data_3PQR # _model_server_result.job_id FRZK-EqR5v5MmtYLjCLuHg _model_server_result.datetime_utc '2024-11-22 09:39:46' _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 3pqr # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"F","auth_seq_id":501}' # _entry.id 3PQR # _exptl.entry_id 3PQR _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 221.208 _entity.id 6 _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 120 _cell.entry_id 3PQR _cell.length_a 241.55 _cell.length_b 241.55 _cell.length_c 109.87 _cell.Z_PDB 18 _cell.pdbx_unique_axis ? # _symmetry.entry_id 3PQR _symmetry.cell_setting ? _symmetry.Int_Tables_number 155 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'H 3 2' # 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 dimeric 2 author_and_software_defined_assembly 1 PISA tetrameric 4 software_defined_assembly 2 # loop_ _pdbx_struct_assembly_gen.asym_id_list _pdbx_struct_assembly_gen.assembly_id _pdbx_struct_assembly_gen.oper_expression A,B,C,D,E,F,G,H,I,J,K,L,M,N 1 1 A,B,C,D,E,F,G,H,I,J,K,L,M,N 2 1,2 # loop_ _pdbx_struct_oper_list.id _pdbx_struct_oper_list.type _pdbx_struct_oper_list.name _pdbx_struct_oper_list.symmetry_operation _pdbx_struct_oper_list.matrix[1][1] _pdbx_struct_oper_list.matrix[1][2] _pdbx_struct_oper_list.matrix[1][3] _pdbx_struct_oper_list.matrix[2][1] _pdbx_struct_oper_list.matrix[2][2] _pdbx_struct_oper_list.matrix[2][3] _pdbx_struct_oper_list.matrix[3][1] _pdbx_struct_oper_list.matrix[3][2] _pdbx_struct_oper_list.matrix[3][3] _pdbx_struct_oper_list.vector[1] _pdbx_struct_oper_list.vector[2] _pdbx_struct_oper_list.vector[3] 1 'identity operation' 1_555 x,y,z 1 0 0 0 1 0 0 0 1 0 0 0 2 'crystal symmetry operation' 5_556 x-y,-y,-z+1 1 0 0 0 -1 0 0 0 -1 0 0 109.87 # _struct_asym.details ? _struct_asym.entity_id 6 _struct_asym.id F _struct_asym.pdbx_modified N _struct_asym.pdbx_blank_PDB_chainid_flag 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 NAG NAG C1 O1 . O4 HO4 . sing 2 ? 3 3 2 BMA NAG C1 O1 . O4 HO4 . sing 3 ? 3 4 3 MAN BMA C1 O1 . O3 HO3 . sing 4 ? 4 1 2 GLC GLC C1 O1 . O1 HO1 . 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 C NAG 1 C 1 NAG A 402 NAG 3 n C NAG 2 C 2 NAG A 403 NAG 3 n C BMA 3 C 3 BMA A 404 BMA 3 n C MAN 4 C 4 MAN A 405 MAN 4 n D GLC 1 D 1 GLC A 1001 TRE 4 n D GLC 2 D 2 GLC A 1001 TRE # 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 110 A CYS 110 1_555 A SG CYS 187 A CYS 187 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.047 ? covale ? covale1 A ND2 ASN 2 A ASN 2 1_555 F C1 NAG . A NAG 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.334 ? covale ? covale2 A ND2 ASN 15 A ASN 15 1_555 C C1 NAG . C NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.334 ? covale ? covale3 A NZ LYS 296 A LYS 296 1_555 E C15 RET . A RET 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.337 ? covale ? covale4 A SG CYS 323 A CYS 323 1_555 I C1 PLM . A PLM 701 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.833 ? covale ? covale5 C O4 NAG . C NAG 1 1_555 C C1 NAG . C NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.424 ? covale ? covale6 C O4 NAG . C NAG 2 1_555 C C1 BMA . C BMA 3 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.43 ? covale ? covale7 C O3 BMA . C BMA 3 1_555 C C1 MAN . C MAN 4 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.453 ? covale ? covale8 D C1 GLC . D GLC 1 1_555 D O1 GLC . D GLC 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.449 sing # _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 363 n n C1 O1 NAG sing 364 n n C1 O5 NAG sing 365 n n C1 H1 NAG sing 366 n n C2 C3 NAG sing 367 n n C2 N2 NAG sing 368 n n C2 H2 NAG sing 369 n n C3 C4 NAG sing 370 n n C3 O3 NAG sing 371 n n C3 H3 NAG sing 372 n n C4 C5 NAG sing 373 n n C4 O4 NAG sing 374 n n C4 H4 NAG sing 375 n n C5 C6 NAG sing 376 n n C5 O5 NAG sing 377 n n C5 H5 NAG sing 378 n n C6 O6 NAG sing 379 n n C6 H61 NAG sing 380 n n C6 H62 NAG sing 381 n n C7 C8 NAG sing 382 n n C7 N2 NAG sing 383 n n C7 O7 NAG doub 384 n n C8 H81 NAG sing 385 n n C8 H82 NAG sing 386 n n C8 H83 NAG sing 387 n n N2 HN2 NAG sing 388 n n O1 HO1 NAG sing 389 n n O3 HO3 NAG sing 390 n n O4 HO4 NAG sing 391 n n O6 HO6 NAG sing 392 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 3PQR _atom_sites.fract_transf_matrix[1][1] 0.00414 _atom_sites.fract_transf_matrix[1][2] 0.00239 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.00478 _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] 0.009102 _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 E 5 RET A 1 401 401 RET RET . F 6 NAG A 1 501 501 NAG NAG . G 7 BOG A 1 601 601 BOG BOG . H 7 BOG A 1 602 602 BOG BOG . I 8 PLM A 1 701 701 PLM PLM . J 9 SO4 A 1 801 801 SO4 SO4 . K 10 ACT A 1 901 901 ACT ACT . L 10 ACT A 1 902 902 ACT ACT . M 11 HOH A 1 349 1 HOH HOH . M 11 HOH A 2 350 2 HOH HOH . M 11 HOH A 3 351 3 HOH HOH . M 11 HOH A 4 352 6 HOH HOH . M 11 HOH A 5 353 7 HOH HOH . M 11 HOH A 6 354 8 HOH HOH . M 11 HOH A 7 355 9 HOH HOH . M 11 HOH A 8 356 10 HOH HOH . M 11 HOH A 9 357 11 HOH HOH . M 11 HOH A 10 358 12 HOH HOH . M 11 HOH A 11 359 13 HOH HOH . M 11 HOH A 12 360 14 HOH HOH . M 11 HOH A 13 361 15 HOH HOH . M 11 HOH A 14 362 16 HOH HOH . M 11 HOH A 15 363 17 HOH HOH . M 11 HOH A 16 364 18 HOH HOH . M 11 HOH A 17 365 19 HOH HOH . M 11 HOH A 18 366 20 HOH HOH . M 11 HOH A 19 367 22 HOH HOH . N 11 HOH B 1 4 4 HOH HOH . N 11 HOH B 2 5 5 HOH HOH . N 11 HOH B 3 21 21 HOH HOH . N 11 HOH B 4 23 23 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 . . . F 6 -64.129 -25.411 42.561 1 114.21 ? C1 NAG 501 A 1 HETATM 2 C C2 NAG . . . F 6 -63.525 -26.605 41.788 1 114.09 ? C2 NAG 501 A 1 HETATM 3 C C3 NAG . . . F 6 -63.417 -27.857 42.66 1 117.93 ? C3 NAG 501 A 1 HETATM 4 C C4 NAG . . . F 6 -63.049 -27.468 44.092 1 123.39 ? C4 NAG 501 A 1 HETATM 5 C C5 NAG . . . F 6 -64.203 -26.687 44.733 1 124.02 ? C5 NAG 501 A 1 HETATM 6 C C6 NAG . . . F 6 -63.792 -26.345 46.181 1 122.62 ? C6 NAG 501 A 1 HETATM 7 C C7 NAG . . . F 6 -64.075 -26.545 39.371 1 113.66 ? C7 NAG 501 A 1 HETATM 8 C C8 NAG . . . F 6 -65.144 -26.927 38.339 1 109.59 ? C8 NAG 501 A 1 HETATM 9 N N2 NAG . . . F 6 -64.382 -26.887 40.624 1 114.98 ? N2 NAG 501 A 1 HETATM 10 O O3 NAG . . . F 6 -62.425 -28.734 42.127 1 118.96 ? O3 NAG 501 A 1 HETATM 11 O O4 NAG . . . F 6 -62.756 -28.634 44.871 1 126.36 ? O4 NAG 501 A 1 HETATM 12 O O5 NAG . . . F 6 -64.556 -25.482 43.973 1 119.78 ? O5 NAG 501 A 1 HETATM 13 O O6 NAG . . . F 6 -64.945 -26.299 47.025 1 121.5 ? O6 NAG 501 A 1 HETATM 14 O O7 NAG . . . F 6 -63.033 -25.976 39.033 1 109.48 ? O7 NAG 501 A 1 # _model_server_stats.io_time_ms 7 _model_server_stats.parse_time_ms 7 _model_server_stats.create_model_time_ms 3 _model_server_stats.query_time_ms 328 _model_server_stats.encode_time_ms 9 _model_server_stats.element_count 14 #