data_5DYS # _model_server_result.job_id 6-GRKQRnyn5XBtP85QY6zA _model_server_result.datetime_utc '2024-12-01 20:49:00' _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 5dys # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"D","auth_seq_id":402}' # _entry.id 5DYS # _exptl.entry_id 5DYS _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 59.044 _entity.id 4 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description 'ACETATE ION' _entity.pdbx_number_of_molecules 2 _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 5DYS _cell.length_a 242.301 _cell.length_b 242.301 _cell.length_c 112.055 _cell.Z_PDB 18 _cell.pdbx_unique_axis ? # _symmetry.entry_id 5DYS _symmetry.cell_setting ? _symmetry.Int_Tables_number 155 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'H 3 2' # _pdbx_struct_assembly.method_details PISA _pdbx_struct_assembly.oligomeric_details monomeric _pdbx_struct_assembly.oligomeric_count 1 _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 _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 D N N ? 4 E N N # _pdbx_entity_branch.entity_id 2 _pdbx_entity_branch.type 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 ? 2 5 3 BMA 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 B NAG 1 B 1 NAG S 301 NAG 2 n B NAG 2 B 2 NAG S 302 NAG 2 n B BMA 3 B 3 BMA S 303 BMA 2 n B MAN 4 B 4 MAN S 304 MAN 2 n B BMA 5 B 5 BMA S 305 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 3 A CYS 2 1_555 A SG CYS 283 A CYS 282 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.096 ? disulf ? disulf2 A SG CYS 111 A CYS 110 1_555 A SG CYS 188 A CYS 187 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.128 ? covale ? covale1 A C ACE 1 A ACE 0 1_555 A N MET 2 A MET 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.384 ? covale ? covale2 A ND2 ASN 16 A ASN 15 1_555 B C1 NAG . B NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.44 ? covale ? covale3 A NZ LYS 297 A LYS 296 1_555 C C15 RET . A RET 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.273 ? covale ? covale4 A SG CYS 323 A CYS 322 1_555 G C1 PLM . A PLM 405 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.705 ? covale ? covale5 A SG CYS 324 A CYS 323 1_555 H C1 PLM . A PLM 406 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.692 ? covale ? covale6 B O4 NAG . B NAG 1 1_555 B C1 NAG . B NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.417 ? covale ? covale7 B O4 NAG . B NAG 2 1_555 B C1 BMA . B BMA 3 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.431 ? covale ? covale8 B O3 BMA . B BMA 3 1_555 B C1 MAN . B MAN 4 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.445 ? covale ? covale9 B O6 BMA . B BMA 3 1_555 B C1 BMA . B BMA 5 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.47 ? # _chem_comp.formula 'C2 H3 O2 -1' _chem_comp.formula_weight 59.044 _chem_comp.id ACT _chem_comp.mon_nstd_flag . _chem_comp.name 'ACETATE ION' _chem_comp.type non-polymer _chem_comp.pdbx_synonyms ? # 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 C O ACT doub 7 n n C OXT ACT sing 8 n n C CH3 ACT sing 9 n n CH3 H1 ACT sing 10 n n CH3 H2 ACT sing 11 n n CH3 H3 ACT sing 12 n n # _atom_sites.entry_id 5DYS _atom_sites.fract_transf_matrix[1][1] 0.004127 _atom_sites.fract_transf_matrix[1][2] 0.002383 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.004766 _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] 0.008924 _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 C 3 RET A 1 401 401 RET RET . D 4 ACT A 1 402 102 ACT ACT . E 4 ACT A 1 403 103 ACT ACT . F 5 BOG A 1 404 204 BOG BOG . G 6 PLM A 1 405 205 PLM PLM . H 6 PLM A 1 406 206 PLM PLM . I 5 BOG A 1 412 601 BOG BOG . J 7 SO4 A 1 413 801 SO4 SO4 . K 8 HOH A 1 501 25 HOH HOH . K 8 HOH A 2 502 21 HOH HOH . K 8 HOH A 3 503 43 HOH HOH . K 8 HOH A 4 504 5 HOH HOH . K 8 HOH A 5 505 41 HOH HOH . K 8 HOH A 6 506 4 HOH HOH . K 8 HOH A 7 507 14 HOH HOH . K 8 HOH A 8 508 44 HOH HOH . K 8 HOH A 9 509 46 HOH HOH . K 8 HOH A 10 510 3 HOH HOH . K 8 HOH A 11 511 26 HOH HOH . K 8 HOH A 12 512 18 HOH HOH . K 8 HOH A 13 513 13 HOH HOH . K 8 HOH A 14 514 19 HOH HOH . K 8 HOH A 15 515 20 HOH HOH . K 8 HOH A 16 516 27 HOH HOH . K 8 HOH A 17 517 8 HOH HOH . K 8 HOH A 18 518 28 HOH HOH . K 8 HOH A 19 519 45 HOH HOH . K 8 HOH A 20 520 12 HOH HOH . K 8 HOH A 21 521 35 HOH HOH . K 8 HOH A 22 522 32 HOH HOH . K 8 HOH A 23 523 10 HOH HOH . K 8 HOH A 24 524 39 HOH HOH . K 8 HOH A 25 525 11 HOH HOH . K 8 HOH A 26 526 1 HOH HOH . K 8 HOH A 27 527 40 HOH HOH . K 8 HOH A 28 528 7 HOH HOH . K 8 HOH A 29 529 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 C ACT . . . D 4 -46.772 -24.613 31.757 1 103.16 ? C ACT 402 A 1 HETATM 2 O O ACT . . . D 4 -46.79 -24.283 30.552 1 113.53 ? O ACT 402 A 1 HETATM 3 O OXT ACT . . . D 4 -46.882 -23.728 32.68 1 83.55 ? OXT ACT 402 A 1 HETATM 4 C CH3 ACT . . . D 4 -46.625 -26.108 31.993 1 95.58 ? CH3 ACT 402 A 1 # _model_server_stats.io_time_ms 9 _model_server_stats.parse_time_ms 11 _model_server_stats.create_model_time_ms 4 _model_server_stats.query_time_ms 346 _model_server_stats.encode_time_ms 1 _model_server_stats.element_count 4 #