data_4K63 # _model_server_result.job_id aO7vqtPS3nJLYtke-vmNDw _model_server_result.datetime_utc '2024-10-17 03:21:34' _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 4k63 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"M","auth_seq_id":601}' # _entry.id 4K63 # _exptl.entry_id 4K63 _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 120 _cell.entry_id 4K63 _cell.length_a 70.555 _cell.length_b 70.555 _cell.length_c 506.295 _cell.Z_PDB 12 _cell.pdbx_unique_axis ? # _symmetry.entry_id 4K63 _symmetry.cell_setting ? _symmetry.Int_Tables_number 143 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 3' # loop_ _pdbx_struct_assembly.method_details _pdbx_struct_assembly.oligomeric_details _pdbx_struct_assembly.oligomeric_count _pdbx_struct_assembly.details _pdbx_struct_assembly.id PISA hexameric 6 author_and_software_defined_assembly 1 PISA hexameric 6 author_and_software_defined_assembly 2 PISA hexameric 6 author_and_software_defined_assembly 3 PISA hexameric 6 author_and_software_defined_assembly 4 # loop_ _pdbx_struct_assembly_gen.asym_id_list _pdbx_struct_assembly_gen.assembly_id _pdbx_struct_assembly_gen.oper_expression A,B,I,M 1 1,2,3 C,D,J 2 1,4,5 E,F,K,N 3 1,6,7 G,H,L 4 1,4,5 # 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_575 -y,x-y+2,z -0.5 -0.866025 0 0.866025 -0.5 0 0 0 1 -70.555 122.204845 0 3 'crystal symmetry operation' 3_355 -x+y-2,-x,z -0.5 0.866025 0 -0.866025 -0.5 0 0 0 1 -141.11 0 0 4 'crystal symmetry operation' 2_685 -y+1,x-y+3,z -0.5 -0.866025 0 0.866025 -0.5 0 0 0 1 -35.2775 183.307267 0 5 'crystal symmetry operation' 3_365 -x+y-2,-x+1,z -0.5 0.866025 0 -0.866025 -0.5 0 0 0 1 -176.3875 61.102422 0 6 'crystal symmetry operation' 2_585 -y,x-y+3,z -0.5 -0.866025 0 0.866025 -0.5 0 0 0 1 -105.8325 183.307267 0 7 'crystal symmetry operation' 3_255 -x+y-3,-x,z -0.5 0.866025 0 -0.866025 -0.5 0 0 0 1 -211.665 0 0 # loop_ _struct_asym.details _struct_asym.entity_id _struct_asym.id _struct_asym.pdbx_modified _struct_asym.pdbx_blank_PDB_chainid_flag ? 5 M N N ? 5 N N N # loop_ _pdbx_entity_branch.entity_id _pdbx_entity_branch.type 3 oligosaccharide 4 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 ? 3 2 1 GAL NAG C1 O1 . O4 HO4 . sing 2 ? 3 3 2 SIA GAL C2 O2 . O3 HO3 . sing 3 ? 4 2 1 SIA GAL C2 O2 . O3 HO3 . 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 3 n I NAG 1 I 1 NAG A 803 NAG 3 n I GAL 2 I 2 GAL A 802 GAL 3 n I SIA 3 I 3 SIA A 801 SIA 3 n J NAG 1 J 1 NAG C 803 NAG 3 n J GAL 2 J 2 GAL C 802 GAL 3 n J SIA 3 J 3 SIA C 801 SIA 4 n K GAL 1 K 1 GAL E 802 GAL 4 n K SIA 2 K 2 SIA E 801 SIA 3 n L NAG 1 L 1 NAG G 803 NAG 3 n L GAL 2 L 2 GAL G 802 GAL 3 n L SIA 3 L 3 SIA G 801 SIA # 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 5 A CYS 8 1_555 B SG CYS 137 B CYS 471 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.031 ? disulf ? disulf2 A SG CYS 43 A CYS 46 1_555 A SG CYS 275 A CYS 278 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.029 ? disulf ? disulf3 A SG CYS 56 A CYS 59 1_555 A SG CYS 68 A CYS 71 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.03 ? disulf ? disulf4 A SG CYS 91 A CYS 94 1_555 A SG CYS 136 A CYS 139 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.035 ? disulf ? disulf5 A SG CYS 279 A CYS 282 1_555 A SG CYS 303 A CYS 306 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.026 ? disulf ? disulf6 B SG CYS 144 B CYS 478 1_555 B SG CYS 148 B CYS 482 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.031 ? disulf ? disulf7 C SG CYS 5 C CYS 8 1_555 D SG CYS 137 D CYS 471 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.032 ? disulf ? disulf8 C SG CYS 43 C CYS 46 1_555 C SG CYS 275 C CYS 278 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.031 ? disulf ? disulf9 C SG CYS 56 C CYS 59 1_555 C SG CYS 68 C CYS 71 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.034 ? disulf ? disulf10 C SG CYS 91 C CYS 94 1_555 C SG CYS 136 C CYS 139 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.037 ? disulf ? disulf11 C SG CYS 279 C CYS 282 1_555 C SG CYS 303 C CYS 306 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.027 ? disulf ? disulf12 D SG CYS 144 D CYS 478 1_555 D SG CYS 148 D CYS 482 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.03 ? disulf ? disulf13 E SG CYS 5 E CYS 8 1_555 F SG CYS 137 F CYS 471 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.029 ? disulf ? disulf14 E SG CYS 43 E CYS 46 1_555 E SG CYS 275 E CYS 278 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.027 ? disulf ? disulf15 E SG CYS 56 E CYS 59 1_555 E SG CYS 68 E CYS 71 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.028 ? disulf ? disulf16 E SG CYS 91 E CYS 94 1_555 E SG CYS 136 E CYS 139 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.034 ? disulf ? disulf17 E SG CYS 279 E CYS 282 1_555 E SG CYS 303 E CYS 306 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.025 ? disulf ? disulf18 F SG CYS 144 F CYS 478 1_555 F SG CYS 148 F CYS 482 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.031 ? disulf ? disulf19 G SG CYS 5 G CYS 8 1_555 H SG CYS 137 H CYS 471 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.031 ? disulf ? disulf20 G SG CYS 43 G CYS 46 1_555 G SG CYS 275 G CYS 278 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.029 ? disulf ? disulf21 G SG CYS 56 G CYS 59 1_555 G SG CYS 68 G CYS 71 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.026 ? disulf ? disulf22 G SG CYS 91 G CYS 94 1_555 G SG CYS 136 G CYS 139 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.038 ? disulf ? disulf23 G SG CYS 279 G CYS 282 1_555 G SG CYS 303 G CYS 306 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.026 ? disulf ? disulf24 H SG CYS 144 H CYS 478 1_555 H SG CYS 148 H CYS 482 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.029 ? covale ? covale1 A ND2 ASN 166 A ASN 169 1_555 M C1 NAG . A NAG 601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.451 ? covale ? covale2 E ND2 ASN 166 E ASN 169 1_555 N C1 NAG . E NAG 601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.447 ? covale ? covale3 I O4 NAG . I NAG 1 1_555 I C1 GAL . I GAL 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.442 ? covale ? covale4 I O3 GAL . I GAL 2 1_555 I C2 SIA . I SIA 3 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.447 ? covale ? covale5 J O4 NAG . J NAG 1 1_555 J C1 GAL . J GAL 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.442 ? covale ? covale6 J O3 GAL . J GAL 2 1_555 J C2 SIA . J SIA 3 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.439 ? covale ? covale7 K O3 GAL . K GAL 1 1_555 K C2 SIA . K SIA 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.448 ? covale ? covale8 L O4 NAG . L NAG 1 1_555 L C1 GAL . L GAL 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.443 ? covale ? covale9 L O3 GAL . L GAL 2 1_555 L C2 SIA . L SIA 3 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.445 ? # _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 259 n n C1 O1 NAG sing 260 n n C1 O5 NAG sing 261 n n C1 H1 NAG sing 262 n n C2 C3 NAG sing 263 n n C2 N2 NAG sing 264 n n C2 H2 NAG sing 265 n n C3 C4 NAG sing 266 n n C3 O3 NAG sing 267 n n C3 H3 NAG sing 268 n n C4 C5 NAG sing 269 n n C4 O4 NAG sing 270 n n C4 H4 NAG sing 271 n n C5 C6 NAG sing 272 n n C5 O5 NAG sing 273 n n C5 H5 NAG sing 274 n n C6 O6 NAG sing 275 n n C6 H61 NAG sing 276 n n C6 H62 NAG sing 277 n n C7 C8 NAG sing 278 n n C7 N2 NAG sing 279 n n C7 O7 NAG doub 280 n n C8 H81 NAG sing 281 n n C8 H82 NAG sing 282 n n C8 H83 NAG sing 283 n n N2 HN2 NAG sing 284 n n O1 HO1 NAG sing 285 n n O3 HO3 NAG sing 286 n n O4 HO4 NAG sing 287 n n O6 HO6 NAG sing 288 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 4K63 _atom_sites.fract_transf_matrix[1][1] 0.014173 _atom_sites.fract_transf_matrix[1][2] 0.008183 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.016366 _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] 0.001975 _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 M 5 NAG A 1 601 601 NAG NAG . N 5 NAG E 1 601 601 NAG NAG . # 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 . . . M 5 -97.016 25.571 26.523 1 51.4 ? C1 NAG 601 A 1 HETATM 2 C C2 NAG . . . M 5 -95.81 24.727 26.945 1 47.49 ? C2 NAG 601 A 1 HETATM 3 C C3 NAG . . . M 5 -95.792 23.327 26.328 1 46.98 ? C3 NAG 601 A 1 HETATM 4 C C4 NAG . . . M 5 -97.153 22.657 26.439 1 47.04 ? C4 NAG 601 A 1 HETATM 5 C C5 NAG . . . M 5 -98.243 23.591 25.919 1 44.1 ? C5 NAG 601 A 1 HETATM 6 C C6 NAG . . . M 5 -99.618 22.96 26.088 1 43.53 ? C6 NAG 601 A 1 HETATM 7 C C7 NAG . . . M 5 -93.518 25.373 27.386 1 48.21 ? C7 NAG 601 A 1 HETATM 8 C C8 NAG . . . M 5 -92.241 25.851 26.762 1 43 ? C8 NAG 601 A 1 HETATM 9 N N2 NAG . . . M 5 -94.594 25.439 26.607 1 33.98 ? N2 NAG 601 A 1 HETATM 10 O O3 NAG . . . M 5 -94.829 22.533 26.982 1 31.89 ? O3 NAG 601 A 1 HETATM 11 O O4 NAG . . . M 5 -97.149 21.441 25.719 1 41.02 ? O4 NAG 601 A 1 HETATM 12 O O5 NAG . . . M 5 -98.228 24.833 26.604 1 50.87 ? O5 NAG 601 A 1 HETATM 13 O O6 NAG . . . M 5 -100.584 23.981 26.159 1 45.46 ? O6 NAG 601 A 1 HETATM 14 O O7 NAG . . . M 5 -93.534 24.947 28.544 1 44.58 ? O7 NAG 601 A 1 # _model_server_stats.io_time_ms 167 _model_server_stats.parse_time_ms 11 _model_server_stats.create_model_time_ms 16 _model_server_stats.query_time_ms 269 _model_server_stats.encode_time_ms 4 _model_server_stats.element_count 14 #