data_4GZ8 # _model_server_result.job_id RPeJNZvV7mTb0jjEhE16kw _model_server_result.datetime_utc '2024-12-20 18:52:10' _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 4gz8 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"L","auth_seq_id":807}' # _entry.id 4GZ8 # _exptl.entry_id 4GZ8 _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 221.208 _entity.id 7 _entity.src_method man _entity.type non-polymer _entity.pdbx_description 2-acetamido-2-deoxy-beta-D-glucopyranose _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 4GZ8 _cell.length_a 97.63 _cell.length_b 126.17 _cell.length_c 161.48 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 4GZ8 _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 dimeric _pdbx_struct_assembly.oligomeric_count 2 _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 _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 7 _struct_asym.id L _struct_asym.pdbx_modified N _struct_asym.pdbx_blank_PDB_chainid_flag N # loop_ _pdbx_entity_branch.entity_id _pdbx_entity_branch.type 2 oligosaccharide 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 ? 2 2 1 NAG NAG C1 O1 . O4 HO4 . sing 2 ? 2 3 2 BMA NAG C1 O1 . O4 HO4 . sing 3 ? 2 4 3 MAN BMA C1 O1 . O3 HO3 . sing 4 ? 3 2 1 NAG NAG C1 O1 . O4 HO4 . sing 5 ? 4 2 1 NAG NAG C1 O1 . O4 HO4 . sing 6 ? 4 3 2 BMA NAG C1 O1 . O4 HO4 . sing 7 ? 4 4 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 2 n C NAG 1 C 1 NAG A 701 NAG 2 n C NAG 2 C 2 NAG A 702 NAG 2 n C BMA 3 C 3 BMA A 703 BMA 2 n C MAN 4 C 4 MAN A 704 MAN 3 n D NAG 1 D 1 NAG A 706 NAG 3 n D NAG 2 D 2 NAG A 707 NAG 4 n E NAG 1 E 1 NAG B 703 NAG 4 n E NAG 2 E 2 NAG B 704 NAG 4 n E BMA 3 E 3 BMA B 705 BMA 4 n E MAN 4 E 4 MAN B 706 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 86 A CYS 103 1_555 A SG CYS 97 A CYS 114 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.107 ? disulf ? disulf2 A SG CYS 115 A CYS 132 1_555 A SG CYS 124 A CYS 141 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.086 ? disulf ? disulf3 A SG CYS 252 A CYS 269 1_555 A SG CYS 364 A CYS 381 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.057 ? disulf ? disulf4 A SG CYS 276 A CYS 293 1_555 A SG CYS 324 A CYS 341 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.044 ? disulf ? disulf5 A SG CYS 500 A CYS 517 1_555 A SG CYS 518 A CYS 535 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.051 ? disulf ? disulf6 A SG CYS 507 A CYS 524 1_555 A SG CYS 550 A CYS 567 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.042 ? disulf ? disulf7 A SG CYS 510 A CYS 527 1_555 A SG CYS 525 A CYS 542 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.06 ? disulf ? disulf8 B SG CYS 86 B CYS 103 1_555 B SG CYS 97 B CYS 114 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.108 ? disulf ? disulf9 B SG CYS 115 B CYS 132 1_555 B SG CYS 124 B CYS 141 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.097 ? disulf ? disulf10 B SG CYS 252 B CYS 269 1_555 B SG CYS 364 B CYS 381 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.053 ? disulf ? disulf11 B SG CYS 276 B CYS 293 1_555 B SG CYS 324 B CYS 341 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.047 ? disulf ? disulf12 B SG CYS 500 B CYS 517 1_555 B SG CYS 518 B CYS 535 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.068 ? disulf ? disulf13 B SG CYS 507 B CYS 524 1_555 B SG CYS 550 B CYS 567 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.046 ? disulf ? disulf14 B SG CYS 510 B CYS 527 1_555 B SG CYS 525 B CYS 542 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.039 ? covale ? covale1 A ND2 ASN 36 A ASN 53 1_555 C C1 NAG . C NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.428 ? covale ? covale2 A ND2 ASN 108 A ASN 125 1_555 D C1 NAG . D NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.448 ? covale ? covale3 B ND2 ASN 36 B ASN 53 1_555 E C1 NAG . E NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.433 ? covale ? covale4 B ND2 ASN 108 B ASN 125 1_555 L C1 NAG . B NAG 807 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.468 ? covale ? covale5 C O4 NAG . C NAG 1 1_555 C C1 NAG . C NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.444 ? covale ? covale6 C O4 NAG . C NAG 2 1_555 C C1 BMA . C BMA 3 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.474 ? covale ? covale7 C O3 BMA . C BMA 3 1_555 C C1 MAN . C MAN 4 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.444 ? covale ? covale8 D O4 NAG . D NAG 1 1_555 D C1 NAG . D NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.439 ? covale ? covale9 E O4 NAG . E NAG 1 1_555 E C1 NAG . E NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.442 ? covale ? covale10 E O4 NAG . E NAG 2 1_555 E C1 BMA . E BMA 3 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.451 ? covale ? covale11 E O6 BMA . E BMA 3 1_555 E C1 MAN . E MAN 4 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.461 ? metalc ? metalc1 A O SER 37 A SER 54 1_555 H CA CA . A CA 809 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.94 ? metalc ? metalc2 A OE2 GLU 105 A GLU 122 1_555 G CA CA . A CA 808 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.379 ? metalc ? metalc3 A OE1 GLU 105 A GLU 122 1_555 G CA CA . A CA 808 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.525 ? metalc ? metalc4 A OD1 ASP 293 A ASP 310 1_555 F CA CA . A CA 807 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.421 ? metalc ? metalc5 A OD2 ASP 293 A ASP 310 1_555 F CA CA . A CA 807 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.478 ? metalc ? metalc6 B OE1 GLU 105 B GLU 122 1_555 K CA CA . B CA 802 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.576 ? metalc ? metalc7 B OE2 GLU 105 B GLU 122 1_555 K CA CA . B CA 802 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.593 ? metalc ? metalc8 B OD2 ASP 293 B ASP 310 1_555 J CA CA . B CA 801 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.455 ? metalc ? metalc9 B OD1 ASP 293 B ASP 310 1_555 J CA CA . B CA 801 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.502 ? metalc ? metalc10 B OE1 GLN 416 B GLN 433 1_555 J CA CA . B CA 801 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.26 ? # _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 289 n n C1 O1 NAG sing 290 n n C1 O5 NAG sing 291 n n C1 H1 NAG sing 292 n n C2 C3 NAG sing 293 n n C2 N2 NAG sing 294 n n C2 H2 NAG sing 295 n n C3 C4 NAG sing 296 n n C3 O3 NAG sing 297 n n C3 H3 NAG sing 298 n n C4 C5 NAG sing 299 n n C4 O4 NAG sing 300 n n C4 H4 NAG sing 301 n n C5 C6 NAG sing 302 n n C5 O5 NAG sing 303 n n C5 H5 NAG sing 304 n n C6 O6 NAG sing 305 n n C6 H61 NAG sing 306 n n C6 H62 NAG sing 307 n n C7 C8 NAG sing 308 n n C7 N2 NAG sing 309 n n C7 O7 NAG doub 310 n n C8 H81 NAG sing 311 n n C8 H82 NAG sing 312 n n C8 H83 NAG sing 313 n n N2 HN2 NAG sing 314 n n O1 HO1 NAG sing 315 n n O3 HO3 NAG sing 316 n n O4 HO4 NAG sing 317 n n O6 HO6 NAG sing 318 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 4GZ8 _atom_sites.fract_transf_matrix[1][1] 0.010243 _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] 0.007926 _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] 0.006193 _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 F 5 CA A 1 807 708 CA CA . G 5 CA A 1 808 709 CA CA . H 5 CA A 1 809 710 CA CA . I 6 ACT A 1 810 711 ACT ACT . J 5 CA B 1 801 701 CA CA . K 5 CA B 1 802 702 CA CA . L 7 NAG B 1 807 707 NAG NAG . M 6 ACT B 1 808 709 ACT ACT . # 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 . . . L 7 24.426 -24.604 49.279 1 53.42 ? C1 NAG 807 B 1 HETATM 2 C C2 NAG . . . L 7 24.169 -24.942 50.728 1 56.93 ? C2 NAG 807 B 1 HETATM 3 C C3 NAG . . . L 7 25.33 -24.449 51.589 1 60.61 ? C3 NAG 807 B 1 HETATM 4 C C4 NAG . . . L 7 26.607 -25.23 51.277 1 61.53 ? C4 NAG 807 B 1 HETATM 5 C C5 NAG . . . L 7 26.783 -25.244 49.754 1 60.98 ? C5 NAG 807 B 1 HETATM 6 C C6 NAG . . . L 7 27.737 -26.4 49.441 1 64.91 ? C6 NAG 807 B 1 HETATM 7 C C7 NAG . . . L 7 21.783 -25.198 51.307 1 54.6 ? C7 NAG 807 B 1 HETATM 8 C C8 NAG . . . L 7 21.801 -26.719 51.142 1 54 ? C8 NAG 807 B 1 HETATM 9 N N2 NAG . . . L 7 22.871 -24.441 51.122 1 54.14 ? N2 NAG 807 B 1 HETATM 10 O O3 NAG . . . L 7 25.015 -24.681 52.928 1 65.94 ? O3 NAG 807 B 1 HETATM 11 O O4 NAG . . . L 7 27.77 -24.741 51.965 1 59.23 ? O4 NAG 807 B 1 HETATM 12 O O5 NAG . . . L 7 25.574 -25.388 48.98 1 55.52 ? O5 NAG 807 B 1 HETATM 13 O O6 NAG . . . L 7 28.113 -26.392 48.078 1 69.28 ? O6 NAG 807 B 1 HETATM 14 O O7 NAG . . . L 7 20.757 -24.604 51.623 1 49.67 ? O7 NAG 807 B 1 # _model_server_stats.io_time_ms 9 _model_server_stats.parse_time_ms 13 _model_server_stats.create_model_time_ms 54 _model_server_stats.query_time_ms 241 _model_server_stats.encode_time_ms 6 _model_server_stats.element_count 14 #