data_6D8D # _model_server_result.job_id lD1f6PYdCIoR5PCQJBT44A _model_server_result.datetime_utc '2024-11-30 23:29:06' _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 6d8d # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"K","auth_seq_id":405}' # _entry.id 6D8D # _exptl.entry_id 6D8D _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 180.156 _entity.id 6 _entity.src_method man _entity.type non-polymer _entity.pdbx_description beta-D-galactopyranose _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 124.21 _cell.angle_gamma 90 _cell.entry_id 6D8D _cell.length_a 203.571 _cell.length_b 117.866 _cell.length_c 119.86 _cell.Z_PDB 12 _cell.pdbx_unique_axis ? # _symmetry.entry_id 6D8D _symmetry.cell_setting ? _symmetry.Int_Tables_number 5 _symmetry.space_group_name_Hall . _symmetry.space_group_name_H-M 'C 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 _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 ? 6 K N N ? 6 N N N ? 6 R 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 . O3 HO3 . sing 2 ? 3 3 1 SIA NAG C2 O2 . O6 HO6 . sing 3 ? 4 2 1 GAL NAG C1 O1 . 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 G NAG 1 G 1 NAG A 409 NAG 3 n G GAL 2 G 2 GAL A 410 GAL 3 n G SIA 3 G 3 SIA A 408 SIA 3 n H NAG 1 H 1 NAG C 409 NAG 3 n H GAL 2 H 2 GAL C 410 GAL 3 n H SIA 3 H 3 SIA C 408 SIA 4 n I NAG 1 I 1 NAG E 409 NAG 4 n I GAL 2 I 2 GAL E 410 GAL # 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 4 A CYS 4 1_555 B SG CYS 137 B CYS 137 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.029 ? disulf ? disulf2 A SG CYS 42 A CYS 42 1_555 A SG CYS 268 A CYS 268 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.814 ? disulf ? disulf3 A SG CYS 54 A CYS 54 1_555 A SG CYS 66 A CYS 66 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.011 ? disulf ? disulf4 A SG CYS 87 A CYS 87 1_555 A SG CYS 129 A CYS 129 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.021 ? disulf ? disulf5 A SG CYS 272 A CYS 272 1_555 A SG CYS 296 A CYS 296 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.019 ? disulf ? disulf6 B SG CYS 144 B CYS 144 1_555 B SG CYS 148 B CYS 148 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.048 ? disulf ? disulf7 C SG CYS 4 C CYS 4 1_555 D SG CYS 137 D CYS 137 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.029 ? disulf ? disulf8 C SG CYS 42 C CYS 42 1_555 C SG CYS 268 C CYS 268 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.826 ? disulf ? disulf9 C SG CYS 54 C CYS 54 1_555 C SG CYS 66 C CYS 66 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.003 ? disulf ? disulf10 C SG CYS 87 C CYS 87 1_555 C SG CYS 129 C CYS 129 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.017 ? disulf ? disulf11 C SG CYS 272 C CYS 272 1_555 C SG CYS 296 C CYS 296 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.025 ? disulf ? disulf12 D SG CYS 144 D CYS 144 1_555 D SG CYS 148 D CYS 148 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.05 ? disulf ? disulf13 E SG CYS 4 E CYS 4 1_555 F SG CYS 137 F CYS 137 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.019 ? disulf ? disulf14 E SG CYS 42 E CYS 42 1_555 E SG CYS 268 E CYS 268 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.848 ? disulf ? disulf15 E SG CYS 54 E CYS 54 1_555 E SG CYS 66 E CYS 66 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.026 ? disulf ? disulf16 E SG CYS 87 E CYS 87 1_555 E SG CYS 129 E CYS 129 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.019 ? disulf ? disulf17 E SG CYS 272 E CYS 272 1_555 E SG CYS 296 E CYS 296 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.017 ? disulf ? disulf18 F SG CYS 144 F CYS 144 1_555 F SG CYS 148 F CYS 148 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.053 ? covale ? covale1 A ND2 ASN 231 A ASN 231 1_555 J C1 NAG . A NAG 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.435 ? covale ? covale2 B ND2 ASN 82 B ASN 82 1_555 L C1 NAG . B NAG 301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.493 ? covale ? covale3 C ND2 ASN 231 C ASN 231 1_555 M C1 NAG . C NAG 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.45 ? covale ? covale4 D ND2 ASN 82 D ASN 82 1_555 O C1 NAG . D NAG 301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.474 ? covale ? covale5 E ND2 ASN 231 E ASN 231 1_555 P C1 NAG . E NAG 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.433 ? covale ? covale6 F ND2 ASN 82 F ASN 82 1_555 S C1 NAG . F NAG 301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.507 ? covale ? covale7 G O3 NAG . G NAG 1 1_555 G C1 GAL . G GAL 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.462 sing covale ? covale8 G O6 NAG . G NAG 1 1_555 G C2 SIA . G SIA 3 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.468 ? covale ? covale9 H O3 NAG . H NAG 1 1_555 H C1 GAL . H GAL 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.462 sing covale ? covale10 H O6 NAG . H NAG 1 1_555 H C2 SIA . H SIA 3 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.468 ? covale ? covale11 I O3 NAG . I NAG 1 1_555 I C1 GAL . I GAL 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.449 sing # _chem_comp.formula 'C6 H12 O6' _chem_comp.formula_weight 180.156 _chem_comp.id GAL _chem_comp.mon_nstd_flag . _chem_comp.name beta-D-galactopyranose _chem_comp.type 'd-saccharide, beta linking' _chem_comp.pdbx_synonyms beta-D-galactose;D-galactose;galactose # 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 GAL sing 83 n n C1 O1 GAL sing 84 n n C1 O5 GAL sing 85 n n C1 H1 GAL sing 86 n n C2 C3 GAL sing 87 n n C2 O2 GAL sing 88 n n C2 H2 GAL sing 89 n n C3 C4 GAL sing 90 n n C3 O3 GAL sing 91 n n C3 H3 GAL sing 92 n n C4 C5 GAL sing 93 n n C4 O4 GAL sing 94 n n C4 H4 GAL sing 95 n n C5 C6 GAL sing 96 n n C5 O5 GAL sing 97 n n C5 H5 GAL sing 98 n n C6 O6 GAL sing 99 n n C6 H61 GAL sing 100 n n C6 H62 GAL sing 101 n n O1 HO1 GAL sing 102 n n O2 HO2 GAL sing 103 n n O3 HO3 GAL sing 104 n n O4 HO4 GAL sing 105 n n O6 HO6 GAL sing 106 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 GAL DGalpb 'CONDENSED IUPAC CARBOHYDRATE SYMBOL' GMML 1 GAL b-D-galactopyranose 'COMMON NAME' GMML 1 GAL b-D-Galp 'IUPAC CARBOHYDRATE SYMBOL' PDB-CARE 1 GAL Gal 'SNFG CARBOHYDRATE SYMBOL' GMML 1 # _atom_sites.entry_id 6D8D _atom_sites.fract_transf_matrix[1][1] 0.004912 _atom_sites.fract_transf_matrix[1][2] 0 _atom_sites.fract_transf_matrix[1][3] 0.00334 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.008484 _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] 0.010089 _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 J 5 NAG A 1 401 404 NAG NAG . K 6 GAL A 1 405 411 GAL GAL . L 5 NAG B 1 301 201 NAG NAG . M 5 NAG C 1 401 404 NAG NAG . N 6 GAL C 1 405 411 GAL GAL . O 5 NAG D 1 301 201 NAG NAG . P 5 NAG E 1 401 404 NAG NAG . Q 7 SIA E 1 402 408 SIA SIA . R 6 GAL E 1 405 411 GAL GAL . S 5 NAG F 1 301 201 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 GAL . . . K 6 28.301 -25.423 -36.143 1 134.95 ? C1 GAL 405 A 1 HETATM 2 C C2 GAL . . . K 6 28.881 -26.129 -37.363 1 133.21 ? C2 GAL 405 A 1 HETATM 3 C C3 GAL . . . K 6 27.975 -27.309 -37.729 1 133.78 ? C3 GAL 405 A 1 HETATM 4 C C4 GAL . . . K 6 27.724 -28.252 -36.545 1 135.47 ? C4 GAL 405 A 1 HETATM 5 C C5 GAL . . . K 6 27.511 -27.539 -35.178 1 135.22 ? C5 GAL 405 A 1 HETATM 6 C C6 GAL . . . K 6 27.717 -28.473 -33.95 1 129.48 ? C6 GAL 405 A 1 HETATM 7 O O1 GAL . . . K 6 29.082 -24.245 -35.868 1 132.92 ? O1 GAL 405 A 1 HETATM 8 O O2 GAL . . . K 6 29.03 -25.18 -38.431 1 129.72 ? O2 GAL 405 A 1 HETATM 9 O O3 GAL . . . K 6 28.584 -28.067 -38.782 1 130.98 ? O3 GAL 405 A 1 HETATM 10 O O4 GAL . . . K 6 28.83 -29.165 -36.502 1 140.58 ? O4 GAL 405 A 1 HETATM 11 O O5 GAL . . . K 6 28.32 -26.348 -35.038 1 139.92 ? O5 GAL 405 A 1 HETATM 12 O O6 GAL . . . K 6 28.966 -28.27 -33.262 1 122.91 ? O6 GAL 405 A 1 # _model_server_stats.io_time_ms 30 _model_server_stats.parse_time_ms 14 _model_server_stats.create_model_time_ms 25 _model_server_stats.query_time_ms 308 _model_server_stats.encode_time_ms 7 _model_server_stats.element_count 12 #