› 8vdh

X-ray diffraction
1.64Å resolution

Human PU.1 ETS-Domain (165-270) Bound to d(AATAGAAGGAAGTGGG) in Ternary Complex with DB2447

Released:
DOI: 10.2210/pdb8vdh/pdb
Model geometry
Fit model/data
PDB entry 8vdh coloured by chain, front view.
PDB entry 8vdh coloured by chain, side view.
PDB entry 8vdh coloured by chain, top view.
Source organisms:
Primary publication:
Single GC base pair recognition by a heterocyclic diamidine: structures, affinities, and dynamics.
Ogbonna EN, Terrell JR, Paul A, Farahat AA, Poon GMK, Boykin DW, Wilson WD
RSC Adv 14 29675-29682 (2024)
PMID: 39297050

Function and Biology Details

Biochemical function:
Biological process:
Cellular component:
  • not assigned

Structure analysis Details

Assembly composition:
hetero trimer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-270883 (preferred)
Entry contents:
1 distinct polypeptide molecule
2 distinct DNA molecules
Macromolecules (3 distinct):
Transcription factor PU.1 Chain: F
Molecule details ›
Chain: F
Length: 106 amino acids
Theoretical weight: 12.44 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli
UniProt:
  • Canonical: P17947 (Residues: 165-270; Coverage: 39%)
Gene name: SPI1
Sequence domains: Ets-domain
DNA (5'-D(*AP*AP*TP*AP*GP*AP*AP*GP*GP*AP*AP*GP*TP*GP*GP*G)-3') Chain: C
Molecule details ›
Chain: C
Length: 16 nucleotides
Theoretical weight: 5.06 KDa
Source organism: DNA molecule
Expression system: Not provided
DNA (5'-D(*TP*CP*CP*CP*AP*CP*TP*TP*CP*CP*TP*TP*CP*TP*AP*T)-3') Chain: D

Ligands and Environments

1 bound ligand:
Ligand A1AAQ 1 x A1AAQ
No modified residues

Experiments and Validation Details

wwPDB Validation report is not available for this entry.
X-ray source: NSLS-II BEAMLINE 17-ID-2
Spacegroup: P21
Unit cell:
a: 43.049Å b: 61.062Å c: 44.178Å
α: 90° β: 116.306° γ: 90°
R-values:
R R work R free
0.184 0.182 0.208
Expression systems:
  • Escherichia coli
  • Not provided

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