data_3E8H
#
_model_server_result.job_id            ZcUcZlJEkk-mo_b2ilX05w 
_model_server_result.datetime_utc      '2025-09-09 18:11:19' 
_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          3e8h 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"L","auth_seq_id":503}' 
#
_entry.id    3E8H 
#
_exptl.entry_id    3E8H 
_exptl.method      'X-RAY DIFFRACTION' 
#
_entity.details                     ? 
_entity.formula_weight              118.174 
_entity.id                          2 
_entity.src_method                  syn 
_entity.type                        non-polymer 
_entity.pdbx_description            (4S)-2-METHYL-2,4-PENTANEDIOL 
_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         90 
_cell.entry_id            3E8H 
_cell.length_a            68.194 
_cell.length_b            68.194 
_cell.length_c            89.294 
_cell.Z_PDB               16 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 3E8H 
_symmetry.cell_setting             ? 
_symmetry.Int_Tables_number        79 
_symmetry.space_group_name_Hall    ? 
_symmetry.space_group_name_H-M     'I 4' 
#
loop_
_pdbx_struct_assembly.method_details
_pdbx_struct_assembly.oligomeric_details
_pdbx_struct_assembly.oligomeric_count
_pdbx_struct_assembly.details
_pdbx_struct_assembly.id
PISA tetrameric 4 author_and_software_defined_assembly 1 
PISA tetrameric 4 author_and_software_defined_assembly 2 
#
loop_
_pdbx_struct_assembly_gen.asym_id_list
_pdbx_struct_assembly_gen.assembly_id
_pdbx_struct_assembly_gen.oper_expression
A,C,D,E,F,G,H,I,J,Q 1 1,2,3,4 
B,K,L,M,N,O,P,R 2 1,2,3,4 
#
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' 2_445 -x-1,-y-1,z -1 0 0 0 -1 0 0 0 1 -68.194 -68.194 0 
3 'crystal symmetry operation' 3_455 -y-1,x,z 0 -1 0 1 0 0 0 0 1 -68.194 0 0 
4 'crystal symmetry operation' 4_545 y,-x-1,z 0 1 0 -1 0 0 0 0 1 0 -68.194 0 
#
loop_
_struct_asym.details
_struct_asym.entity_id
_struct_asym.id
_struct_asym.pdbx_modified
_struct_asym.pdbx_blank_PDB_chainid_flag
? 2 C N N 
? 2 D N N 
? 2 K N N 
? 2 L 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 E K K . A K 1 1_555 A O THR 45 A THR 63 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.831 ? 
metalc ? metalc2 E K K . A K 1 1_555 A O VAL 46 A VAL 64 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.805 ? 
metalc ? metalc3 F K K . A K 3 1_555 A O GLY 49 A GLY 67 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.523 ? 
metalc ? metalc4 G K K . A K 4 1_555 A O VAL 46 A VAL 64 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.995 ? 
metalc ? metalc5 G K K . A K 4 1_555 Q O HOH . A HOH 511 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.956 ? 
metalc ? metalc6 H K K . A K 5 1_555 A O THR 45 A THR 63 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.973 ? 
metalc ? metalc7 H K K . A K 5 1_555 A OG1 THR 45 A THR 63 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.793 ? 
metalc ? metalc8 I K K . A K 9 1_555 Q O HOH . A HOH 511 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.712 ? 
metalc ? metalc9 M K K . B K 2 1_555 B O THR 45 B THR 63 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.746 ? 
metalc ? metalc10 M K K . B K 2 1_555 B O VAL 46 B VAL 64 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.959 ? 
metalc ? metalc11 N K K . B K 6 1_555 B O THR 45 B THR 63 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.965 ? 
metalc ? metalc12 N K K . B K 6 1_555 B OG1 THR 45 B THR 63 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.835 ? 
metalc ? metalc13 O K K . B K 7 1_555 R O HOH . B HOH 504 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.877 ? 
metalc ? metalc14 P K K . B K 8 1_555 B O GLY 49 B GLY 67 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.702 ? 
#
_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 205 n n 
C1 H11 MPD sing 206 n n 
C1 H12 MPD sing 207 n n 
C1 H13 MPD sing 208 n n 
C2 O2 MPD sing 209 n n 
C2 CM MPD sing 210 n n 
C2 C3 MPD sing 211 n n 
O2 HO2 MPD sing 212 n n 
CM HM1 MPD sing 213 n n 
CM HM2 MPD sing 214 n n 
CM HM3 MPD sing 215 n n 
C3 C4 MPD sing 216 n n 
C3 H31 MPD sing 217 n n 
C3 H32 MPD sing 218 n n 
C4 O4 MPD sing 219 n n 
C4 C5 MPD sing 220 n n 
C4 H4 MPD sing 221 n n 
O4 HO4 MPD sing 222 n n 
C5 H51 MPD sing 223 n n 
C5 H52 MPD sing 224 n n 
C5 H53 MPD sing 225 n n 
#
_atom_sites.entry_id                     3E8H 
_atom_sites.fract_transf_matrix[1][1]    0.014664 
_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]    0.014664 
_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]    0.011199 
_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 MPD A 1 501 501 MPD MPD . 
D 2 MPD A 1 504 504 MPD MPD . 
E 3 K A 1 1 1 K K . 
F 3 K A 1 3 3 K K . 
G 3 K A 1 4 4 K K . 
H 3 K A 1 5 5 K K . 
I 3 K A 1 9 9 K K . 
J 3 K A 1 10 10 K K . 
K 2 MPD B 1 502 502 MPD MPD . 
L 2 MPD B 1 503 503 MPD MPD . 
M 3 K B 1 2 2 K K . 
N 3 K B 1 6 6 K K . 
O 3 K B 1 7 7 K K . 
P 3 K B 1 8 8 K K . 
Q 4 HOH A 1 505 1 HOH HOH . 
Q 4 HOH A 2 506 2 HOH HOH . 
Q 4 HOH A 3 507 3 HOH HOH . 
Q 4 HOH A 4 508 4 HOH HOH . 
Q 4 HOH A 5 509 5 HOH HOH . 
Q 4 HOH A 6 510 6 HOH HOH . 
Q 4 HOH A 7 511 7 HOH HOH . 
Q 4 HOH A 8 512 10 HOH HOH . 
Q 4 HOH A 9 513 13 HOH HOH . 
Q 4 HOH A 10 514 15 HOH HOH . 
Q 4 HOH A 11 515 16 HOH HOH . 
Q 4 HOH A 12 516 17 HOH HOH . 
Q 4 HOH A 13 517 18 HOH HOH . 
Q 4 HOH A 14 518 19 HOH HOH . 
Q 4 HOH A 15 519 20 HOH HOH . 
Q 4 HOH A 16 520 21 HOH HOH . 
Q 4 HOH A 17 521 22 HOH HOH . 
Q 4 HOH A 18 522 23 HOH HOH . 
Q 4 HOH A 19 523 26 HOH HOH . 
Q 4 HOH A 20 524 28 HOH HOH . 
Q 4 HOH A 21 525 29 HOH HOH . 
Q 4 HOH A 22 526 30 HOH HOH . 
Q 4 HOH A 23 527 32 HOH HOH . 
Q 4 HOH A 24 528 35 HOH HOH . 
Q 4 HOH A 25 529 36 HOH HOH . 
Q 4 HOH A 26 530 37 HOH HOH . 
Q 4 HOH A 27 531 38 HOH HOH . 
Q 4 HOH A 28 532 39 HOH HOH . 
Q 4 HOH A 29 533 42 HOH HOH . 
Q 4 HOH A 30 534 43 HOH HOH . 
Q 4 HOH A 31 535 48 HOH HOH . 
Q 4 HOH A 32 536 50 HOH HOH . 
Q 4 HOH A 33 537 53 HOH HOH . 
Q 4 HOH A 34 538 54 HOH HOH . 
Q 4 HOH A 35 539 57 HOH HOH . 
Q 4 HOH A 36 540 63 HOH HOH . 
Q 4 HOH A 37 541 64 HOH HOH . 
Q 4 HOH A 38 542 67 HOH HOH . 
Q 4 HOH A 39 543 68 HOH HOH . 
Q 4 HOH A 40 544 72 HOH HOH . 
Q 4 HOH A 41 545 73 HOH HOH . 
Q 4 HOH A 42 546 75 HOH HOH . 
Q 4 HOH A 43 547 77 HOH HOH . 
Q 4 HOH A 44 548 79 HOH HOH . 
Q 4 HOH A 45 549 80 HOH HOH . 
Q 4 HOH A 46 550 84 HOH HOH . 
Q 4 HOH A 47 551 85 HOH HOH . 
Q 4 HOH A 48 552 87 HOH HOH . 
Q 4 HOH A 49 553 88 HOH HOH . 
Q 4 HOH A 50 554 91 HOH HOH . 
Q 4 HOH A 51 555 92 HOH HOH . 
Q 4 HOH A 52 556 95 HOH HOH . 
Q 4 HOH A 53 557 96 HOH HOH . 
Q 4 HOH A 54 558 31 HOH HOH . 
Q 4 HOH A 55 559 55 HOH HOH . 
R 4 HOH B 1 504 8 HOH HOH . 
R 4 HOH B 2 505 9 HOH HOH . 
R 4 HOH B 3 506 11 HOH HOH . 
R 4 HOH B 4 507 12 HOH HOH . 
R 4 HOH B 5 508 14 HOH HOH . 
R 4 HOH B 6 509 24 HOH HOH . 
R 4 HOH B 7 510 25 HOH HOH . 
R 4 HOH B 8 511 27 HOH HOH . 
R 4 HOH B 9 513 33 HOH HOH . 
R 4 HOH B 10 514 34 HOH HOH . 
R 4 HOH B 11 515 40 HOH HOH . 
R 4 HOH B 12 516 41 HOH HOH . 
R 4 HOH B 13 517 44 HOH HOH . 
R 4 HOH B 14 518 45 HOH HOH . 
R 4 HOH B 15 519 46 HOH HOH . 
R 4 HOH B 16 520 47 HOH HOH . 
R 4 HOH B 17 521 49 HOH HOH . 
R 4 HOH B 18 522 51 HOH HOH . 
R 4 HOH B 19 523 52 HOH HOH . 
R 4 HOH B 20 525 56 HOH HOH . 
R 4 HOH B 21 526 58 HOH HOH . 
R 4 HOH B 22 527 59 HOH HOH . 
R 4 HOH B 23 528 60 HOH HOH . 
R 4 HOH B 24 529 61 HOH HOH . 
R 4 HOH B 25 530 62 HOH HOH . 
R 4 HOH B 26 531 65 HOH HOH . 
R 4 HOH B 27 532 66 HOH HOH . 
R 4 HOH B 28 533 69 HOH HOH . 
R 4 HOH B 29 534 70 HOH HOH . 
R 4 HOH B 30 535 71 HOH HOH . 
R 4 HOH B 31 536 74 HOH HOH . 
R 4 HOH B 32 537 76 HOH HOH . 
R 4 HOH B 33 538 78 HOH HOH . 
R 4 HOH B 34 539 81 HOH HOH . 
R 4 HOH B 35 540 82 HOH HOH . 
R 4 HOH B 36 541 83 HOH HOH . 
R 4 HOH B 37 542 86 HOH HOH . 
R 4 HOH B 38 543 89 HOH HOH . 
R 4 HOH B 39 544 90 HOH HOH . 
R 4 HOH B 40 545 93 HOH HOH . 
R 4 HOH B 41 546 94 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 . . . L 2 -16.157 -14.158 43.05 1 27.04 ? C1 MPD 503 B 1 
HETATM 2 C C2 MPD . . . L 2 -14.738 -14.644 42.748 1 33.22 ? C2 MPD 503 B 1 
HETATM 3 O O2 MPD . . . L 2 -14.629 -14.937 41.352 1 44.87 ? O2 MPD 503 B 1 
HETATM 4 C CM MPD . . . L 2 -13.745 -13.541 43.12 1 33.3 ? CM MPD 503 B 1 
HETATM 5 C C3 MPD . . . L 2 -14.41 -15.918 43.577 1 34.89 ? C3 MPD 503 B 1 
HETATM 6 C C4 MPD . . . L 2 -15.368 -17.104 43.273 1 37.91 ? C4 MPD 503 B 1 
HETATM 7 O O4 MPD . . . L 2 -15.3 -17.466 41.889 1 52.66 ? O4 MPD 503 B 1 
HETATM 8 C C5 MPD . . . L 2 -14.984 -18.314 44.128 1 37.04 ? C5 MPD 503 B 1 
#
_model_server_stats.io_time_ms              61 
_model_server_stats.parse_time_ms           6 
_model_server_stats.create_model_time_ms    4 
_model_server_stats.query_time_ms           272 
_model_server_stats.encode_time_ms          2 
_model_server_stats.element_count           8 
#