data_4K67 # _model_server_result.job_id WoDH-kxXmvO22D117NvYnA _model_server_result.datetime_utc '2024-11-26 15:21:40' _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 4k67 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"O","auth_seq_id":601}' # _entry.id 4K67 # _exptl.entry_id 4K67 _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 4 _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 4K67 _cell.length_a 70.626 _cell.length_b 70.626 _cell.length_c 494.52 _cell.Z_PDB 12 _cell.pdbx_unique_axis ? # _symmetry.entry_id 4K67 _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,N 2 1,2,3 E,F,K,O 3 1,4,5 G,H,L,P 4 1,6,7 # 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_555 -y,x-y,z -0.5 -0.866025 0 0.866025 -0.5 0 0 0 1 0 0 0 3 'crystal symmetry operation' 3_555 -x+y,-x,z -0.5 0.866025 0 -0.866025 -0.5 0 0 0 1 0 0 0 4 'crystal symmetry operation' 2_545 -y,x-y-1,z -0.5 -0.866025 0 0.866025 -0.5 0 0 0 1 35.313 -61.16391 0 5 'crystal symmetry operation' 3_655 -x+y+1,-x,z -0.5 0.866025 0 -0.866025 -0.5 0 0 0 1 70.626 0 0 6 'crystal symmetry operation' 2_655 -y+1,x-y,z -0.5 -0.866025 0 0.866025 -0.5 0 0 0 1 70.626 0 0 7 'crystal symmetry operation' 3_665 -x+y+1,-x+1,z -0.5 0.866025 0 -0.866025 -0.5 0 0 0 1 35.313 61.16391 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 ? 5 O N N ? 5 P 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 SIA GAL C2 O2 . O6 HO6 . sing 2 ? 4 2 1 GAL NAG C1 O1 . O4 HO4 . sing 3 ? 4 3 2 SIA GAL C2 O2 . O6 HO6 . 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 GAL 1 I 1 GAL A 802 GAL 3 n I SIA 2 I 2 SIA A 801 SIA 3 n J GAL 1 J 1 GAL C 802 GAL 3 n J SIA 2 J 2 SIA C 801 SIA 4 n K NAG 1 K 1 NAG E 803 NAG 4 n K GAL 2 K 2 GAL E 802 GAL 4 n K SIA 3 K 3 SIA E 801 SIA 4 n L NAG 1 L 1 NAG G 803 NAG 4 n L GAL 2 L 2 GAL G 802 GAL 4 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 ? ? ? ? ? ? ? ? ? ? ? ? 2.051 ? disulf ? disulf2 A SG CYS 43 A CYS 46 1_555 A SG CYS 275 A CYS 278 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.044 ? disulf ? disulf3 A SG CYS 56 A CYS 59 1_555 A SG CYS 68 A CYS 71 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.025 ? disulf ? disulf4 A SG CYS 91 A CYS 94 1_555 A SG CYS 136 A CYS 139 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.055 ? disulf ? disulf5 A SG CYS 279 A CYS 282 1_555 A SG CYS 303 A CYS 306 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.042 ? disulf ? disulf6 B SG CYS 144 B CYS 478 1_555 B SG CYS 148 B CYS 482 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.035 ? disulf ? disulf7 C SG CYS 5 C CYS 8 1_555 D SG CYS 137 D CYS 471 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.051 ? disulf ? disulf8 C SG CYS 43 C CYS 46 1_555 C SG CYS 275 C CYS 278 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.039 ? disulf ? disulf9 C SG CYS 56 C CYS 59 1_555 C SG CYS 68 C CYS 71 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.027 ? disulf ? disulf10 C SG CYS 91 C CYS 94 1_555 C SG CYS 136 C CYS 139 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.056 ? disulf ? disulf11 C SG CYS 279 C CYS 282 1_555 C SG CYS 303 C CYS 306 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.04 ? disulf ? disulf12 D SG CYS 144 D CYS 478 1_555 D SG CYS 148 D CYS 482 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.036 ? disulf ? disulf13 E SG CYS 5 E CYS 8 1_555 F SG CYS 137 F CYS 471 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.022 ? disulf ? disulf14 E SG CYS 43 E CYS 46 1_555 E SG CYS 275 E CYS 278 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.041 ? disulf ? disulf15 E SG CYS 56 E CYS 59 1_555 E SG CYS 68 E CYS 71 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.032 ? disulf ? disulf16 E SG CYS 91 E CYS 94 1_555 E SG CYS 136 E CYS 139 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.055 ? disulf ? disulf17 E SG CYS 279 E CYS 282 1_555 E SG CYS 303 E CYS 306 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.036 ? disulf ? disulf18 F SG CYS 144 F CYS 478 1_555 F SG CYS 148 F CYS 482 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.035 ? disulf ? disulf19 G SG CYS 5 G CYS 8 1_555 H SG CYS 137 H CYS 471 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.029 ? disulf ? disulf20 G SG CYS 43 G CYS 46 1_555 G SG CYS 275 G CYS 278 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.04 ? disulf ? disulf21 G SG CYS 56 G CYS 59 1_555 G SG CYS 68 G CYS 71 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.036 ? disulf ? disulf22 G SG CYS 91 G CYS 94 1_555 G SG CYS 136 G CYS 139 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.058 ? disulf ? disulf23 G SG CYS 279 G CYS 282 1_555 G SG CYS 303 G CYS 306 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.032 ? disulf ? disulf24 H SG CYS 144 H CYS 478 1_555 H SG CYS 148 H CYS 482 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.034 ? covale ? covale1 A ND2 ASN 166 A ASN 169 1_555 M C1 NAG . A NAG 601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.454 ? covale ? covale2 C ND2 ASN 166 C ASN 169 1_555 N C1 NAG . C NAG 601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.45 ? covale ? covale3 E ND2 ASN 166 E ASN 169 1_555 O C1 NAG . E NAG 601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.447 ? covale ? covale4 G ND2 ASN 166 G ASN 169 1_555 P C1 NAG . G NAG 601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.445 ? covale ? covale5 I O6 GAL . I GAL 1 1_555 I C2 SIA . I SIA 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.426 ? covale ? covale6 J O6 GAL . J GAL 1 1_555 J C2 SIA . J SIA 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.436 ? covale ? covale7 K O4 NAG . K NAG 1 1_555 K C1 GAL . K GAL 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.447 ? covale ? covale8 K O6 GAL . K GAL 2 1_555 K C2 SIA . K SIA 3 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.436 ? covale ? covale9 L O4 NAG . L NAG 1 1_555 L C1 GAL . L GAL 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.439 ? covale ? covale10 L O6 GAL . L GAL 2 1_555 L C2 SIA . L SIA 3 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.428 ? # _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 4K67 _atom_sites.fract_transf_matrix[1][1] 0.014159 _atom_sites.fract_transf_matrix[1][2] 0.008175 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.01635 _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] 0.002022 _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 C 1 601 601 NAG NAG . O 5 NAG E 1 601 601 NAG NAG . P 5 NAG G 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 . . . O 5 9.534 -4.927 397.779 1 68.63 ? C1 NAG 601 E 1 HETATM 2 C C2 NAG . . . O 5 9.114 -6.193 398.514 1 67.76 ? C2 NAG 601 E 1 HETATM 3 C C3 NAG . . . O 5 7.743 -6.717 398.083 1 79.15 ? C3 NAG 601 E 1 HETATM 4 C C4 NAG . . . O 5 6.727 -5.591 397.94 1 85.11 ? C4 NAG 601 E 1 HETATM 5 C C5 NAG . . . O 5 7.318 -4.532 397.014 1 75.74 ? C5 NAG 601 E 1 HETATM 6 C C6 NAG . . . O 5 6.343 -3.396 396.704 1 81.72 ? C6 NAG 601 E 1 HETATM 7 C C7 NAG . . . O 5 10.817 -7.811 399.169 1 44.73 ? C7 NAG 601 E 1 HETATM 8 C C8 NAG . . . O 5 11.69 -8.899 398.653 1 53.41 ? C8 NAG 601 E 1 HETATM 9 N N2 NAG . . . O 5 10.115 -7.195 398.229 1 48.99 ? N2 NAG 601 E 1 HETATM 10 O O3 NAG . . . O 5 7.28 -7.674 399.014 1 68.59 ? O3 NAG 601 E 1 HETATM 11 O O4 NAG . . . O 5 5.501 -6.099 397.445 1 76.65 ? O4 NAG 601 E 1 HETATM 12 O O5 NAG . . . O 5 8.477 -4.001 397.619 1 71.13 ? O5 NAG 601 E 1 HETATM 13 O O6 NAG . . . O 5 6.218 -2.527 397.81 1 84.1 ? O6 NAG 601 E 1 HETATM 14 O O7 NAG . . . O 5 10.789 -7.547 400.369 1 45.42 ? O7 NAG 601 E 1 # _model_server_stats.io_time_ms 158 _model_server_stats.parse_time_ms 25 _model_server_stats.create_model_time_ms 17 _model_server_stats.query_time_ms 315 _model_server_stats.encode_time_ms 4 _model_server_stats.element_count 14 #