data_5JPN # _model_server_result.job_id eQzKCNbIbcbJmp5yhqPWVg _model_server_result.datetime_utc '2025-01-08 07:16:48' _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 5jpn # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"I","auth_seq_id":1508}' # _entry.id 5JPN # _exptl.entry_id 5JPN _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 221.208 _entity.id 8 _entity.src_method man _entity.type non-polymer _entity.pdbx_description 2-acetamido-2-deoxy-alpha-D-galactopyranose _entity.pdbx_number_of_molecules 1 _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 5JPN _cell.length_a 85.45 _cell.length_b 103.31 _cell.length_c 256.03 _cell.Z_PDB 4 _cell.pdbx_unique_axis ? # _symmetry.entry_id 5JPN _symmetry.cell_setting ? _symmetry.Int_Tables_number 19 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 21 21 21' # _pdbx_struct_assembly.method_details PISA _pdbx_struct_assembly.oligomeric_details trimeric _pdbx_struct_assembly.oligomeric_count 3 _pdbx_struct_assembly.details 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 _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 # _struct_asym.details ? _struct_asym.entity_id 8 _struct_asym.id I _struct_asym.pdbx_modified N _struct_asym.pdbx_blank_PDB_chainid_flag N # loop_ _pdbx_entity_branch.entity_id _pdbx_entity_branch.type 4 oligosaccharide 5 oligosaccharide 6 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 ? 5 2 1 NAG NAG C1 O1 . O4 HO4 . sing 4 ? 6 2 1 NAG NAG C1 O1 . O4 HO4 . sing 5 ? 6 3 2 BMA NAG C1 O1 . O4 HO4 . sing 6 ? 6 4 3 MAN BMA C1 O1 . O3 HO3 . sing 7 ? 6 5 3 MAN BMA C1 O1 . 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 4 n D NAG 1 D 1 NAG A 701 NAG 4 n D NAG 2 D 2 NAG A 702 NAG 4 n D BMA 3 D 3 BMA A 703 BMA 5 n E NAG 1 E 1 NAG B 1810 NAG 5 n E NAG 2 E 2 NAG B 1811 NAG 6 n F NAG 1 F 1 NAG B 1801 NAG 6 n F NAG 2 F 2 NAG B 1802 NAG 6 n F BMA 3 F 3 BMA B 1803 BMA 6 n F MAN 4 F 4 MAN B 1805 MAN 6 n F MAN 5 F 5 MAN B 1804 MAN 6 n G NAG 1 G 1 NAG B 1820 NAG 6 n G NAG 2 G 2 NAG B 1821 NAG 6 n G BMA 3 G 3 BMA B 1822 BMA 6 n G MAN 4 G 4 MAN B 1824 MAN 6 n G MAN 5 G 5 MAN B 1823 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 49 A CYS 68 1_555 A SG CYS 78 A CYS 97 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.033 ? disulf ? disulf2 A SG CYS 548 A CYS 567 1_555 B SG CYS 141 B CYS 820 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.029 ? disulf ? disulf3 A SG CYS 616 A CYS 635 1_555 A SG CYS 650 A CYS 669 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.031 ? disulf ? disulf4 B SG CYS 23 B CYS 702 1_555 B SG CYS 49 B CYS 728 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.03 ? disulf ? disulf5 B SG CYS 24 B CYS 703 1_555 B SG CYS 56 B CYS 735 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.031 ? disulf ? disulf6 B SG CYS 37 B CYS 716 1_555 B SG CYS 57 B CYS 736 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.034 ? disulf ? disulf7 B SG CYS 197 B CYS 876 1_555 C SG CYS 136 C CYS 1590 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.033 ? disulf ? disulf8 B SG CYS 715 B CYS 1394 1_555 C SG CYS 112 C CYS 1566 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.032 ? disulf ? disulf9 C SG CYS 17 C CYS 1471 1_555 C SG CYS 81 C CYS 1535 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.032 ? disulf ? disulf10 C SG CYS 129 C CYS 1583 1_555 C SG CYS 134 C CYS 1588 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.032 ? disulf ? disulf11 C SG CYS 141 C CYS 1595 1_555 C SG CYS 219 C CYS 1673 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.03 ? disulf ? disulf12 C SG CYS 164 C CYS 1618 1_555 C SG CYS 288 C CYS 1742 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.031 ? disulf ? disulf13 C SG CYS 264 C CYS 1718 1_555 C SG CYS 273 C CYS 1727 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.032 ? covale ? covale1 A ND2 ASN 207 A ASN 226 1_555 D C1 NAG . D NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.443 ? covale ? covale2 B ND2 ASN 183 B ASN 862 1_555 F C1 NAG . F NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.439 ? covale ? covale3 B OG1 THR 565 B THR 1244 1_555 I C1 A2G . B A2G 1508 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.375 ? covale ? covale4 B ND2 ASN 649 B ASN 1328 1_555 E C1 NAG . E NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.443 ? covale ? covale5 B ND2 ASN 712 B ASN 1391 1_555 G C1 NAG . G NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.44 ? covale ? covale6 D O4 NAG . D NAG 1 1_555 D C1 NAG . D NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.44 ? covale ? covale7 D O4 NAG . D NAG 2 1_555 D C1 BMA . D BMA 3 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.452 ? covale ? covale8 E O4 NAG . E NAG 1 1_555 E C1 NAG . E NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.447 ? covale ? covale9 F O4 NAG . F NAG 1 1_555 F C1 NAG . F NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.437 ? covale ? covale10 F O4 NAG . F NAG 2 1_555 F C1 BMA . F BMA 3 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.445 ? covale ? covale11 F O3 BMA . F BMA 3 1_555 F C1 MAN . F MAN 4 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.443 ? covale ? covale12 F O6 BMA . F BMA 3 1_555 F C1 MAN . F MAN 5 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.44 ? covale ? covale13 G O4 NAG . G NAG 1 1_555 G C1 NAG . G NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.43 ? covale ? covale14 G O4 NAG . G NAG 2 1_555 G C1 BMA . G BMA 3 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.447 ? covale ? covale15 G O3 BMA . G BMA 3 1_555 G C1 MAN . G MAN 4 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.439 ? covale ? covale16 G O6 BMA . G BMA 3 1_555 G C1 MAN . G MAN 5 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.441 ? metalc ? metalc1 A OD2 ASP 202 A ASP 221 1_555 H PB PBM . A PBM 704 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.749 ? metalc ? metalc2 B OD1 ASP 111 B ASP 790 1_555 L PB PBM . C PBM 1801 4_445 ? ? ? ? ? ? ? ? ? ? ? ? 2.751 ? metalc ? metalc3 B OD2 ASP 111 B ASP 790 1_555 L PB PBM . C PBM 1801 4_445 ? ? ? ? ? ? ? ? ? ? ? ? 2.749 ? metalc ? metalc4 B OE1 GLU 128 B GLU 807 1_555 J PB PBM . B PBM 1514 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.75 ? metalc ? metalc5 B OE2 GLU 128 B GLU 807 1_555 J PB PBM . B PBM 1514 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.75 ? metalc ? metalc6 B OE1 GLU 678 B GLU 1357 1_555 K PB PBM . B PBM 1515 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.75 ? metalc ? metalc7 B OE2 GLU 678 B GLU 1357 1_555 K PB PBM . B PBM 1515 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.751 ? metalc ? metalc8 C OE1 GLU 138 C GLU 1592 1_555 L PB PBM . C PBM 1801 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.749 ? metalc ? metalc9 C OE2 GLU 138 C GLU 1592 1_555 L PB PBM . C PBM 1801 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.75 ? # _chem_comp.formula 'C8 H15 N O6' _chem_comp.formula_weight 221.208 _chem_comp.id A2G _chem_comp.mon_nstd_flag . _chem_comp.name 2-acetamido-2-deoxy-alpha-D-galactopyranose _chem_comp.type 'd-saccharide, alpha linking' _chem_comp.pdbx_synonyms N-acetyl-alpha-D-galactosamine;2-acetamido-2-deoxy-alpha-D-galactose;2-acetamido-2-deoxy-D-galactose;2-acetamido-2-deoxy-galactose;N-ACETYL-2-DEOXY-2-AMINO-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 O5 C5 A2G sing 1 n n C1 O5 A2G sing 2 n n C1 C2 A2G sing 3 n n C1 H1 A2G sing 4 n n O1 C1 A2G sing 5 n n O1 HO1 A2G sing 6 n n C2 C3 A2G sing 7 n n C2 H2 A2G sing 8 n n N2 C2 A2G sing 9 n n N2 HN2 A2G sing 10 n n C3 C4 A2G sing 11 n n C3 O3 A2G sing 12 n n C3 H3 A2G sing 13 n n O3 HO3 A2G sing 14 n n C4 O4 A2G sing 15 n n C4 H4 A2G sing 16 n n O4 HO4 A2G sing 17 n n C5 C4 A2G sing 18 n n C5 C6 A2G sing 19 n n C5 H5 A2G sing 20 n n C6 O6 A2G sing 21 n n C6 H61 A2G sing 22 n n C7 N2 A2G sing 23 n n O7 C7 A2G doub 24 n n C8 C7 A2G sing 25 n n C8 H81 A2G sing 26 n n C8 H82 A2G sing 27 n n C8 H83 A2G sing 28 n n C6 H62 A2G sing 29 n n O6 HO6 A2G sing 30 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 A2G DGalpNAca 'CONDENSED IUPAC CARBOHYDRATE SYMBOL' GMML 1 A2G N-acetyl-a-D-galactopyranosamine 'COMMON NAME' GMML 1 A2G a-D-GalpNAc 'IUPAC CARBOHYDRATE SYMBOL' PDB-CARE 1 A2G GalNAc 'SNFG CARBOHYDRATE SYMBOL' GMML 1 # _atom_sites.entry_id 5JPN _atom_sites.fract_transf_matrix[1][1] 0.011703 _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] 0.00968 _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] 0.003906 _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 H 7 PBM A 1 704 2 PBM PBM . I 8 A2G B 1 1508 1830 A2G A2G . J 7 PBM B 1 1514 3 PBM PBM . K 7 PBM B 1 1515 4 PBM PBM . L 7 PBM C 1 1801 1 PBM PBM . # 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 O O5 A2G . . . I 8 -49.909 31.743 24.763 0.74 180.31 ? O5 A2G 1508 B 1 HETATM 2 C C1 A2G . . . I 8 -51.368 31.674 24.928 0.74 180.14 ? C1 A2G 1508 B 1 HETATM 3 C C2 A2G . . . I 8 -51.7 31.169 26.339 0.74 177.41 ? C2 A2G 1508 B 1 HETATM 4 N N2 A2G . . . I 8 -53.18 31.036 26.492 0.74 174.56 ? N2 A2G 1508 B 1 HETATM 5 C C3 A2G . . . I 8 -51.156 32.093 27.349 0.74 183.52 ? C3 A2G 1508 B 1 HETATM 6 O O3 A2G . . . I 8 -51.443 31.567 28.697 0.74 183.18 ? O3 A2G 1508 B 1 HETATM 7 C C4 A2G . . . I 8 -49.698 32.251 27.205 0.74 184.41 ? C4 A2G 1508 B 1 HETATM 8 O O4 A2G . . . I 8 -49.059 31.013 27.574 0.74 182.44 ? O4 A2G 1508 B 1 HETATM 9 C C5 A2G . . . I 8 -49.28 32.611 25.768 0.74 183.67 ? C5 A2G 1508 B 1 HETATM 10 C C6 A2G . . . I 8 -47.793 32.487 25.652 0.74 178.05 ? C6 A2G 1508 B 1 HETATM 11 O O6 A2G . . . I 8 -47.175 33.485 26.417 0.74 178.55 ? O6 A2G 1508 B 1 HETATM 12 C C7 A2G . . . I 8 -53.725 30.059 27.418 0.74 166.37 ? C7 A2G 1508 B 1 HETATM 13 O O7 A2G . . . I 8 -52.997 29.375 28.056 0.74 157.18 ? O7 A2G 1508 B 1 HETATM 14 C C8 A2G . . . I 8 -55.237 29.923 27.576 0.74 168.67 ? C8 A2G 1508 B 1 # _model_server_stats.io_time_ms 32 _model_server_stats.parse_time_ms 28 _model_server_stats.create_model_time_ms 43 _model_server_stats.query_time_ms 327 _model_server_stats.encode_time_ms 7 _model_server_stats.element_count 14 #