data_3LXA # _model_server_result.job_id wlL-GcCZhUW9AfikoqALFg _model_server_result.datetime_utc '2024-11-22 22:28:54' _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 3lxa # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"J","auth_seq_id":715}' # _entry.id 3LXA # _exptl.entry_id 3LXA _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 3 _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 3LXA _cell.length_a 59.241 _cell.length_b 104.959 _cell.length_c 181.038 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 3LXA _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,N _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 ? 4 F N N ? 4 I N N ? 4 J 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 ? 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 # 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 D 692 NAG 2 n C NAG 2 C 2 NAG D 693 NAG 2 n C BMA 3 C 3 BMA D 694 BMA 2 n C MAN 4 C 4 MAN D 695 MAN 3 n D NAG 1 D 1 NAG E 715 NAG 3 n D NAG 2 D 2 NAG E 716 NAG 2 n E NAG 1 E 1 NAG G 692 NAG 2 n E NAG 2 E 2 NAG G 693 NAG 2 n E BMA 3 E 3 BMA G 694 BMA 2 n E MAN 4 E 4 MAN G 695 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 21 A CYS 52 1_555 A SG CYS 63 A CYS 94 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.029 ? disulf ? disulf2 A SG CYS 25 A CYS 56 1_555 A SG CYS 32 A CYS 63 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.037 ? disulf ? disulf3 A SG CYS 111 A CYS 142 1_555 A SG CYS 141 A CYS 172 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.045 ? disulf ? disulf4 A SG CYS 171 A CYS 202 1_555 A SG CYS 192 A CYS 223 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.04 ? disulf ? disulf5 A SG CYS 347 A CYS 378 1_555 A SG CYS 351 A CYS 382 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.032 ? disulf ? disulf6 B SG CYS 21 B CYS 52 1_555 B SG CYS 63 B CYS 94 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.038 ? disulf ? disulf7 B SG CYS 25 B CYS 56 1_555 B SG CYS 32 B CYS 63 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.048 ? disulf ? disulf8 B SG CYS 111 B CYS 142 1_555 B SG CYS 141 B CYS 172 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.023 ? disulf ? disulf9 B SG CYS 171 B CYS 202 1_555 B SG CYS 192 B CYS 223 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.042 ? disulf ? disulf10 B SG CYS 347 B CYS 378 1_555 B SG CYS 351 B CYS 382 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.031 ? covale ? covale1 A ND2 ASN 108 A ASN 139 1_555 F C1 NAG . A NAG 639 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.462 ? covale ? covale2 A ND2 ASN 161 A ASN 192 1_555 C C1 NAG . C NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.454 ? covale ? covale3 A ND2 ASN 184 A ASN 215 1_555 D C1 NAG . D NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.455 ? covale ? covale4 B ND2 ASN 108 B ASN 139 1_555 I C1 NAG . B NAG 639 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.442 ? covale ? covale5 B ND2 ASN 161 B ASN 192 1_555 E C1 NAG . E NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.434 ? covale ? covale6 B ND2 ASN 184 B ASN 215 1_555 J C1 NAG . B NAG 715 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.448 ? covale ? covale7 C O4 NAG . C NAG 1 1_555 C C1 NAG . C NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.437 ? covale ? covale8 C O4 NAG . C NAG 2 1_555 C C1 BMA . C BMA 3 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.439 ? covale ? covale9 C O3 BMA . C BMA 3 1_555 C C1 MAN . C MAN 4 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.453 ? covale ? covale10 D O4 NAG . D NAG 1 1_555 D C1 NAG . D NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.449 ? covale ? covale11 E O4 NAG . E NAG 1 1_555 E C1 NAG . E NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.442 ? covale ? covale12 E O4 NAG . E NAG 2 1_555 E C1 BMA . E BMA 3 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.447 ? covale ? covale13 E O3 BMA . E BMA 3 1_555 E C1 MAN . E MAN 4 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.467 ? # _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 309 n n C1 O1 NAG sing 310 n n C1 O5 NAG sing 311 n n C1 H1 NAG sing 312 n n C2 C3 NAG sing 313 n n C2 N2 NAG sing 314 n n C2 H2 NAG sing 315 n n C3 C4 NAG sing 316 n n C3 O3 NAG sing 317 n n C3 H3 NAG sing 318 n n C4 C5 NAG sing 319 n n C4 O4 NAG sing 320 n n C4 H4 NAG sing 321 n n C5 C6 NAG sing 322 n n C5 O5 NAG sing 323 n n C5 H5 NAG sing 324 n n C6 O6 NAG sing 325 n n C6 H61 NAG sing 326 n n C6 H62 NAG sing 327 n n C7 C8 NAG sing 328 n n C7 N2 NAG sing 329 n n C7 O7 NAG doub 330 n n C8 H81 NAG sing 331 n n C8 H82 NAG sing 332 n n C8 H83 NAG sing 333 n n N2 HN2 NAG sing 334 n n O1 HO1 NAG sing 335 n n O3 HO3 NAG sing 336 n n O4 HO4 NAG sing 337 n n O6 HO6 NAG sing 338 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 3LXA _atom_sites.fract_transf_matrix[1][1] 0.01688 _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] 0.009528 _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] 0.005524 _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 4 NAG A 1 639 639 NAG NAG . G 5 GLA A 1 801 801 GLA GLA . H 5 GLA A 1 803 803 GLA GLA . I 4 NAG B 1 639 639 NAG NAG . J 4 NAG B 1 715 715 NAG NAG . K 5 GLA B 1 802 802 GLA GLA . L 5 GLA B 1 804 804 GLA GLA . M 6 HOH A 1 8 8 HOH HOH . M 6 HOH A 2 10 10 HOH HOH . M 6 HOH A 3 13 13 HOH HOH . M 6 HOH A 4 14 14 HOH HOH . M 6 HOH A 5 15 15 HOH HOH . M 6 HOH A 6 17 17 HOH HOH . M 6 HOH A 7 19 19 HOH HOH . M 6 HOH A 8 20 20 HOH HOH . M 6 HOH A 9 21 21 HOH HOH . M 6 HOH A 10 25 25 HOH HOH . M 6 HOH A 11 28 28 HOH HOH . M 6 HOH A 12 436 32 HOH HOH . M 6 HOH A 13 437 35 HOH HOH . M 6 HOH A 14 438 36 HOH HOH . M 6 HOH A 15 439 37 HOH HOH . M 6 HOH A 16 440 40 HOH HOH . M 6 HOH A 17 441 41 HOH HOH . M 6 HOH A 18 442 45 HOH HOH . M 6 HOH A 19 443 46 HOH HOH . N 6 HOH B 1 3 3 HOH HOH . N 6 HOH B 2 5 5 HOH HOH . N 6 HOH B 3 9 9 HOH HOH . N 6 HOH B 4 18 18 HOH HOH . N 6 HOH B 5 23 23 HOH HOH . N 6 HOH B 6 24 24 HOH HOH . N 6 HOH B 7 26 26 HOH HOH . N 6 HOH B 8 27 27 HOH HOH . N 6 HOH B 9 29 29 HOH HOH . N 6 HOH B 10 31 31 HOH HOH . N 6 HOH B 11 436 33 HOH HOH . N 6 HOH B 12 437 38 HOH HOH . N 6 HOH B 13 438 39 HOH HOH . N 6 HOH B 14 439 42 HOH HOH . N 6 HOH B 15 440 47 HOH HOH . N 6 HOH B 16 441 48 HOH HOH . N 6 HOH B 17 442 49 HOH HOH . # 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 . . . J 4 22.773 29.398 66.329 1 59.98 ? C1 NAG 715 B 1 HETATM 2 C C2 NAG . . . J 4 22.804 30.881 65.924 1 68.08 ? C2 NAG 715 B 1 HETATM 3 C C3 NAG . . . J 4 23.573 31.755 66.926 1 70.99 ? C3 NAG 715 B 1 HETATM 4 C C4 NAG . . . J 4 23.33 31.371 68.398 1 70.33 ? C4 NAG 715 B 1 HETATM 5 C C5 NAG . . . J 4 23.294 29.853 68.616 1 67.8 ? C5 NAG 715 B 1 HETATM 6 C C6 NAG . . . J 4 22.82 29.506 70.026 1 68.01 ? C6 NAG 715 B 1 HETATM 7 C C7 NAG . . . J 4 22.641 31.397 63.53 1 67.94 ? C7 NAG 715 B 1 HETATM 8 C C8 NAG . . . J 4 23.352 31.441 62.205 1 66.95 ? C8 NAG 715 B 1 HETATM 9 N N2 NAG . . . J 4 23.376 31.055 64.592 1 67.9 ? N2 NAG 715 B 1 HETATM 10 O O3 NAG . . . J 4 23.224 33.114 66.7 1 74.17 ? O3 NAG 715 B 1 HETATM 11 O O4 NAG . . . J 4 24.333 31.936 69.222 1 71.03 ? O4 NAG 715 B 1 HETATM 12 O O5 NAG . . . J 4 22.407 29.247 67.691 1 64.43 ? O5 NAG 715 B 1 HETATM 13 O O6 NAG . . . J 4 23.571 28.413 70.511 1 69.1 ? O6 NAG 715 B 1 HETATM 14 O O7 NAG . . . J 4 21.441 31.665 63.603 1 68.77 ? O7 NAG 715 B 1 # _model_server_stats.io_time_ms 16 _model_server_stats.parse_time_ms 10 _model_server_stats.create_model_time_ms 7 _model_server_stats.query_time_ms 248 _model_server_stats.encode_time_ms 8 _model_server_stats.element_count 14 #