data_1NCA # _model_server_result.job_id -hQ4RurWK3aUEljrrtUJgg _model_server_result.datetime_utc '2024-11-25 17:06:05' _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 1nca # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"F","auth_seq_id":476}' # _entry.id 1NCA # _exptl.entry_id 1NCA _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 221.208 _entity.id 5 _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 1NCA _cell.length_a 167 _cell.length_b 167 _cell.length_c 124 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 1NCA _symmetry.cell_setting ? _symmetry.Int_Tables_number 90 _symmetry.space_group_name_Hall . _symmetry.space_group_name_H-M 'P 4 21 2' # loop_ _pdbx_struct_assembly.method_details _pdbx_struct_assembly.oligomeric_details _pdbx_struct_assembly.oligomeric_count _pdbx_struct_assembly.details _pdbx_struct_assembly.id PQS dodecameric 12 author_and_software_defined_assembly 1 PISA eicosameric 20 software_defined_assembly 2 # loop_ _pdbx_struct_assembly_gen.asym_id_list _pdbx_struct_assembly_gen.assembly_id _pdbx_struct_assembly_gen.oper_expression A,B,C,D,E,F,G,H,I,J 1 1,2,3,4 A,C,D,E,F,G,H,J 2 1,2,3,4 A,B,C,D,E,F,G,H,I,J 2 5,6,7,8 # loop_ _pdbx_struct_oper_list.id _pdbx_struct_oper_list.type _pdbx_struct_oper_list.name _pdbx_struct_oper_list.symmetry_operation _pdbx_struct_oper_list.matrix[1][1] _pdbx_struct_oper_list.matrix[1][2] _pdbx_struct_oper_list.matrix[1][3] _pdbx_struct_oper_list.matrix[2][1] _pdbx_struct_oper_list.matrix[2][2] _pdbx_struct_oper_list.matrix[2][3] _pdbx_struct_oper_list.matrix[3][1] _pdbx_struct_oper_list.matrix[3][2] _pdbx_struct_oper_list.matrix[3][3] _pdbx_struct_oper_list.vector[1] _pdbx_struct_oper_list.vector[2] _pdbx_struct_oper_list.vector[3] 1 'identity operation' 1_555 x,y,z 1 0 0 0 1 0 0 0 1 0 0 0 2 'crystal symmetry operation' 2_655 -x+1,-y,z -1 0 0 0 -1 0 0 0 1 167 0 0 3 'crystal symmetry operation' 3_545 -y+1/2,x-1/2,z 0 -1 0 1 0 0 0 0 1 83.5 -83.5 0 4 'crystal symmetry operation' 4_555 y+1/2,-x+1/2,z 0 1 0 -1 0 0 0 0 1 83.5 83.5 0 5 'crystal symmetry operation' 5_547 -x+1/2,y-1/2,-z+2 -1 0 0 0 1 0 0 0 -1 83.5 -83.5 248 6 'crystal symmetry operation' 6_557 x+1/2,-y+1/2,-z+2 1 0 0 0 -1 0 0 0 -1 83.5 83.5 248 7 'crystal symmetry operation' 7_557 y,x,-z+2 0 1 0 1 0 0 0 0 -1 0 0 248 8 'crystal symmetry operation' 8_657 -y+1,-x,-z+2 0 -1 0 -1 0 0 0 0 -1 167 0 248 # loop_ _struct_asym.details _struct_asym.entity_id _struct_asym.id _struct_asym.pdbx_modified _struct_asym.pdbx_blank_PDB_chainid_flag ? 5 E N N ? 5 F N N # _pdbx_entity_branch.entity_id 4 _pdbx_entity_branch.type 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 ? 4 2 1 NAG NAG C1 O1 . O4 HO4 . sing 2 ? 4 3 2 BMA NAG C1 O1 . O4 HO4 . sing 3 ? 4 4 3 MAN BMA C1 O1 . O3 HO3 . sing 4 ? 4 5 4 MAN MAN C1 O1 . O2 HO2 . sing 5 ? 4 6 5 MAN MAN C1 O1 . O2 HO2 . 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 4 n D NAG 1 A 1 NAG N 200 NAG 4 n D NAG 2 A 2 NAG N 200 NAG 4 n D BMA 3 A 3 BMA N 200 MAN 4 n D MAN 4 A 4 MAN N 200 MAN 4 n D MAN 5 A 5 MAN N 200 MAN 4 n D MAN 6 A 6 MAN N 200 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 12 N CYS 92 1_555 A SG CYS 338 N CYS 417 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.005 ? disulf ? disulf2 A SG CYS 44 N CYS 124 1_555 A SG CYS 49 N CYS 129 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.014 ? disulf ? disulf3 A SG CYS 96 N CYS 175 1_555 A SG CYS 114 N CYS 193 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.004 ? disulf ? disulf4 A SG CYS 104 N CYS 183 1_555 A SG CYS 151 N CYS 230 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.998 ? disulf ? disulf5 A SG CYS 153 N CYS 232 1_555 A SG CYS 158 N CYS 237 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.015 ? disulf ? disulf6 A SG CYS 199 N CYS 278 1_555 A SG CYS 212 N CYS 291 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.008 ? disulf ? disulf7 A SG CYS 201 N CYS 280 1_555 A SG CYS 210 N CYS 289 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.016 ? disulf ? disulf8 A SG CYS 239 N CYS 318 1_555 A SG CYS 257 N CYS 337 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.983 ? disulf ? disulf9 A SG CYS 342 N CYS 421 1_555 A SG CYS 368 N CYS 447 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.011 ? disulf ? disulf10 B SG CYS 23 L CYS 23 1_555 B SG CYS 88 L CYS 88 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.03 ? disulf ? disulf11 B SG CYS 134 L CYS 134 1_555 B SG CYS 194 L CYS 194 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.018 ? disulf ? disulf12 B SG CYS 214 L CYS 214 1_555 C SG CYS 135 H CYS 128 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.015 ? disulf ? disulf13 C SG CYS 22 H CYS 22 1_555 C SG CYS 96 H CYS 92 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.975 ? disulf ? disulf14 C SG CYS 147 H CYS 142 1_555 C SG CYS 202 H CYS 208 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.015 ? covale ? covale1 A ND2 ASN 6 N ASN 86 1_555 E C1 NAG . N NAG 475 1_555 ? ? ? A ? ? ? ? ? ? ? ? 1.452 ? covale ? covale2 A ND2 ASN 66 N ASN 146 1_555 F C1 NAG . N NAG 476 1_555 ? ? ? A ? ? ? ? ? ? ? ? 1.432 ? covale ? covale3 A ND2 ASN 121 N ASN 200 1_555 D C1 NAG . A NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.469 ? covale ? covale4 D O4 NAG . A NAG 1 1_555 D C1 NAG . A NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.444 ? covale ? covale5 D O4 NAG . A NAG 2 1_555 D C1 BMA . A BMA 3 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.416 ? covale ? covale6 D O3 BMA . A BMA 3 1_555 D C1 MAN . A MAN 4 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.424 ? covale ? covale7 D O2 MAN . A MAN 4 1_555 D C1 MAN . A MAN 5 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.423 ? covale ? covale8 D O2 MAN . A MAN 5 1_555 D C1 MAN . A MAN 6 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.439 ? metalc ? metalc1 G CA CA . N CA 1 1_555 A O ASP 214 N ASP 293 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.033 ? metalc ? metalc2 G CA CA . N CA 1 1_555 A O GLY 218 N GLY 297 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.659 ? metalc ? metalc3 G CA CA . N CA 1 1_555 A OD2 ASP 245 N ASP 324 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.679 ? metalc ? metalc4 G CA CA . N CA 1 1_555 A O ASN 267 N ASN 347 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 3.013 ? # _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 1NCA _atom_sites.fract_transf_matrix[1][1] 0.005988 _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] 0.005988 _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] 0.008065 _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 5 NAG N 1 475 86 NAG NAG A F 5 NAG N 1 476 146 NAG NAG A G 6 CA N 1 1 1 CA CA . H 7 HOH N 1 5 5 HOH HOH . H 7 HOH N 2 8 8 HOH HOH . H 7 HOH N 3 9 9 HOH HOH . H 7 HOH N 4 10 10 HOH HOH . H 7 HOH N 5 11 11 HOH HOH . H 7 HOH N 6 13 13 HOH HOH . H 7 HOH N 7 14 14 HOH HOH . H 7 HOH N 8 15 15 HOH HOH . H 7 HOH N 9 16 16 HOH HOH . H 7 HOH N 10 17 17 HOH HOH . H 7 HOH N 11 18 18 HOH HOH . H 7 HOH N 12 19 19 HOH HOH . H 7 HOH N 13 20 20 HOH HOH . H 7 HOH N 14 21 21 HOH HOH . H 7 HOH N 15 22 22 HOH HOH . H 7 HOH N 16 23 23 HOH HOH . H 7 HOH N 17 24 24 HOH HOH . H 7 HOH N 18 25 25 HOH HOH . H 7 HOH N 19 26 26 HOH HOH . H 7 HOH N 20 27 27 HOH HOH . H 7 HOH N 21 28 28 HOH HOH . H 7 HOH N 22 29 29 HOH HOH . H 7 HOH N 23 30 30 HOH HOH . H 7 HOH N 24 31 31 HOH HOH . H 7 HOH N 25 32 32 HOH HOH . H 7 HOH N 26 33 33 HOH HOH . H 7 HOH N 27 34 34 HOH HOH . H 7 HOH N 28 35 35 HOH HOH . H 7 HOH N 29 36 36 HOH HOH . H 7 HOH N 30 37 37 HOH HOH . H 7 HOH N 31 38 38 HOH HOH . H 7 HOH N 32 39 39 HOH HOH . H 7 HOH N 33 40 40 HOH HOH . H 7 HOH N 34 41 41 HOH HOH . H 7 HOH N 35 42 42 HOH HOH . H 7 HOH N 36 43 43 HOH HOH . H 7 HOH N 37 44 44 HOH HOH . H 7 HOH N 38 45 45 HOH HOH . H 7 HOH N 39 46 46 HOH HOH . H 7 HOH N 40 47 47 HOH HOH . H 7 HOH N 41 48 48 HOH HOH . H 7 HOH N 42 49 49 HOH HOH . H 7 HOH N 43 50 50 HOH HOH . H 7 HOH N 44 51 51 HOH HOH . H 7 HOH N 45 52 52 HOH HOH . H 7 HOH N 46 53 53 HOH HOH . H 7 HOH N 47 54 54 HOH HOH . H 7 HOH N 48 55 55 HOH HOH . H 7 HOH N 49 56 56 HOH HOH . H 7 HOH N 50 57 57 HOH HOH . H 7 HOH N 51 58 58 HOH HOH . H 7 HOH N 52 59 59 HOH HOH . H 7 HOH N 53 60 60 HOH HOH . H 7 HOH N 54 61 61 HOH HOH . H 7 HOH N 55 62 62 HOH HOH . H 7 HOH N 56 63 63 HOH HOH . H 7 HOH N 57 64 64 HOH HOH . H 7 HOH N 58 65 65 HOH HOH . H 7 HOH N 59 66 66 HOH HOH . H 7 HOH N 60 67 67 HOH HOH . H 7 HOH N 61 68 68 HOH HOH . H 7 HOH N 62 69 69 HOH HOH . H 7 HOH N 63 70 70 HOH HOH . H 7 HOH N 64 71 71 HOH HOH . H 7 HOH N 65 72 72 HOH HOH . H 7 HOH N 66 73 73 HOH HOH . I 7 HOH L 1 215 2 HOH HOH . I 7 HOH L 2 216 7 HOH HOH . J 7 HOH H 1 228 3 HOH HOH . J 7 HOH H 2 229 4 HOH HOH . J 7 HOH H 3 230 6 HOH HOH . J 7 HOH H 4 231 12 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 . . A F 5 63.448 0.587 109.099 1 40.16 ? C1 NAG 476 N 1 HETATM 2 C C2 NAG . . A F 5 61.988 0.502 108.528 1 44.52 ? C2 NAG 476 N 1 HETATM 3 C C3 NAG . . A F 5 61.931 0.037 107.071 1 44.82 ? C3 NAG 476 N 1 HETATM 4 C C4 NAG . . A F 5 62.812 1.065 106.34 1 44.45 ? C4 NAG 476 N 1 HETATM 5 C C5 NAG . . A F 5 64.268 0.954 106.887 1 43.39 ? C5 NAG 476 N 1 HETATM 6 C C6 NAG . . A F 5 65.376 1.721 106.18 1 43.13 ? C6 NAG 476 N 1 HETATM 7 C C7 NAG . . A F 5 61.482 -1.692 109.574 1 54.21 ? C7 NAG 476 N 1 HETATM 8 C C8 NAG . . A F 5 60.643 -2.558 110.511 1 54.72 ? C8 NAG 476 N 1 HETATM 9 N N2 NAG . . A F 5 61.159 -0.402 109.331 1 49.94 ? N2 NAG 476 N 1 HETATM 10 O O3 NAG . . A F 5 60.566 0.008 106.712 1 46.14 ? O3 NAG 476 N 1 HETATM 11 O O4 NAG . . A F 5 62.801 0.87 104.911 1 45.59 ? O4 NAG 476 N 1 HETATM 12 O O5 NAG . . A F 5 64.281 1.38 108.26 1 40.84 ? O5 NAG 476 N 1 HETATM 13 O O6 NAG . . A F 5 66.5 1.783 107.053 1 41.5 ? O6 NAG 476 N 1 HETATM 14 O O7 NAG . . A F 5 62.46 -2.206 109.028 1 57.64 ? O7 NAG 476 N 1 # _model_server_stats.io_time_ms 9 _model_server_stats.parse_time_ms 10 _model_server_stats.create_model_time_ms 7 _model_server_stats.query_time_ms 315 _model_server_stats.encode_time_ms 6 _model_server_stats.element_count 14 #