data_6Z13
#
_model_server_result.job_id            OCPTKdjgnXXsr3dOfm7liA 
_model_server_result.datetime_utc      '2024-11-25 20:12:50' 
_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          6z13 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"K","auth_seq_id":203}' 
#
_entry.id    6Z13 
#
_exptl.entry_id    6Z13 
_exptl.method      'X-RAY DIFFRACTION' 
#
_entity.details                     ? 
_entity.formula_weight              118.174 
_entity.id                          5 
_entity.src_method                  syn 
_entity.type                        non-polymer 
_entity.pdbx_description            (4S)-2-METHYL-2,4-PENTANEDIOL 
_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         90 
_cell.entry_id            6Z13 
_cell.length_a            54.256 
_cell.length_b            55.691 
_cell.length_c            76.979 
_cell.Z_PDB               8 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 6Z13 
_symmetry.cell_setting             ? 
_symmetry.Int_Tables_number        19 
_symmetry.space_group_name_Hall    'P 2ac 2ab' 
_symmetry.space_group_name_H-M     'P 21 21 21' 
#
_pdbx_struct_assembly.method_details        PISA 
_pdbx_struct_assembly.oligomeric_details    trimeric 
_pdbx_struct_assembly.oligomeric_count      3 
_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
? 5 H N N 
? 5 K 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
disulf ? disulf1 A SG CYS 1 P CYS 1 1_555 A SG CYS 11 P CYS 11 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.045 ? 
disulf ? disulf2 B SG CYS 14 V CYS 26 1_555 B SG CYS 56 V CYS 68 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.082 ? 
disulf ? disulf3 B SG CYS 39 V CYS 51 1_555 C SG CYS 48 W CYS 60 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.064 ? 
disulf ? disulf4 B SG CYS 45 V CYS 57 1_555 B SG CYS 90 V CYS 102 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.944 ? 
disulf ? disulf5 B SG CYS 48 V CYS 60 1_555 C SG CYS 39 W CYS 51 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.094 ? 
disulf ? disulf6 B SG CYS 49 V CYS 61 1_555 B SG CYS 92 V CYS 104 1_555 ? A ? ? A ? ? ? ? ? ? ? 2.021 ? 
disulf ? disulf7 B SG CYS 49 V CYS 61 1_555 B SG CYS 92 V CYS 104 1_555 ? B ? ? B ? ? ? ? ? ? ? 2.016 ? 
disulf ? disulf8 C SG CYS 14 W CYS 26 1_555 C SG CYS 56 W CYS 68 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.011 ? 
disulf ? disulf9 C SG CYS 45 W CYS 57 1_555 C SG CYS 90 W CYS 102 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.023 ? 
disulf ? disulf10 C SG CYS 49 W CYS 61 1_555 C SG CYS 92 W CYS 104 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.993 ? 
covale ? covale1 A C VAL 5 P VAL 5 1_555 A N NLE 6 P NLE 6 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.346 ? 
covale ? covale2 A C NLE 6 P NLE 6 1_555 A N TRP 7 P TRP 7 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.338 ? 
covale ? covale3 A C LEU 15 P LEU 15 1_555 D N NH2 . P NH2 101 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.327 ? 
#
_chem_comp.formula           'C6 H14 O2' 
_chem_comp.formula_weight    118.174 
_chem_comp.id                MPD 
_chem_comp.mon_nstd_flag     . 
_chem_comp.name              (4S)-2-METHYL-2,4-PENTANEDIOL 
_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
C1 C2 MPD sing 232 n n 
C1 H11 MPD sing 233 n n 
C1 H12 MPD sing 234 n n 
C1 H13 MPD sing 235 n n 
C2 O2 MPD sing 236 n n 
C2 CM MPD sing 237 n n 
C2 C3 MPD sing 238 n n 
O2 HO2 MPD sing 239 n n 
CM HM1 MPD sing 240 n n 
CM HM2 MPD sing 241 n n 
CM HM3 MPD sing 242 n n 
C3 C4 MPD sing 243 n n 
C3 H31 MPD sing 244 n n 
C3 H32 MPD sing 245 n n 
C4 O4 MPD sing 246 n n 
C4 C5 MPD sing 247 n n 
C4 H4 MPD sing 248 n n 
O4 HO4 MPD sing 249 n n 
C5 H51 MPD sing 250 n n 
C5 H52 MPD sing 251 n n 
C5 H53 MPD sing 252 n n 
#
_atom_sites.entry_id                     6Z13 
_atom_sites.fract_transf_matrix[1][1]    0.018431 
_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]    0.017956 
_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]    0.012991 
_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
D 3 NH2 P 1 101 16 NH2 NH2 . 
E 4 ACY V 1 201 1 ACY ACY . 
F 4 ACY V 1 202 2 ACY ACY . 
G 4 ACY V 1 203 4 ACY ACY . 
H 5 MPD V 1 204 6 MPD MPD . 
I 4 ACY W 1 201 3 ACY ACY . 
J 4 ACY W 1 202 5 ACY ACY . 
K 5 MPD W 1 203 7 MPD MPD . 
L 6 HOH P 1 201 82 HOH HOH . 
L 6 HOH P 2 202 72 HOH HOH . 
L 6 HOH P 3 203 127 HOH HOH . 
L 6 HOH P 4 204 18 HOH HOH . 
L 6 HOH P 5 205 103 HOH HOH . 
M 6 HOH V 1 301 28 HOH HOH . 
M 6 HOH V 2 302 86 HOH HOH . 
M 6 HOH V 3 303 10 HOH HOH . 
M 6 HOH V 4 304 110 HOH HOH . 
M 6 HOH V 5 305 134 HOH HOH . 
M 6 HOH V 6 306 50 HOH HOH . 
M 6 HOH V 7 307 52 HOH HOH . 
M 6 HOH V 8 308 12 HOH HOH . 
M 6 HOH V 9 309 33 HOH HOH . 
M 6 HOH V 10 310 98 HOH HOH . 
M 6 HOH V 11 311 8 HOH HOH . 
M 6 HOH V 12 312 27 HOH HOH . 
M 6 HOH V 13 313 36 HOH HOH . 
M 6 HOH V 14 314 100 HOH HOH . 
M 6 HOH V 15 315 41 HOH HOH . 
M 6 HOH V 16 316 111 HOH HOH . 
M 6 HOH V 17 317 73 HOH HOH . 
M 6 HOH V 18 318 56 HOH HOH . 
M 6 HOH V 19 319 14 HOH HOH . 
M 6 HOH V 20 320 46 HOH HOH . 
M 6 HOH V 21 321 67 HOH HOH . 
M 6 HOH V 22 322 1 HOH HOH . 
M 6 HOH V 23 323 97 HOH HOH . 
M 6 HOH V 24 324 101 HOH HOH . 
M 6 HOH V 25 325 78 HOH HOH . 
M 6 HOH V 26 326 121 HOH HOH . 
M 6 HOH V 27 327 49 HOH HOH . 
M 6 HOH V 28 328 96 HOH HOH . 
M 6 HOH V 29 329 109 HOH HOH . 
M 6 HOH V 30 330 13 HOH HOH . 
M 6 HOH V 31 331 34 HOH HOH . 
M 6 HOH V 32 332 54 HOH HOH . 
M 6 HOH V 33 333 16 HOH HOH . 
M 6 HOH V 34 334 105 HOH HOH . 
M 6 HOH V 35 335 7 HOH HOH . 
M 6 HOH V 36 336 43 HOH HOH . 
M 6 HOH V 37 337 130 HOH HOH . 
M 6 HOH V 38 338 108 HOH HOH . 
M 6 HOH V 39 339 128 HOH HOH . 
M 6 HOH V 40 340 58 HOH HOH . 
M 6 HOH V 41 341 63 HOH HOH . 
M 6 HOH V 42 342 118 HOH HOH . 
M 6 HOH V 43 343 115 HOH HOH . 
M 6 HOH V 44 344 3 HOH HOH . 
M 6 HOH V 45 345 24 HOH HOH . 
M 6 HOH V 46 346 68 HOH HOH . 
M 6 HOH V 47 347 132 HOH HOH . 
M 6 HOH V 48 348 129 HOH HOH . 
M 6 HOH V 49 349 91 HOH HOH . 
M 6 HOH V 50 350 122 HOH HOH . 
M 6 HOH V 51 351 75 HOH HOH . 
M 6 HOH V 52 352 124 HOH HOH . 
M 6 HOH V 53 353 146 HOH HOH . 
M 6 HOH V 54 354 138 HOH HOH . 
M 6 HOH V 55 355 90 HOH HOH . 
M 6 HOH V 56 356 117 HOH HOH . 
M 6 HOH V 57 357 35 HOH HOH . 
N 6 HOH W 1 301 6 HOH HOH . 
N 6 HOH W 2 302 116 HOH HOH . 
N 6 HOH W 3 303 17 HOH HOH . 
N 6 HOH W 4 304 11 HOH HOH . 
N 6 HOH W 5 305 37 HOH HOH . 
N 6 HOH W 6 306 114 HOH HOH . 
N 6 HOH W 7 307 62 HOH HOH . 
N 6 HOH W 8 308 19 HOH HOH . 
N 6 HOH W 9 309 99 HOH HOH . 
N 6 HOH W 10 310 60 HOH HOH . 
N 6 HOH W 11 311 61 HOH HOH . 
N 6 HOH W 12 312 84 HOH HOH . 
N 6 HOH W 13 313 29 HOH HOH . 
N 6 HOH W 14 314 20 HOH HOH . 
N 6 HOH W 15 315 55 HOH HOH . 
N 6 HOH W 16 316 77 HOH HOH . 
N 6 HOH W 17 317 113 HOH HOH . 
N 6 HOH W 18 318 59 HOH HOH . 
N 6 HOH W 19 319 44 HOH HOH . 
N 6 HOH W 20 320 135 HOH HOH . 
N 6 HOH W 21 321 30 HOH HOH . 
N 6 HOH W 22 322 87 HOH HOH . 
N 6 HOH W 23 323 4 HOH HOH . 
N 6 HOH W 24 324 85 HOH HOH . 
N 6 HOH W 25 325 125 HOH HOH . 
N 6 HOH W 26 326 47 HOH HOH . 
N 6 HOH W 27 327 21 HOH HOH . 
N 6 HOH W 28 328 2 HOH HOH . 
N 6 HOH W 29 329 140 HOH HOH . 
N 6 HOH W 30 330 15 HOH HOH . 
N 6 HOH W 31 331 92 HOH HOH . 
N 6 HOH W 32 332 48 HOH HOH . 
N 6 HOH W 33 333 23 HOH HOH . 
N 6 HOH W 34 334 133 HOH HOH . 
N 6 HOH W 35 335 94 HOH HOH . 
N 6 HOH W 36 336 131 HOH HOH . 
N 6 HOH W 37 337 81 HOH HOH . 
N 6 HOH W 38 338 89 HOH HOH . 
N 6 HOH W 39 339 51 HOH HOH . 
N 6 HOH W 40 340 57 HOH HOH . 
N 6 HOH W 41 341 106 HOH HOH . 
N 6 HOH W 42 342 144 HOH HOH . 
N 6 HOH W 43 343 31 HOH HOH . 
N 6 HOH W 44 344 83 HOH HOH . 
N 6 HOH W 45 345 88 HOH HOH . 
N 6 HOH W 46 346 38 HOH HOH . 
N 6 HOH W 47 347 25 HOH HOH . 
N 6 HOH W 48 348 65 HOH HOH . 
N 6 HOH W 49 349 69 HOH HOH . 
N 6 HOH W 50 350 9 HOH HOH . 
N 6 HOH W 51 351 64 HOH HOH . 
N 6 HOH W 52 352 22 HOH HOH . 
N 6 HOH W 53 353 123 HOH HOH . 
N 6 HOH W 54 354 5 HOH HOH . 
N 6 HOH W 55 355 40 HOH HOH . 
N 6 HOH W 56 356 45 HOH HOH . 
N 6 HOH W 57 357 39 HOH HOH . 
N 6 HOH W 58 358 42 HOH HOH . 
N 6 HOH W 59 359 79 HOH HOH . 
N 6 HOH W 60 360 26 HOH HOH . 
N 6 HOH W 61 361 107 HOH HOH . 
N 6 HOH W 62 362 136 HOH HOH . 
N 6 HOH W 63 363 142 HOH HOH . 
N 6 HOH W 64 364 143 HOH HOH . 
N 6 HOH W 65 365 71 HOH HOH . 
N 6 HOH W 66 366 53 HOH HOH . 
N 6 HOH W 67 367 145 HOH HOH . 
N 6 HOH W 68 368 102 HOH HOH . 
N 6 HOH W 69 369 95 HOH HOH . 
N 6 HOH W 70 370 76 HOH HOH . 
N 6 HOH W 71 371 32 HOH HOH . 
N 6 HOH W 72 372 66 HOH HOH . 
N 6 HOH W 73 373 70 HOH HOH . 
N 6 HOH W 74 374 137 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 MPD . . . K 5 22.086 18.663 7.512 1 26.45 ? C1 MPD 203 W 1 
HETATM 2 C C2 MPD . . . K 5 21.458 17.976 8.733 1 33.61 ? C2 MPD 203 W 1 
HETATM 3 O O2 MPD . . . K 5 22.47 17.786 9.763 1 33.41 ? O2 MPD 203 W 1 
HETATM 4 C CM MPD . . . K 5 20.378 18.917 9.271 1 48.52 ? CM MPD 203 W 1 
HETATM 5 C C3 MPD . . . K 5 21.001 16.578 8.303 1 45.75 ? C3 MPD 203 W 1 
HETATM 6 C C4 MPD . . . K 5 20.053 15.907 9.287 1 56.13 ? C4 MPD 203 W 1 
HETATM 7 O O4 MPD . . . K 5 20.03 14.529 9.007 1 51.07 ? O4 MPD 203 W 1 
HETATM 8 C C5 MPD . . . K 5 20.493 16.089 10.724 1 52.18 ? C5 MPD 203 W 1 
HETATM 9 H H11 MPD . . . K 5 22.006 18.008 6.645 1 31.74 ? H11 MPD 203 W 1 
HETATM 10 H H12 MPD . . . K 5 21.562 19.597 7.311 1 31.74 ? H12 MPD 203 W 1 
HETATM 11 H H13 MPD . . . K 5 23.137 18.872 7.714 1 31.74 ? H13 MPD 203 W 1 
HETATM 12 H HO2 MPD . . . K 5 22.735 16.843 9.79 1 40.09 ? HO2 MPD 203 W 1 
HETATM 13 H HM1 MPD . . . K 5 19.557 18.33 9.684 1 58.22 ? HM1 MPD 203 W 1 
HETATM 14 H HM2 MPD . . . K 5 20.005 19.542 8.46 1 58.22 ? HM2 MPD 203 W 1 
HETATM 15 H HM3 MPD . . . K 5 20.802 19.548 10.052 1 58.22 ? HM3 MPD 203 W 1 
HETATM 16 H H31 MPD . . . K 5 20.504 16.656 7.336 1 54.9 ? H31 MPD 203 W 1 
HETATM 17 H H32 MPD . . . K 5 21.88 15.946 8.178 1 54.9 ? H32 MPD 203 W 1 
HETATM 18 H H4 MPD . . . K 5 19.068 16.36 9.172 1 67.36 ? H4 MPD 203 W 1 
HETATM 19 H HO4 MPD . . . K 5 19.277 14.129 9.486 1 61.28 ? HO4 MPD 203 W 1 
HETATM 20 H H51 MPD . . . K 5 21.379 15.481 10.912 1 62.62 ? H51 MPD 203 W 1 
HETATM 21 H H52 MPD . . . K 5 20.728 17.138 10.902 1 62.62 ? H52 MPD 203 W 1 
HETATM 22 H H53 MPD . . . K 5 19.69 15.777 11.392 1 62.62 ? H53 MPD 203 W 1 
#
_model_server_stats.io_time_ms              10 
_model_server_stats.parse_time_ms           8 
_model_server_stats.create_model_time_ms    4 
_model_server_stats.query_time_ms           278 
_model_server_stats.encode_time_ms          9 
_model_server_stats.element_count           22 
#