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MolNFT v1 · #141209 · protein + DNA

ATVAL1 B3 domain in complex with 13BP-DNA

5YZY · DNA (5'-D(*AP*TP*TP*CP*TP*GP*CP*AP*TP*GP*GP*AP*T)-3'): “ATVAL1 B3 domain in complex with 13BP-DNA”. X-ray diffraction, 1 ligand (HG), 1 pocket (best druggability 0.43). MolNFT v1 #141209 on GenesisL1: 3D structure, binding sites and…

PDB
5YZY
Type
protein + DNA
Length
137 residues
Chains
3
Method
x-ray diffraction
Collection
MolNFT v1 / PDB
Contract
0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner
0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule
DNA (5'-D(*AP*TP*TP*CP*TP*GP*CP*AP*TP*GP*GP*AP*T)-3'); DNA…
UniProt
Q8W4L5
Ligands
HG
Pockets
1 · best druggability 0.43

Structure

x-ray diffraction · 3 distinct chains · 15% helix, 48% strand (DSSP).

ChainMoleculeTypeResiduesSecondary structureUniProt
ADNA (5'-D(*AP*TP*TP*CP*TP*GP*CP*AP*TP*GP*GP*AP*T)-3')dna13——
BDNA (5'-D(*TP*AP*TP*CP*CP*AP*TP*GP*CP*AP*GP*AP*A)-3')dna13——
CB3 domain-containing transcription repressor VAL1protein11115% helix, 48% strandQ8W4L5

Ligands and binding sites

  • HG · Mercury (II) ion · metal · chains C

Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.

Pockets

1 pocket found on a 1 Å grid, 0 with a druggability of 0.5 or more.

PocketVolume (ų)DruggabilityBuriednessLining residuesInside
11080.430.7820empty

Interfaces

3 interfaces between chains.

  • A–B · 553 Ų buried · 55 hydrogen bonds · nucleic-nucleic
  • B–C · 393 Ų buried · 7 hydrogen bonds · protein-nucleic
  • A–C · 365 Ų buried · 4 hydrogen bonds · protein-nucleic

Compared structures

  • 5YZY · AtVAL1 B3 domain in complex with 13bp-DNA · the same entry in another collection · chain C against C, TM-score 1.00
  • Q8W4L5 · AlphaFold monomer V2.0 prediction for B3 domain-containing transcription repressor VAL1… · a predicted model of the same protein · chain C against A, TM-score 0.97

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