A 48 1148 128 HOH HOH . Q 5 HOH A 49 1149 69 HOH HOH . Q 5 HOH A 50 1150 96 HOH HOH . Q 5 HOH A 51 1151 52 HOH HOH . Q 5 HOH A 52 1152 129 HOH HOH . Q 5 HOH A 53 1153 98 HOH HOH . Q 5 HOH A 54 1154 102 HOH HOH . Q 5 HOH A 55 1155 28 HOH HOH . Q 5 HOH A 56 1156 19 HOH HOH . Q 5 HOH A 57 1157 90 HOH HOH . Q 5 HOH A 58 1158 61 HOH HOH . Q 5 HOH A 59 1159 124 HOH HOH . Q 5 HOH A 60 1160 79 HOH HOH . Q 5 HOH A 61 1161 57 HOH HOH . Q 5 HOH A 62 1162 110 HOH HOH . R 5 HOH E 1 101 109 HOH HOH . S 5 HOH F 1 101 131 HOH HOH . S 5 HOH F 2 102 84 HOH HOH . S 5 HOH F 3 103 89 HOH HOH . T 5 HOH B 1 1101 44 HOH HOH . T 5 HOH B 2 1102 67 HOH HOH . T 5 HOH B 3 1103 73 HOH HOH . T 5 HOH B 4 1104 66 HOH HOH . T 5 HOH B 5 1105 65 HOH HOH . T 5 HOH B 6 1106 14 HOH HOH . T 5 HOH B 7 1107 97 HOH HOH . T 5 HOH B 8 1108 108 HOH HOH . T 5 HOH B 9 1109 68 HOH HOH . T 5 HOH B 10 1110 77 HOH HOH . T 5 HOH B 11 1111 27 HOH HOH . T 5 HOH B 12 1112 54 HOH HOH . T 5 HOH B 13 1113 122 HOH HOH . T 5 HOH B 14 1114 99 HOH HOH . T 5 HOH B 15 1115 4 HOH HOH . T 5 HOH B 16 1116 133 HOH HOH . T 5 HOH B 17 1117 59 HOH HOH . T 5 HOH B 18 1118 113 HOH HOH . T 5 HOH B 19 1119 100 HOH HOH . T 5 HOH B 20 1120 30 HOH HOH . T 5 HOH B 21 1121 48 HOH HOH . T 5 HOH B 22 1122 50 HOH HOH . T 5 HOH B 23 1123 117 HOH HOH . T 5 HOH B 24 1124 121 HOH HOH . T 5 HOH B 25 1125 53 HOH HOH . T 5 HOH B 26 1126 5 HOH HOH . T 5 HOH B 27 1127 34 HOH HOH . T 5 HOH B 28 1128 58 HOH HOH . T 5 HOH B 29 1129 24 HOH HOH . T 5 HOH B 30 1130 82 HOH HOH . T 5 HOH B 31 1131 15 HOH HOH . T 5 HOH B 32 1132 16 HOH HOH . T 5 HOH B 33 1133 29 HOH HOH . T 5 HOH B 34 1134 40 HOH HOH . T 5 HOH B 35 1135 31 HOH HOH . T 5 HOH B 36 1136 22 HOH HOH . T 5 HOH B 37 1137 42 HOH HOH . T 5 HOH B 38 1138 114 HOH HOH . T 5 HOH B 39 1139 126 HOH HOH . T 5 HOH B 40 1140 26 HOH HOH . T 5 HOH B 41 1141 56 HOH HOH . T 5 HOH B 42 1142 88 HOH HOH . T 5 HOH B 43 1143 35 HOH HOH . T 5 HOH B 44 1144 13 HOH HOH . T 5 HOH B 45 1145 64 HOH HOH . T 5 HOH B 46 1146 130 HOH HOH . T 5 HOH B 47 1147 8 HOH HOH . T 5 HOH B 48 1148 86 HOH HOH . T 5 HOH B 49 1149 1 HOH HOH . T 5 HOH B 50 1150 41 HOH HOH . T 5 HOH B 51 1151 38 HOH HOH . T 5 HOH B 52 1152 9 HOH HOH . T 5 HOH B 53 1153 125 HOH HOH . T 5 HOH B 54 1154 80 HOH HOH . T 5 HOH B 55 1155 134 HOH HOH . T 5 HOH B 56 1156 10 HOH HOH . T 5 HOH B 57 1157 71 HOH HOH . T 5 HOH B 58 1158 111 HOH HOH . T 5 HOH B 59 1159 94 HOH HOH . T 5 HOH B 60 1160 92 HOH HOH . T 5 HOH B 61 1161 33 HOH HOH . T 5 HOH B 62 1162 12 HOH HOH . T 5 HOH B 63 1163 51 HOH HOH . T 5 HOH B 64 1164 120 HOH HOH . T 5 HOH B 65 1165 93 HOH HOH . T 5 HOH B 66 1166 47 HOH HOH . T 5 HOH B 67 1167 37 HOH HOH . T 5 HOH B 68 1168 74 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 -17.154 -26.461 47.311 1 35.79 ? C1 NAG 1003 B 1 HETATM 2 C C2 NAG . . . O 4 -18.147 -25.572 48.051 1 37.27 ? C2 NAG 1003 B 1 HETATM 3 C C3 NAG . . . O 4 -18.803 -26.398 49.158 1 37.76 ? C3 NAG 1003 B 1 HETATM 4 C C4 NAG . . . O 4 -19.516 -27.592 48.51 1 37.94 ? C4 NAG 1003 B 1 HETATM 5 C C5 NAG . . . O 4 -18.495 -28.409 47.71 1 37.69 ? C5 NAG 1003 B 1 HETATM 6 C C6 NAG . . . O 4 -19.094 -29.611 46.985 1 37.96 ? C6 NAG 1003 B 1 HETATM 7 C C7 NAG . . . O 4 -18.019 -23.156 48.565 1 39.43 ? C7 NAG 1003 B 1 HETATM 8 C C8 NAG . . . O 4 -17.14 -22.07 49.123 1 39.56 ? C8 NAG 1003 B 1 HETATM 9 N N2 NAG . . . O 4 -17.471 -24.384 48.562 1 38.37 ? N2 NAG 1003 B 1 HETATM 10 O O3 NAG . . . O 4 -19.689 -25.582 49.934 1 37.9 ? O3 NAG 1003 B 1 HETATM 11 O O4 NAG . . . O 4 -20.13 -28.414 49.506 1 38.53 ? O4 NAG 1003 B 1 HETATM 12 O O5 NAG . . . O 4 -17.875 -27.553 46.745 1 36.8 ? O5 NAG 1003 B 1 HETATM 13 O O6 NAG . . . O 4 -19.307 -29.301 45.601 1 38.16 ? O6 NAG 1003 B 1 HETATM 14 O O7 NAG . . . O 4 -19.149 -22.907 48.15 1 39.52 ? O7 NAG 1003 B 1 # _model_server_stats.io_time_ms 32 _model_server_stats.parse_time_ms 30 _model_server_stats.create_model_time_ms 65 _model_server_stats.query_time_ms 345 _model_server_stats.encode_time_ms 8 _model_server_stats.element_count 14 #