data_5CKV # _model_server_result.job_id g_xl8DVQaFk8qntR4O0N3w _model_server_result.datetime_utc '2024-11-18 21:28:29' _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 5ckv # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"R","auth_seq_id":507}' # _entry.id 5CKV # _exptl.entry_id 5CKV _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 92.094 _entity.id 4 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description GLYCEROL _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 120 _cell.entry_id 5CKV _cell.length_a 204.76 _cell.length_b 204.76 _cell.length_c 66.774 _cell.Z_PDB 12 _cell.pdbx_unique_axis ? # _symmetry.entry_id 5CKV _symmetry.cell_setting ? _symmetry.Int_Tables_number 154 _symmetry.space_group_name_Hall . _symmetry.space_group_name_H-M 'P 32 2 1' # _pdbx_struct_assembly.method_details PISA _pdbx_struct_assembly.oligomeric_details tetrameric _pdbx_struct_assembly.oligomeric_count 4 _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,O,P,Q,R,S,T,U,V,W _pdbx_struct_assembly_gen.assembly_id 1 _pdbx_struct_assembly_gen.oper_expression 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_554 x-y,-y,-z-2/3 1 0 0 0 -1 0 0 0 -1 0 0 -44.516 # loop_ _struct_asym.details _struct_asym.entity_id _struct_asym.id _struct_asym.pdbx_modified _struct_asym.pdbx_blank_PDB_chainid_flag ? 4 G N N ? 4 H N N ? 4 P N N ? 4 Q N N ? 4 R N N # 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 metalc ? metalc1 A SG CYS 97 A CYS 87 1_555 J MN MN . A MN 508 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.693 ? metalc ? metalc2 A NE2 HIS 379 A HIS 369 1_555 J MN MN . A MN 508 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.203 ? metalc ? metalc3 A OE2 GLU 421 A GLU 411 1_555 J MN MN . A MN 508 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.132 ? metalc ? metalc4 A OD2 ASP 451 A ASP 441 1_555 J MN MN . A MN 508 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.149 ? metalc ? metalc5 J MN MN . A MN 508 1_555 V O HOH . A HOH 604 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.25 ? metalc ? metalc6 B SG CYS 97 B CYS 87 1_555 M MN MN . B MN 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.599 ? metalc ? metalc7 B NE2 HIS 379 B HIS 369 1_555 M MN MN . B MN 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.173 ? metalc ? metalc8 B OE2 GLU 421 B GLU 411 1_555 M MN MN . B MN 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.134 ? metalc ? metalc9 B OD2 ASP 451 B ASP 441 1_555 M MN MN . B MN 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.173 ? # _chem_comp.formula 'C3 H8 O3' _chem_comp.formula_weight 92.094 _chem_comp.id GOL _chem_comp.mon_nstd_flag . _chem_comp.name GLYCEROL _chem_comp.type non-polymer _chem_comp.pdbx_synonyms GLYCERIN;PROPANE-1,2,3-TRIOL # 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 O1 GOL sing 129 n n C1 C2 GOL sing 130 n n C1 H11 GOL sing 131 n n C1 H12 GOL sing 132 n n O1 HO1 GOL sing 133 n n C2 O2 GOL sing 134 n n C2 C3 GOL sing 135 n n C2 H2 GOL sing 136 n n O2 HO2 GOL sing 137 n n C3 O3 GOL sing 138 n n C3 H31 GOL sing 139 n n C3 H32 GOL sing 140 n n O3 HO3 GOL sing 141 n n # _atom_sites.entry_id 5CKV _atom_sites.fract_transf_matrix[1][1] 0.004884 _atom_sites.fract_transf_matrix[1][2] 0.00282 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.005639 _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] 0.014976 _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 2 CL A 1 501 5 CL CL . D 3 SO4 A 1 502 2 SO4 SO4 . E 3 SO4 A 1 503 3 SO4 SO4 . F 3 SO4 A 1 504 1 SO4 SO4 . G 4 GOL A 1 505 4 GOL GOL . H 4 GOL A 1 506 7 GOL GOL . I 5 TRP A 1 507 1 TRP TRP . J 6 MN A 1 508 2 MN MN . K 7 PHE A 1 509 3 PHE PHE . L 2 CL B 1 501 4 CL CL . M 6 MN B 1 502 1 MN MN . N 3 SO4 B 1 503 1 SO4 SO4 . O 3 SO4 B 1 504 4 SO4 SO4 . P 4 GOL B 1 505 6 GOL GOL . Q 4 GOL B 1 506 11 GOL GOL . R 4 GOL B 1 507 15 GOL GOL . S 8 TYR B 1 508 1 TYR TYR . T 5 TRP B 1 509 2 TRP TRP . U 7 PHE B 1 510 2 PHE PHE . V 9 HOH A 1 601 25 HOH HOH . V 9 HOH A 2 602 54 HOH HOH . V 9 HOH A 3 603 14 HOH HOH . V 9 HOH A 4 604 48 HOH HOH . V 9 HOH A 5 605 49 HOH HOH . V 9 HOH A 6 606 12 HOH HOH . V 9 HOH A 7 607 15 HOH HOH . V 9 HOH A 8 608 6 HOH HOH . V 9 HOH A 9 609 23 HOH HOH . V 9 HOH A 10 610 39 HOH HOH . V 9 HOH A 11 611 4 HOH HOH . V 9 HOH A 12 612 29 HOH HOH . V 9 HOH A 13 613 33 HOH HOH . V 9 HOH A 14 614 51 HOH HOH . V 9 HOH A 15 615 16 HOH HOH . V 9 HOH A 16 616 34 HOH HOH . V 9 HOH A 17 617 18 HOH HOH . V 9 HOH A 18 618 61 HOH HOH . W 9 HOH B 1 601 63 HOH HOH . W 9 HOH B 2 602 11 HOH HOH . W 9 HOH B 3 603 5 HOH HOH . W 9 HOH B 4 604 2 HOH HOH . W 9 HOH B 5 605 30 HOH HOH . W 9 HOH B 6 606 9 HOH HOH . W 9 HOH B 7 607 1 HOH HOH . W 9 HOH B 8 608 26 HOH HOH . W 9 HOH B 9 609 10 HOH HOH . W 9 HOH B 10 610 32 HOH HOH . W 9 HOH B 11 611 56 HOH HOH . W 9 HOH B 12 612 41 HOH HOH . W 9 HOH B 13 613 62 HOH HOH . W 9 HOH B 14 614 3 HOH HOH . W 9 HOH B 15 615 31 HOH HOH . W 9 HOH B 16 616 57 HOH HOH . W 9 HOH B 17 617 40 HOH HOH . W 9 HOH B 18 618 60 HOH HOH . W 9 HOH B 19 619 59 HOH HOH . W 9 HOH B 20 620 24 HOH HOH . W 9 HOH B 21 621 19 HOH HOH . W 9 HOH B 22 622 58 HOH HOH . W 9 HOH B 23 623 52 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 GOL . . . R 4 104.325 -34 -48.223 1 45.83 ? C1 GOL 507 B 1 HETATM 2 O O1 GOL . . . R 4 104.129 -34.8 -47.081 1 61.13 ? O1 GOL 507 B 1 HETATM 3 C C2 GOL . . . R 4 104.573 -34.89 -49.435 1 69.08 ? C2 GOL 507 B 1 HETATM 4 O O2 GOL . . . R 4 103.712 -34.487 -50.478 1 64.05 ? O2 GOL 507 B 1 HETATM 5 C C3 GOL . . . R 4 106.048 -34.858 -49.859 1 66.66 ? C3 GOL 507 B 1 HETATM 6 O O3 GOL . . . R 4 106.182 -34.97 -51.264 1 61.37 ? O3 GOL 507 B 1 HETATM 7 H H11 GOL . . . R 4 105.18 -33.341 -48.069 1 54.99 ? H11 GOL 507 B 1 HETATM 8 H H12 GOL . . . R 4 103.445 -33.38 -48.395 1 54.99 ? H12 GOL 507 B 1 HETATM 9 H HO1 GOL . . . R 4 104.035 -34.227 -46.292 1 73.35 ? HO1 GOL 507 B 1 HETATM 10 H H2 GOL . . . R 4 104.33 -35.915 -49.152 1 82.89 ? H2 GOL 507 B 1 HETATM 11 H HO2 GOL . . . R 4 103.939 -33.575 -50.755 1 76.86 ? HO2 GOL 507 B 1 HETATM 12 H H31 GOL . . . R 4 106.581 -35.678 -49.378 1 79.99 ? H31 GOL 507 B 1 HETATM 13 H H32 GOL . . . R 4 106.5 -33.924 -49.525 1 79.99 ? H32 GOL 507 B 1 HETATM 14 H HO3 GOL . . . R 4 107.101 -34.746 -51.523 1 73.65 ? HO3 GOL 507 B 1 # _model_server_stats.io_time_ms 12 _model_server_stats.parse_time_ms 10 _model_server_stats.create_model_time_ms 14 _model_server_stats.query_time_ms 275 _model_server_stats.encode_time_ms 6 _model_server_stats.element_count 14 #