data_3LPO # _model_server_result.job_id PvFg76aj-ecFRkYCgJSMyA _model_server_result.datetime_utc '2024-12-01 18:30:09' _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 3lpo # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"M","auth_seq_id":3001}' # _entry.id 3LPO # _exptl.entry_id 3LPO _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 221.208 _entity.id 4 _entity.src_method man _entity.type non-polymer _entity.pdbx_description 2-acetamido-2-deoxy-beta-D-glucopyranose _entity.pdbx_number_of_molecules 5 _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 3LPO _cell.length_a 76.344 _cell.length_b 172.586 _cell.length_c 343.874 _cell.Z_PDB 16 _cell.pdbx_unique_axis ? # _symmetry.entry_id 3LPO _symmetry.cell_setting ? _symmetry.Int_Tables_number 19 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 21 21 21' # 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 monomeric 1 author_and_software_defined_assembly 1 PISA monomeric 1 author_and_software_defined_assembly 2 PISA monomeric 1 author_and_software_defined_assembly 3 PISA monomeric 1 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,E,F,I 1 1 B,J 2 1 C,G,H,K 3 1 D,L,M 4 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 ? 4 I N N ? 4 J N N ? 4 K N N ? 4 L N N ? 4 M N N # loop_ _pdbx_entity_branch.entity_id _pdbx_entity_branch.type 2 oligosaccharide 3 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 ? 3 2 1 NAG NAG C1 O1 . O4 HO4 . sing 3 ? 3 3 2 BMA NAG C1 O1 . O4 HO4 . sing 4 ? 3 4 3 MAN BMA C1 O1 . O3 HO3 . sing 5 ? 3 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 2 n E NAG 1 E 1 NAG A 3001 NAG 2 n E NAG 2 E 2 NAG A 3002 NAG 3 n F NAG 1 F 1 NAG A 1001 NAG 3 n F NAG 2 F 2 NAG A 1002 NAG 3 n F BMA 3 F 3 BMA A 1003 BMA 3 n F MAN 4 F 4 MAN A 1004 MAN 3 n F MAN 5 F 5 MAN A 1005 MAN 2 n G NAG 1 G 1 NAG C 3001 NAG 2 n G NAG 2 G 2 NAG C 3002 NAG 3 n H NAG 1 H 1 NAG C 1001 NAG 3 n H NAG 2 H 2 NAG C 1002 NAG 3 n H BMA 3 H 3 BMA C 1003 BMA 3 n H MAN 4 H 4 MAN C 1004 MAN 3 n H MAN 5 H 5 MAN C 1005 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 30 A CYS 30 1_555 A SG CYS 61 A CYS 61 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.065 ? disulf ? disulf2 A SG CYS 44 A CYS 44 1_555 A SG CYS 60 A CYS 60 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.035 ? disulf ? disulf3 A SG CYS 55 A CYS 55 1_555 A SG CYS 73 A CYS 73 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.096 ? disulf ? disulf4 A SG CYS 602 A CYS 602 1_555 A SG CYS 613 A CYS 613 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.042 ? disulf ? disulf5 B SG CYS 30 B CYS 30 1_555 B SG CYS 61 B CYS 61 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.051 ? disulf ? disulf6 B SG CYS 44 B CYS 44 1_555 B SG CYS 60 B CYS 60 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.068 ? disulf ? disulf7 B SG CYS 55 B CYS 55 1_555 B SG CYS 73 B CYS 73 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.076 ? disulf ? disulf8 B SG CYS 602 B CYS 602 1_555 B SG CYS 613 B CYS 613 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.052 ? disulf ? disulf9 C SG CYS 30 C CYS 30 1_555 C SG CYS 61 C CYS 61 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.078 ? disulf ? disulf10 C SG CYS 44 C CYS 44 1_555 C SG CYS 60 C CYS 60 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.05 ? disulf ? disulf11 C SG CYS 55 C CYS 55 1_555 C SG CYS 73 C CYS 73 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.09 ? disulf ? disulf12 C SG CYS 602 C CYS 602 1_555 C SG CYS 613 C CYS 613 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.046 ? disulf ? disulf13 D SG CYS 30 D CYS 30 1_555 D SG CYS 61 D CYS 61 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.066 ? disulf ? disulf14 D SG CYS 44 D CYS 44 1_555 D SG CYS 60 D CYS 60 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.056 ? disulf ? disulf15 D SG CYS 55 D CYS 55 1_555 D SG CYS 73 D CYS 73 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.103 ? disulf ? disulf16 D SG CYS 602 D CYS 602 1_555 D SG CYS 613 D CYS 613 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.049 ? covale ? covale1 A ND2 ASN 66 A ASN 66 1_555 I C1 NAG . A NAG 2001 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.449 ? covale ? covale2 A ND2 ASN 422 A ASN 422 1_555 E C1 NAG . E NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.442 ? covale ? covale3 A ND2 ASN 822 A ASN 822 1_555 F C1 NAG . F NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.457 ? covale ? covale4 B ND2 ASN 66 B ASN 66 1_555 J C1 NAG . B NAG 2001 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.44 ? covale ? covale5 C ND2 ASN 66 C ASN 66 1_555 K C1 NAG . C NAG 2001 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.457 ? covale ? covale6 C ND2 ASN 422 C ASN 422 1_555 G C1 NAG . G NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.429 ? covale ? covale7 D ND2 ASN 66 D ASN 66 1_555 L C1 NAG . D NAG 2001 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.472 ? covale ? covale8 D ND2 ASN 422 D ASN 422 1_555 M C1 NAG . D NAG 3001 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.45 ? covale ? covale9 E O4 NAG . E NAG 1 1_555 E C1 NAG . E NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.451 ? covale ? covale10 F O4 NAG . F NAG 1 1_555 F C1 NAG . F NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.445 ? covale ? covale11 F O4 NAG . F NAG 2 1_555 F C1 BMA . F BMA 3 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.449 ? covale ? covale12 F O3 BMA . F BMA 3 1_555 F C1 MAN . F MAN 4 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.458 ? covale ? covale13 F O6 BMA . F BMA 3 1_555 F C1 MAN . F MAN 5 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.461 ? covale ? covale14 G O4 NAG . G NAG 1 1_555 G C1 NAG . G NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.449 ? covale ? covale15 H O4 NAG . H NAG 1 1_555 H C1 NAG . H NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.441 ? covale ? covale16 H O4 NAG . H NAG 2 1_555 H C1 BMA . H BMA 3 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.447 ? covale ? covale17 H O3 BMA . H BMA 3 1_555 H C1 MAN . H MAN 4 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.443 ? covale ? covale18 H O6 BMA . H BMA 3 1_555 H C1 MAN . H MAN 5 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.454 ? # _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 283 n n C1 O1 NAG sing 284 n n C1 O5 NAG sing 285 n n C1 H1 NAG sing 286 n n C2 C3 NAG sing 287 n n C2 N2 NAG sing 288 n n C2 H2 NAG sing 289 n n C3 C4 NAG sing 290 n n C3 O3 NAG sing 291 n n C3 H3 NAG sing 292 n n C4 C5 NAG sing 293 n n C4 O4 NAG sing 294 n n C4 H4 NAG sing 295 n n C5 C6 NAG sing 296 n n C5 O5 NAG sing 297 n n C5 H5 NAG sing 298 n n C6 O6 NAG sing 299 n n C6 H61 NAG sing 300 n n C6 H62 NAG sing 301 n n C7 C8 NAG sing 302 n n C7 N2 NAG sing 303 n n C7 O7 NAG doub 304 n n C8 H81 NAG sing 305 n n C8 H82 NAG sing 306 n n C8 H83 NAG sing 307 n n N2 HN2 NAG sing 308 n n O1 HO1 NAG sing 309 n n O3 HO3 NAG sing 310 n n O4 HO4 NAG sing 311 n n O6 HO6 NAG sing 312 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 3LPO _atom_sites.fract_transf_matrix[1][1] 0.013099 _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] 0.005794 _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] 0.002908 _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 I 4 NAG A 1 2001 2001 NAG NAG . J 4 NAG B 1 2001 2001 NAG NAG . K 4 NAG C 1 2001 2001 NAG NAG . L 4 NAG D 1 2001 2001 NAG NAG . M 4 NAG D 1 3001 3001 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 4 -54.676 -102.692 21.546 1 60.37 ? C1 NAG 3001 D 1 HETATM 2 C C2 NAG . . . M 4 -53.209 -102.835 21.921 1 60.27 ? C2 NAG 3001 D 1 HETATM 3 C C3 NAG . . . M 4 -52.892 -104.164 22.641 1 61.47 ? C3 NAG 3001 D 1 HETATM 4 C C4 NAG . . . M 4 -53.923 -104.574 23.705 1 61.73 ? C4 NAG 3001 D 1 HETATM 5 C C5 NAG . . . M 4 -55.29 -104.452 23.034 1 61.51 ? C5 NAG 3001 D 1 HETATM 6 C C6 NAG . . . M 4 -56.409 -104.801 23.986 1 62.25 ? C6 NAG 3001 D 1 HETATM 7 C C7 NAG . . . M 4 -51.551 -101.724 20.504 1 60.96 ? C7 NAG 3001 D 1 HETATM 8 C C8 NAG . . . M 4 -50.228 -102.116 19.91 1 60.86 ? C8 NAG 3001 D 1 HETATM 9 N N2 NAG . . . M 4 -52.435 -102.704 20.7 1 60.07 ? N2 NAG 3001 D 1 HETATM 10 O O3 NAG . . . M 4 -51.629 -104.063 23.259 1 62.68 ? O3 NAG 3001 D 1 HETATM 11 O O4 NAG . . . M 4 -53.666 -105.864 24.272 1 60.89 ? O4 NAG 3001 D 1 HETATM 12 O O5 NAG . . . M 4 -55.488 -103.107 22.627 1 61 ? O5 NAG 3001 D 1 HETATM 13 O O6 NAG . . . M 4 -57.487 -103.852 23.671 1 63.04 ? O6 NAG 3001 D 1 HETATM 14 O O7 NAG . . . M 4 -51.769 -100.543 20.783 1 62.33 ? O7 NAG 3001 D 1 # _model_server_stats.io_time_ms 55 _model_server_stats.parse_time_ms 34 _model_server_stats.create_model_time_ms 113 _model_server_stats.query_time_ms 951 _model_server_stats.encode_time_ms 39 _model_server_stats.element_count 14 #