data_5VJM # _model_server_result.job_id cYBb-x2AUA3HX_NT_LX6VQ _model_server_result.datetime_utc '2024-11-24 13:08:12' _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 5vjm # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"D","auth_seq_id":502}' # _entry.id 5VJM # _exptl.entry_id 5VJM _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 221.208 _entity.id 3 _entity.src_method man _entity.type non-polymer _entity.pdbx_description 2-acetamido-2-deoxy-beta-D-glucopyranose _entity.pdbx_number_of_molecules 3 _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 120 _cell.entry_id 5VJM _cell.length_a 115.942 _cell.length_b 115.942 _cell.length_c 295.757 _cell.Z_PDB 18 _cell.pdbx_unique_axis ? # _symmetry.entry_id 5VJM _symmetry.cell_setting ? _symmetry.Int_Tables_number 155 _symmetry.space_group_name_Hall . _symmetry.space_group_name_H-M 'H 3 2' # _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 _pdbx_struct_assembly_gen.assembly_id 1 _pdbx_struct_assembly_gen.oper_expression 1,2,3 # 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_565 -y,x-y+1,z -0.5 -0.866025 0 0.866025 -0.5 0 0 0 1 -57.971 100.408717 0 3 'crystal symmetry operation' 3_455 -x+y-1,-x,z -0.5 0.866025 0 -0.866025 -0.5 0 0 0 1 -115.942 0 0 # loop_ _struct_asym.details _struct_asym.entity_id _struct_asym.id _struct_asym.pdbx_modified _struct_asym.pdbx_blank_PDB_chainid_flag ? 3 C N N ? 3 D N N ? 3 G 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 8 A CYS 14 1_555 B SG CYS 137 B CYS 137 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.03 ? disulf ? disulf2 A SG CYS 46 A CYS 52 1_555 A SG CYS 272 A CYS 277 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.063 ? disulf ? disulf3 A SG CYS 58 A CYS 64 1_555 A SG CYS 70 A CYS 76 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.069 ? disulf ? disulf4 A SG CYS 91 A CYS 97 1_555 A SG CYS 133 A CYS 139 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.054 ? disulf ? disulf5 A SG CYS 276 A CYS 281 1_555 A SG CYS 300 A CYS 305 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.05 ? disulf ? disulf6 B SG CYS 144 B CYS 144 1_555 B SG CYS 148 B CYS 148 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.042 ? covale ? covale1 A ND2 ASN 32 A ASN 38 1_555 D C1 NAG . A NAG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.424 ? covale ? covale2 A ND2 ASN 235 A ASN 240 1_555 C C1 NAG . A NAG 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.461 ? covale ? covale3 E C2 SIA . A SIA 503 1_555 F O MOH . A MOH 504 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.379 ? covale ? covale4 B ND2 ASN 82 B ASN 82 1_555 G C1 NAG . B NAG 201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.442 ? # _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 242 n n C1 O1 NAG sing 243 n n C1 O5 NAG sing 244 n n C1 H1 NAG sing 245 n n C2 C3 NAG sing 246 n n C2 N2 NAG sing 247 n n C2 H2 NAG sing 248 n n C3 C4 NAG sing 249 n n C3 O3 NAG sing 250 n n C3 H3 NAG sing 251 n n C4 C5 NAG sing 252 n n C4 O4 NAG sing 253 n n C4 H4 NAG sing 254 n n C5 C6 NAG sing 255 n n C5 O5 NAG sing 256 n n C5 H5 NAG sing 257 n n C6 O6 NAG sing 258 n n C6 H61 NAG sing 259 n n C6 H62 NAG sing 260 n n C7 C8 NAG sing 261 n n C7 N2 NAG sing 262 n n C7 O7 NAG doub 263 n n C8 H81 NAG sing 264 n n C8 H82 NAG sing 265 n n C8 H83 NAG sing 266 n n N2 HN2 NAG sing 267 n n O1 HO1 NAG sing 268 n n O3 HO3 NAG sing 269 n n O4 HO4 NAG sing 270 n n O6 HO6 NAG sing 271 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 5VJM _atom_sites.fract_transf_matrix[1][1] 0.008625 _atom_sites.fract_transf_matrix[1][2] 0.00498 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.009959 _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] 0.003381 _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 C 3 NAG A 1 501 501 NAG NAG . D 3 NAG A 1 502 502 NAG NAG . E 4 SIA A 1 503 3001 SIA SIA . F 5 MOH A 1 504 3002 MOH GAL . G 3 NAG B 1 201 502 NAG NAG . H 6 HOH A 1 601 10 HOH HOH . H 6 HOH A 2 602 8 HOH HOH . H 6 HOH A 3 603 1 HOH HOH . H 6 HOH A 4 604 3 HOH HOH . H 6 HOH A 5 605 4 HOH HOH . I 6 HOH B 1 301 9 HOH HOH . I 6 HOH B 2 302 2 HOH HOH . I 6 HOH B 3 303 5 HOH HOH . I 6 HOH B 4 304 6 HOH HOH . I 6 HOH B 5 305 7 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 . . . D 3 -44.991 14.362 32.711 1 127.98 ? C1 NAG 502 A 1 HETATM 2 C C2 NAG . . . D 3 -45.287 12.878 33.058 1 142.23 ? C2 NAG 502 A 1 HETATM 3 C C3 NAG . . . D 3 -45.434 12.053 31.782 1 151.49 ? C3 NAG 502 A 1 HETATM 4 C C4 NAG . . . D 3 -46.602 12.527 30.939 1 150.53 ? C4 NAG 502 A 1 HETATM 5 C C5 NAG . . . D 3 -46.235 13.858 30.35 1 151.18 ? C5 NAG 502 A 1 HETATM 6 C C6 NAG . . . D 3 -47.431 14.589 29.82 1 143.66 ? C6 NAG 502 A 1 HETATM 7 C C7 NAG . . . D 3 -44.082 12.427 35.179 1 135.13 ? C7 NAG 502 A 1 HETATM 8 C C8 NAG . . . D 3 -42.816 11.824 35.731 1 129.21 ? C8 NAG 502 A 1 HETATM 9 N N2 NAG . . . D 3 -44.184 12.376 33.849 1 141.3 ? N2 NAG 502 A 1 HETATM 10 O O3 NAG . . . D 3 -45.587 10.678 32.063 1 159.88 ? O3 NAG 502 A 1 HETATM 11 O O4 NAG . . . D 3 -46.887 11.585 29.904 1 144.52 ? O4 NAG 502 A 1 HETATM 12 O O5 NAG . . . D 3 -45.601 14.741 31.306 1 146.27 ? O5 NAG 502 A 1 HETATM 13 O O6 NAG . . . D 3 -48.455 14.653 30.798 1 128.09 ? O6 NAG 502 A 1 HETATM 14 O O7 NAG . . . D 3 -44.955 12.876 35.899 1 127.7 ? O7 NAG 502 A 1 # _model_server_stats.io_time_ms 16 _model_server_stats.parse_time_ms 10 _model_server_stats.create_model_time_ms 5 _model_server_stats.query_time_ms 291 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 14 #