data_3E8B
#
_model_server_result.job_id            3a-0TDpEM5m1XDgCOqHMCQ 
_model_server_result.datetime_utc      '2025-08-31 04:51:17' 
_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          3e8b 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"L","auth_seq_id":503}' 
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_entry.id    3E8B 
#
_exptl.entry_id    3E8B 
_exptl.method      'X-RAY DIFFRACTION' 
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_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            3E8B 
_cell.length_a            68.134 
_cell.length_b            68.134 
_cell.length_c            89.359 
_cell.Z_PDB               16 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 3E8B 
_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,R 1 1,2,3,4 
B,K,L,M,N,O,P,Q,S 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 -68.134 -68.134 0 
3 'crystal symmetry operation' 3_455 -y-1,x,z 0 -1 0 1 0 0 0 0 1 -68.134 0 0 
4 'crystal symmetry operation' 4_545 y,-x-1,z 0 1 0 -1 0 0 0 0 1 0 -68.134 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 
#
_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                     3E8B 
_atom_sites.fract_transf_matrix[1][1]    0.014677 
_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]    0.014677 
_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]    0.011191 
_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 RB A 1 2 2 RB RB . 
F 3 RB A 1 3 3 RB RB . 
G 3 RB A 1 4 4 RB RB . 
H 3 RB A 1 6 6 RB RB . 
I 3 RB A 1 9 9 RB RB . 
J 3 RB A 1 10 10 RB RB . 
K 2 MPD B 1 502 502 MPD MPD . 
L 2 MPD B 1 503 503 MPD MPD . 
M 3 RB B 1 1 1 RB RB . 
N 3 RB B 1 5 5 RB RB . 
O 3 RB B 1 7 7 RB RB . 
P 3 RB B 1 8 8 RB RB . 
Q 3 RB B 1 11 11 RB RB . 
R 4 HOH A 1 505 505 HOH HOH . 
R 4 HOH A 2 506 506 HOH HOH . 
R 4 HOH A 3 507 507 HOH HOH . 
R 4 HOH A 4 508 508 HOH HOH . 
R 4 HOH A 5 509 509 HOH HOH . 
R 4 HOH A 6 510 510 HOH HOH . 
R 4 HOH A 7 511 511 HOH HOH . 
R 4 HOH A 8 512 512 HOH HOH . 
R 4 HOH A 9 513 513 HOH HOH . 
R 4 HOH A 10 514 514 HOH HOH . 
R 4 HOH A 11 515 515 HOH HOH . 
R 4 HOH A 12 516 516 HOH HOH . 
R 4 HOH A 13 517 517 HOH HOH . 
R 4 HOH A 14 518 518 HOH HOH . 
R 4 HOH A 15 519 519 HOH HOH . 
R 4 HOH A 16 520 520 HOH HOH . 
R 4 HOH A 17 521 521 HOH HOH . 
R 4 HOH A 18 522 522 HOH HOH . 
R 4 HOH A 19 523 523 HOH HOH . 
R 4 HOH A 20 524 524 HOH HOH . 
R 4 HOH A 21 525 525 HOH HOH . 
R 4 HOH A 22 526 526 HOH HOH . 
R 4 HOH A 23 527 527 HOH HOH . 
R 4 HOH A 24 528 528 HOH HOH . 
R 4 HOH A 25 529 529 HOH HOH . 
R 4 HOH A 26 530 530 HOH HOH . 
R 4 HOH A 27 531 531 HOH HOH . 
R 4 HOH A 28 532 532 HOH HOH . 
R 4 HOH A 29 533 533 HOH HOH . 
R 4 HOH A 30 534 534 HOH HOH . 
R 4 HOH A 31 535 535 HOH HOH . 
R 4 HOH A 32 536 536 HOH HOH . 
R 4 HOH A 33 537 537 HOH HOH . 
R 4 HOH A 34 538 538 HOH HOH . 
R 4 HOH A 35 539 539 HOH HOH . 
R 4 HOH A 36 540 540 HOH HOH . 
R 4 HOH A 37 541 541 HOH HOH . 
R 4 HOH A 38 542 542 HOH HOH . 
R 4 HOH A 39 543 543 HOH HOH . 
R 4 HOH A 40 544 544 HOH HOH . 
R 4 HOH A 41 545 545 HOH HOH . 
R 4 HOH A 42 546 546 HOH HOH . 
R 4 HOH A 43 547 547 HOH HOH . 
R 4 HOH A 44 548 548 HOH HOH . 
R 4 HOH A 45 549 549 HOH HOH . 
R 4 HOH A 46 550 550 HOH HOH . 
R 4 HOH A 47 551 551 HOH HOH . 
R 4 HOH A 48 552 552 HOH HOH . 
R 4 HOH A 49 553 553 HOH HOH . 
R 4 HOH A 50 554 554 HOH HOH . 
S 4 HOH B 1 504 504 HOH HOH . 
S 4 HOH B 2 505 505 HOH HOH . 
S 4 HOH B 3 506 506 HOH HOH . 
S 4 HOH B 4 507 507 HOH HOH . 
S 4 HOH B 5 508 508 HOH HOH . 
S 4 HOH B 6 509 509 HOH HOH . 
S 4 HOH B 7 510 510 HOH HOH . 
S 4 HOH B 8 511 511 HOH HOH . 
S 4 HOH B 9 512 512 HOH HOH . 
S 4 HOH B 10 513 513 HOH HOH . 
S 4 HOH B 11 514 514 HOH HOH . 
S 4 HOH B 12 515 515 HOH HOH . 
S 4 HOH B 13 516 516 HOH HOH . 
S 4 HOH B 14 517 517 HOH HOH . 
S 4 HOH B 15 518 518 HOH HOH . 
S 4 HOH B 16 519 519 HOH HOH . 
S 4 HOH B 17 520 520 HOH HOH . 
S 4 HOH B 18 521 521 HOH HOH . 
S 4 HOH B 19 522 522 HOH HOH . 
S 4 HOH B 20 523 523 HOH HOH . 
S 4 HOH B 21 524 524 HOH HOH . 
S 4 HOH B 22 525 525 HOH HOH . 
S 4 HOH B 23 526 526 HOH HOH . 
S 4 HOH B 24 527 527 HOH HOH . 
S 4 HOH B 25 528 528 HOH HOH . 
S 4 HOH B 26 529 529 HOH HOH . 
S 4 HOH B 27 530 530 HOH HOH . 
S 4 HOH B 28 531 531 HOH HOH . 
S 4 HOH B 29 532 532 HOH HOH . 
S 4 HOH B 30 534 534 HOH HOH . 
S 4 HOH B 31 535 535 HOH HOH . 
S 4 HOH B 32 536 536 HOH HOH . 
S 4 HOH B 33 537 537 HOH HOH . 
S 4 HOH B 34 538 538 HOH HOH . 
S 4 HOH B 35 539 539 HOH HOH . 
S 4 HOH B 36 540 540 HOH HOH . 
S 4 HOH B 37 541 541 HOH HOH . 
S 4 HOH B 38 542 542 HOH HOH . 
S 4 HOH B 39 543 543 HOH HOH . 
S 4 HOH B 40 544 544 HOH HOH . 
S 4 HOH B 41 545 545 HOH HOH . 
S 4 HOH B 42 546 546 HOH HOH . 
S 4 HOH B 43 547 547 HOH HOH . 
S 4 HOH B 44 548 548 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 -16.055 -13.747 42.626 1 42.68 ? C1 MPD 503 B 1 
HETATM 2 C C2 MPD . . . L 2 -14.74 -14.496 42.646 1 45.31 ? C2 MPD 503 B 1 
HETATM 3 O O2 MPD . . . L 2 -14.445 -15.024 41.342 1 51.13 ? O2 MPD 503 B 1 
HETATM 4 C CM MPD . . . L 2 -13.62 -13.549 43.067 1 43.18 ? CM MPD 503 B 1 
HETATM 5 C C3 MPD . . . L 2 -14.842 -15.635 43.668 1 48.55 ? C3 MPD 503 B 1 
HETATM 6 C C4 MPD . . . L 2 -15.368 -16.934 43.031 1 48.63 ? C4 MPD 503 B 1 
HETATM 7 O O4 MPD . . . L 2 -14.948 -18.075 43.786 1 49.24 ? O4 MPD 503 B 1 
HETATM 8 C C5 MPD . . . L 2 -16.886 -16.888 42.996 1 47.58 ? C5 MPD 503 B 1 
#
_model_server_stats.io_time_ms              3 
_model_server_stats.parse_time_ms           5 
_model_server_stats.create_model_time_ms    2 
_model_server_stats.query_time_ms           359 
_model_server_stats.encode_time_ms          51 
_model_server_stats.element_count           8 
#