data_5JEA
#
_model_server_result.job_id            HmAXPAYp6s4WTTZIJ5Y5-g 
_model_server_result.datetime_utc      '2024-11-09 02:30:00' 
_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          5jea 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"R","auth_seq_id":301}' 
#
_entry.id    5JEA 
#
_exptl.entry_id    5JEA 
_exptl.method      'X-RAY DIFFRACTION' 
#
_entity.details                     ? 
_entity.formula_weight              118.174 
_entity.id                          13 
_entity.src_method                  syn 
_entity.type                        non-polymer 
_entity.pdbx_description            (4S)-2-METHYL-2,4-PENTANEDIOL 
_entity.pdbx_number_of_molecules    7 
_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            5JEA 
_cell.length_a            106.08 
_cell.length_b            182.53 
_cell.length_c            250.55 
_cell.Z_PDB               4 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 5JEA 
_symmetry.cell_setting             ? 
_symmetry.Int_Tables_number        19 
_symmetry.space_group_name_Hall    . 
_symmetry.space_group_name_H-M     'P 21 21 21' 
#
_pdbx_struct_assembly.method_details        PISA 
_pdbx_struct_assembly.oligomeric_details    dodecameric 
_pdbx_struct_assembly.oligomeric_count      12 
_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,X,Y,Z,AA,BA,CA,DA,EA,FA,GA,HA 
_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
? 13 M N N 
? 13 N N N 
? 13 Q N N 
? 13 R N N 
? 13 T N N 
? 13 U N N 
? 13 V 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 B OG SER 162 B SER 159 1_555 O NA NA . B NA 301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.504 ? 
metalc ? metalc2 B O VAL 192 B VAL 189 1_555 O NA NA . B NA 301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.74 ? 
metalc ? metalc3 B O GLY 194 B GLY 191 1_555 O NA NA . B NA 301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.744 ? 
metalc ? metalc4 F OG1 THR 88 F THR 88 1_555 S NA NA . F NA 301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.43 ? 
metalc ? metalc5 F O GLN 90 F GLN 90 1_555 S NA NA . F NA 301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.443 ? 
metalc ? metalc6 F OG1 THR 92 F THR 92 1_555 S NA NA . F NA 301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 3.034 ? 
metalc ? metalc7 F O SER 133 F SER 133 1_555 S NA NA . F NA 301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.482 ? 
metalc ? metalc8 J SG CYS 51 J CYS 47 1_555 W ZN ZN . J ZN 1102 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.414 ? 
metalc ? metalc9 J SG CYS 56 J CYS 52 1_555 W ZN ZN . J ZN 1102 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.314 ? 
metalc ? metalc10 J SG CYS 59 J CYS 55 1_555 W ZN ZN . J ZN 1102 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.341 ? 
metalc ? metalc11 J NE2 HIS 188 J HIS 184 1_555 W ZN ZN . J ZN 1102 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.164 ? 
hydrog 'C-G PAIR' hydrog1 L N4 C 4 R C -39 1_555 L O6 G 12 R G -31 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? 
hydrog WATSON-CRICK hydrog2 L N3 C 5 R C -38 1_555 L N1 G 10 R G -33 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? 
hydrog WATSON-CRICK hydrog3 L N4 C 5 R C -38 1_555 L O6 G 10 R G -33 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? 
hydrog WATSON-CRICK hydrog4 L O2 C 5 R C -38 1_555 L N2 G 10 R G -33 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? 
#
_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 352 n n 
C1 H11 MPD sing 353 n n 
C1 H12 MPD sing 354 n n 
C1 H13 MPD sing 355 n n 
C2 O2 MPD sing 356 n n 
C2 CM MPD sing 357 n n 
C2 C3 MPD sing 358 n n 
O2 HO2 MPD sing 359 n n 
CM HM1 MPD sing 360 n n 
CM HM2 MPD sing 361 n n 
CM HM3 MPD sing 362 n n 
C3 C4 MPD sing 363 n n 
C3 H31 MPD sing 364 n n 
C3 H32 MPD sing 365 n n 
C4 O4 MPD sing 366 n n 
C4 C5 MPD sing 367 n n 
C4 H4 MPD sing 368 n n 
O4 HO4 MPD sing 369 n n 
C5 H51 MPD sing 370 n n 
C5 H52 MPD sing 371 n n 
C5 H53 MPD sing 372 n n 
#
_atom_sites.entry_id                     5JEA 
_atom_sites.fract_transf_matrix[1][1]    0.009427 
_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]    0.005479 
_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]    0.003991 
_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
M 13 MPD A 1 401 1 MPD MPD . 
N 13 MPD A 1 402 8 MPD MPD . 
O 14 NA B 1 301 4 NA NA . 
P 14 NA B 1 302 5 NA NA . 
Q 13 MPD C 1 401 5 MPD MPD . 
R 13 MPD D 1 301 7 MPD MPD . 
S 14 NA F 1 301 6 NA NA . 
T 13 MPD G 1 301 3 MPD MPD . 
U 13 MPD G 1 302 4 MPD MPD . 
V 13 MPD J 1 1101 6 MPD MPD . 
W 15 ZN J 1 1102 1 ZN ZN . 
X 14 NA J 1 1103 2 NA NA . 
Y 16 HOH A 1 501 87 HOH HOH . 
Y 16 HOH A 2 502 56 HOH HOH . 
Y 16 HOH A 3 503 157 HOH HOH . 
Y 16 HOH A 4 504 5 HOH HOH . 
Y 16 HOH A 5 505 14 HOH HOH . 
Y 16 HOH A 6 506 78 HOH HOH . 
Y 16 HOH A 7 507 139 HOH HOH . 
Y 16 HOH A 8 508 149 HOH HOH . 
Y 16 HOH A 9 509 89 HOH HOH . 
Y 16 HOH A 10 510 144 HOH HOH . 
Y 16 HOH A 11 511 126 HOH HOH . 
Y 16 HOH A 12 512 162 HOH HOH . 
Y 16 HOH A 13 513 143 HOH HOH . 
Y 16 HOH A 14 514 142 HOH HOH . 
Y 16 HOH A 15 515 2 HOH HOH . 
Y 16 HOH A 16 516 95 HOH HOH . 
Y 16 HOH A 17 517 85 HOH HOH . 
Y 16 HOH A 18 518 151 HOH HOH . 
Y 16 HOH A 19 519 113 HOH HOH . 
Z 16 HOH B 1 401 97 HOH HOH . 
Z 16 HOH B 2 402 9 HOH HOH . 
Z 16 HOH B 3 403 19 HOH HOH . 
Z 16 HOH B 4 404 4 HOH HOH . 
Z 16 HOH B 5 405 6 HOH HOH . 
Z 16 HOH B 6 406 26 HOH HOH . 
Z 16 HOH B 7 407 13 HOH HOH . 
Z 16 HOH B 8 408 150 HOH HOH . 
Z 16 HOH B 9 409 45 HOH HOH . 
Z 16 HOH B 10 410 178 HOH HOH . 
Z 16 HOH B 11 411 11 HOH HOH . 
Z 16 HOH B 12 412 46 HOH HOH . 
Z 16 HOH B 13 413 187 HOH HOH . 
AA 16 HOH C 1 501 40 HOH HOH . 
AA 16 HOH C 2 502 66 HOH HOH . 
AA 16 HOH C 3 503 48 HOH HOH . 
AA 16 HOH C 4 504 93 HOH HOH . 
AA 16 HOH C 5 505 21 HOH HOH . 
AA 16 HOH C 6 506 138 HOH HOH . 
AA 16 HOH C 7 507 8 HOH HOH . 
AA 16 HOH C 8 508 153 HOH HOH . 
AA 16 HOH C 9 509 27 HOH HOH . 
AA 16 HOH C 10 510 152 HOH HOH . 
AA 16 HOH C 11 511 124 HOH HOH . 
AA 16 HOH C 12 512 129 HOH HOH . 
BA 16 HOH D 1 401 17 HOH HOH . 
BA 16 HOH D 2 402 136 HOH HOH . 
BA 16 HOH D 3 403 50 HOH HOH . 
BA 16 HOH D 4 404 103 HOH HOH . 
BA 16 HOH D 5 405 141 HOH HOH . 
BA 16 HOH D 6 406 44 HOH HOH . 
BA 16 HOH D 7 407 35 HOH HOH . 
BA 16 HOH D 8 408 164 HOH HOH . 
BA 16 HOH D 9 409 155 HOH HOH . 
BA 16 HOH D 10 410 166 HOH HOH . 
BA 16 HOH D 11 411 39 HOH HOH . 
BA 16 HOH D 12 412 73 HOH HOH . 
BA 16 HOH D 13 413 174 HOH HOH . 
BA 16 HOH D 14 414 105 HOH HOH . 
CA 16 HOH E 1 301 137 HOH HOH . 
CA 16 HOH E 2 302 156 HOH HOH . 
CA 16 HOH E 3 303 47 HOH HOH . 
CA 16 HOH E 4 304 31 HOH HOH . 
CA 16 HOH E 5 305 49 HOH HOH . 
CA 16 HOH E 6 306 54 HOH HOH . 
CA 16 HOH E 7 307 107 HOH HOH . 
CA 16 HOH E 8 308 176 HOH HOH . 
DA 16 HOH F 1 401 62 HOH HOH . 
DA 16 HOH F 2 402 140 HOH HOH . 
DA 16 HOH F 3 403 65 HOH HOH . 
DA 16 HOH F 4 404 104 HOH HOH . 
DA 16 HOH F 5 405 186 HOH HOH . 
DA 16 HOH F 6 406 119 HOH HOH . 
EA 16 HOH G 1 401 116 HOH HOH . 
EA 16 HOH G 2 402 123 HOH HOH . 
EA 16 HOH G 3 403 51 HOH HOH . 
EA 16 HOH G 4 404 12 HOH HOH . 
EA 16 HOH G 5 405 159 HOH HOH . 
EA 16 HOH G 6 406 183 HOH HOH . 
EA 16 HOH G 7 407 43 HOH HOH . 
EA 16 HOH G 8 408 98 HOH HOH . 
EA 16 HOH G 9 409 61 HOH HOH . 
EA 16 HOH G 10 410 36 HOH HOH . 
EA 16 HOH G 11 411 77 HOH HOH . 
EA 16 HOH G 12 412 24 HOH HOH . 
EA 16 HOH G 13 413 10 HOH HOH . 
EA 16 HOH G 14 414 177 HOH HOH . 
EA 16 HOH G 15 415 84 HOH HOH . 
EA 16 HOH G 16 416 190 HOH HOH . 
EA 16 HOH G 17 417 71 HOH HOH . 
EA 16 HOH G 18 418 179 HOH HOH . 
EA 16 HOH G 19 419 172 HOH HOH . 
FA 16 HOH H 1 401 109 HOH HOH . 
FA 16 HOH H 2 402 154 HOH HOH . 
FA 16 HOH H 3 403 60 HOH HOH . 
FA 16 HOH H 4 404 91 HOH HOH . 
FA 16 HOH H 5 405 67 HOH HOH . 
FA 16 HOH H 6 406 75 HOH HOH . 
FA 16 HOH H 7 407 148 HOH HOH . 
FA 16 HOH H 8 408 165 HOH HOH . 
FA 16 HOH H 9 409 173 HOH HOH . 
FA 16 HOH H 10 410 28 HOH HOH . 
FA 16 HOH H 11 411 110 HOH HOH . 
FA 16 HOH H 12 412 158 HOH HOH . 
FA 16 HOH H 13 413 189 HOH HOH . 
FA 16 HOH H 14 414 69 HOH HOH . 
FA 16 HOH H 15 415 63 HOH HOH . 
GA 16 HOH I 1 301 168 HOH HOH . 
GA 16 HOH I 2 302 112 HOH HOH . 
HA 16 HOH J 1 1201 185 HOH HOH . 
HA 16 HOH J 2 1202 163 HOH HOH . 
HA 16 HOH J 3 1203 181 HOH HOH . 
HA 16 HOH J 4 1204 122 HOH HOH . 
HA 16 HOH J 5 1205 83 HOH HOH . 
HA 16 HOH J 6 1206 130 HOH HOH . 
HA 16 HOH J 7 1207 33 HOH HOH . 
HA 16 HOH J 8 1208 22 HOH HOH . 
HA 16 HOH J 9 1209 3 HOH HOH . 
HA 16 HOH J 10 1210 7 HOH HOH . 
HA 16 HOH J 11 1211 32 HOH HOH . 
HA 16 HOH J 12 1212 80 HOH HOH . 
HA 16 HOH J 13 1213 99 HOH HOH . 
HA 16 HOH J 14 1214 30 HOH HOH . 
HA 16 HOH J 15 1215 92 HOH HOH . 
HA 16 HOH J 16 1216 101 HOH HOH . 
HA 16 HOH J 17 1217 42 HOH HOH . 
HA 16 HOH J 18 1218 23 HOH HOH . 
HA 16 HOH J 19 1219 52 HOH HOH . 
HA 16 HOH J 20 1220 133 HOH HOH . 
HA 16 HOH J 21 1221 167 HOH HOH . 
HA 16 HOH J 22 1222 188 HOH HOH . 
HA 16 HOH J 23 1223 118 HOH HOH . 
HA 16 HOH J 24 1224 131 HOH HOH . 
HA 16 HOH J 25 1225 135 HOH HOH . 
HA 16 HOH J 26 1226 191 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 . . . R 13 53.38 -13.7 -51.543 1 80.85 ? C1 MPD 301 D 1 
HETATM 2 C C2 MPD . . . R 13 53.651 -14.796 -50.518 1 86.1 ? C2 MPD 301 D 1 
HETATM 3 O O2 MPD . . . R 13 54.419 -14.233 -49.426 1 92.59 ? O2 MPD 301 D 1 
HETATM 4 C CM MPD . . . R 13 52.334 -15.313 -49.954 1 81.12 ? CM MPD 301 D 1 
HETATM 5 C C3 MPD . . . R 13 54.439 -15.941 -51.151 1 86.92 ? C3 MPD 301 D 1 
HETATM 6 C C4 MPD . . . R 13 55.942 -15.866 -50.883 1 87.39 ? C4 MPD 301 D 1 
HETATM 7 O O4 MPD . . . R 13 56.311 -14.579 -50.438 1 71.06 ? O4 MPD 301 D 1 
HETATM 8 C C5 MPD . . . R 13 56.36 -16.902 -49.844 1 94.19 ? C5 MPD 301 D 1 
#
_model_server_stats.io_time_ms              57 
_model_server_stats.parse_time_ms           16 
_model_server_stats.create_model_time_ms    33 
_model_server_stats.query_time_ms           295 
_model_server_stats.encode_time_ms          4 
_model_server_stats.element_count           8 
#