› 7psx

X-ray diffraction
2Å resolution

Structure of HOXB13 bound to hydroxymethylated DNA

Released:
DOI: 10.2210/pdb7psx/pdb
PDB entry 7psx coloured by chain, front view.
PDB entry 7psx coloured by chain, side view.
PDB entry 7psx coloured by chain, top view.
Source organism: Homo sapiens
Entry authors: Morgunova E, Popov A, Yin Y, Taipale J

Function and Biology Details

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

Structure analysis Details

Assembly composition:
hetero trimer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-121827 (preferred)
Entry contents:
1 distinct polypeptide molecule
2 distinct DNA molecules
Macromolecules (3 distinct):
Homeobox protein Hox-B13 Chains: A, B, G, J
Molecule details ›
Chains: A, B, G, J
Length: 61 amino acids
Theoretical weight: 7.41 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: Q92826 (Residues: 217-277; Coverage: 22%)
Gene name: HOXB13
Sequence domains: Homeodomain
DNA (5'-D(P*TP*TP*GP*TP*GP*TP*TP*TP*TP*AP*CP*GP*AP*GP*GP*TP*CP*C)-3') Chains: C, D, H, K
Molecule details ›
Chains: C, D, H, K
Length: 18 nucleotides
Theoretical weight: 5.54 KDa
Source organism: Homo sapiens
Expression system: Not provided
DNA (5'-D(P*GP*GP*AP*CP*CP*TP*5HCP*AP*TP*AP*AP*AP*AP*CP*AP*CP*AP*A)-3') Chains: E, F, I, L
Molecule details ›
Chains: E, F, I, L
Length: 18 nucleotides
Theoretical weight: 5.52 KDa
Source organism: Homo sapiens
Expression system: Not provided

Ligands and Environments

1 bound ligand:
Ligand MG 2 x MG
1 modified residue:
Ligand 5HC 4 x 5HC

Experiments and Validation Details

Entry percentile scores
X-ray source: ESRF BEAMLINE ID23-1
Spacegroup: P1
Unit cell:
a: 38.153Å b: 55.541Å c: 101.08Å
α: 88.02° β: 81.46° γ: 84.94°
R-values:
R R work R free
0.261 0.26 0.283
Expression systems:
  • Escherichia coli BL21(DE3)
  • Not provided

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