data_4YKL
#
_model_server_result.job_id            VNvikYFnO8Pd38EyoAwgww 
_model_server_result.datetime_utc      '2024-10-19 15:26:25' 
_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          4ykl 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"E","auth_seq_id":303}' 
#
_entry.id    4YKL 
#
_exptl.entry_id    4YKL 
_exptl.method      'X-RAY DIFFRACTION' 
#
_entity.details                     ? 
_entity.formula_weight              92.094 
_entity.id                          5 
_entity.src_method                  syn 
_entity.type                        non-polymer 
_entity.pdbx_description            GLYCEROL 
_entity.pdbx_number_of_molecules    4 
_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            4YKL 
_cell.length_a            119.083 
_cell.length_b            119.083 
_cell.length_c            36.564 
_cell.Z_PDB               6 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 4YKL 
_symmetry.cell_setting             ? 
_symmetry.Int_Tables_number        150 
_symmetry.space_group_name_Hall    ? 
_symmetry.space_group_name_H-M     'P 3 2 1' 
#
_pdbx_struct_assembly.method_details        PISA 
_pdbx_struct_assembly.oligomeric_details    tetrameric 
_pdbx_struct_assembly.oligomeric_count      4 
_pdbx_struct_assembly.details               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 
_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' 6_556 -x,-x+y,-z+1 -0.5 -0.866025 0 -0.866025 0.5 0 0 0 -1 0 0 36.564 
#
loop_
_struct_asym.details
_struct_asym.entity_id
_struct_asym.id
_struct_asym.pdbx_modified
_struct_asym.pdbx_blank_PDB_chainid_flag
? 5 E N N 
? 5 F N N 
? 5 G N N 
? 5 H 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 168 B CYS 200 1_555 C ZN ZN . B ZN 301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.309 ? 
metalc ? metalc2 A SG CYS 171 B CYS 203 1_555 C ZN ZN . B ZN 301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.318 ? 
metalc ? metalc3 A NE2 HIS 185 B HIS 217 1_555 C ZN ZN . B ZN 301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.018 ? 
metalc ? metalc4 A OE1 GLU 189 B GLU 221 1_555 C ZN ZN . B ZN 301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.956 ? 
hydrog WATSON-CRICK hydrog1 B N1 DG 1 A DG 1 1_555 B N3 DC 10 A DC 10 6_556 ? ? ? ? ? ? ? ? ? ? ? ? ? ? 
hydrog WATSON-CRICK hydrog2 B N2 DG 1 A DG 1 1_555 B O2 DC 10 A DC 10 6_556 ? ? ? ? ? ? ? ? ? ? ? ? ? ? 
hydrog WATSON-CRICK hydrog3 B O6 DG 1 A DG 1 1_555 B N4 DC 10 A DC 10 6_556 ? ? ? ? ? ? ? ? ? ? ? ? ? ? 
hydrog WATSON-CRICK hydrog4 B N3 DC 10 A DC 10 1_555 B N1 DG 1 A DG 1 6_556 ? ? ? ? ? ? ? ? ? ? ? ? ? ? 
hydrog WATSON-CRICK hydrog5 B N4 DC 10 A DC 10 1_555 B O6 DG 1 A DG 1 6_556 ? ? ? ? ? ? ? ? ? ? ? ? ? ? 
hydrog WATSON-CRICK hydrog6 B O2 DC 10 A DC 10 1_555 B N2 DG 1 A DG 1 6_556 ? ? ? ? ? ? ? ? ? ? ? ? ? ? 
#
_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 313 n n 
C1 C2 GOL sing 314 n n 
C1 H11 GOL sing 315 n n 
C1 H12 GOL sing 316 n n 
O1 HO1 GOL sing 317 n n 
C2 O2 GOL sing 318 n n 
C2 C3 GOL sing 319 n n 
C2 H2 GOL sing 320 n n 
O2 HO2 GOL sing 321 n n 
C3 O3 GOL sing 322 n n 
C3 H31 GOL sing 323 n n 
C3 H32 GOL sing 324 n n 
O3 HO3 GOL sing 325 n n 
#
_atom_sites.entry_id                     4YKL 
_atom_sites.fract_transf_matrix[1][1]    0.008398 
_atom_sites.fract_transf_matrix[1][2]    0.004848 
_atom_sites.fract_transf_matrix[1][3]    0 
_atom_sites.fract_transf_matrix[2][1]    0 
_atom_sites.fract_transf_matrix[2][2]    0.009697 
_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]    0.027349 
_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 ZN B 1 301 1 ZN ZN . 
D 4 GMP B 1 302 1 GMP 5GP . 
E 5 GOL B 1 303 1 GOL GOL . 
F 5 GOL B 1 304 2 GOL GOL . 
G 5 GOL B 1 305 3 GOL GOL . 
H 5 GOL B 1 306 4 GOL GOL . 
I 6 CL B 1 307 1 CL CL . 
J 6 CL B 1 308 1 CL CL . 
K 7 HOH B 1 401 29 HOH HOH . 
K 7 HOH B 2 402 42 HOH HOH . 
K 7 HOH B 3 403 30 HOH HOH . 
K 7 HOH B 4 404 23 HOH HOH . 
K 7 HOH B 5 405 39 HOH HOH . 
K 7 HOH B 6 406 38 HOH HOH . 
K 7 HOH B 7 407 35 HOH HOH . 
K 7 HOH B 8 408 37 HOH HOH . 
K 7 HOH B 9 409 21 HOH HOH . 
K 7 HOH B 10 410 18 HOH HOH . 
K 7 HOH B 11 411 47 HOH HOH . 
K 7 HOH B 12 412 49 HOH HOH . 
K 7 HOH B 13 413 48 HOH HOH . 
K 7 HOH B 14 414 1 HOH HOH . 
K 7 HOH B 15 415 2 HOH HOH . 
K 7 HOH B 16 416 3 HOH HOH . 
K 7 HOH B 17 417 5 HOH HOH . 
K 7 HOH B 18 418 6 HOH HOH . 
K 7 HOH B 19 419 7 HOH HOH . 
K 7 HOH B 20 420 8 HOH HOH . 
K 7 HOH B 21 421 9 HOH HOH . 
K 7 HOH B 22 422 10 HOH HOH . 
K 7 HOH B 23 423 11 HOH HOH . 
K 7 HOH B 24 424 12 HOH HOH . 
K 7 HOH B 25 425 13 HOH HOH . 
K 7 HOH B 26 426 14 HOH HOH . 
K 7 HOH B 27 427 15 HOH HOH . 
K 7 HOH B 28 428 16 HOH HOH . 
K 7 HOH B 29 429 17 HOH HOH . 
K 7 HOH B 30 430 19 HOH HOH . 
K 7 HOH B 31 431 20 HOH HOH . 
K 7 HOH B 32 432 22 HOH HOH . 
K 7 HOH B 33 433 24 HOH HOH . 
K 7 HOH B 34 434 25 HOH HOH . 
K 7 HOH B 35 435 27 HOH HOH . 
K 7 HOH B 36 436 28 HOH HOH . 
K 7 HOH B 37 437 31 HOH HOH . 
K 7 HOH B 38 438 32 HOH HOH . 
K 7 HOH B 39 439 33 HOH HOH . 
K 7 HOH B 40 440 34 HOH HOH . 
K 7 HOH B 41 441 40 HOH HOH . 
K 7 HOH B 42 442 41 HOH HOH . 
K 7 HOH B 43 443 43 HOH HOH . 
K 7 HOH B 44 444 44 HOH HOH . 
K 7 HOH B 45 445 45 HOH HOH . 
K 7 HOH B 46 446 50 HOH HOH . 
K 7 HOH B 47 447 53 HOH HOH . 
L 7 HOH A 1 101 46 HOH HOH . 
L 7 HOH A 2 102 26 HOH HOH . 
L 7 HOH A 3 103 52 HOH HOH . 
L 7 HOH A 4 104 51 HOH HOH . 
L 7 HOH A 5 105 4 HOH HOH . 
L 7 HOH A 6 106 36 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 . . . E 5 -10.348 70.153 13.334 1 76.37 ? C1 GOL 303 B 1 
HETATM 2 O O1 GOL . . . E 5 -11.099 69.926 12.159 1 77.72 ? O1 GOL 303 B 1 
HETATM 3 C C2 GOL . . . E 5 -11.286 70.263 14.531 1 74.29 ? C2 GOL 303 B 1 
HETATM 4 O O2 GOL . . . E 5 -12.549 69.747 14.184 1 73.79 ? O2 GOL 303 B 1 
HETATM 5 C C3 GOL . . . E 5 -10.711 69.463 15.689 1 73.41 ? C3 GOL 303 B 1 
HETATM 6 O O3 GOL . . . E 5 -11.6 69.504 16.78 1 72.62 ? O3 GOL 303 B 1 
#
_model_server_stats.io_time_ms              17 
_model_server_stats.parse_time_ms           11 
_model_server_stats.create_model_time_ms    3 
_model_server_stats.query_time_ms           274 
_model_server_stats.encode_time_ms          4 
_model_server_stats.element_count           6 
#