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MolNFT v1 · #24935 · protein + DNA

Atomic model of a pyrimidine dimer specific excision repair enzyme complexed with a DNA substrate: structural basis for damaged DNA recognition

1VAS · DNA (5'-D(*AP*TP*CP*GP*CP*GP*TP*TP*GP*CP*GP*CP*T)-3'): “Atomic model of a pyrimidine dimer specific excision repair enzyme complexed with a DNA substrate: structural…”. X-ray diffraction, 2 pockets (best druggability 0.58). MolNFT…

PDB
1VAS
Type
protein + DNA
Length
163 residues
Chains
3
Method
x-ray diffraction
Collection
MolNFT v1 / PDB
Contract
0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner
0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule
DNA (5'-D(*AP*TP*CP*GP*CP*GP*TP*TP*GP*CP*GP*CP*T)-3'); DNA…
UniProt
P04418
Pockets
2 · best druggability 0.58

Structure

x-ray diffraction · 3 distinct chains · 51% helix, 1% strand (DSSP).

ChainMoleculeTypeResiduesSecondary structureUniProt
BDNA (5'-D(*AP*TP*CP*GP*CP*GP*TP*TP*GP*CP*GP*CP*T)-3')dna13——
CDNA (5'-D(*TP*AP*GP*CP*GP*CP*AP*AP*CP*GP*CP*GP*A)-3')dna13——
AProtein (T4 endonuclease V (E.C.3.1.25.1))protein13751% helix, 1% strandP04418

Pockets

2 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.

PocketVolume (ų)DruggabilityBuriednessLining residuesInside
1610.580.9014empty
21220.560.8417empty

Interfaces

3 interfaces between chains.

  • B–A · 772 Ų buried · 25 hydrogen bonds · protein-nucleic
  • C–A · 640 Ų buried · 8 hydrogen bonds · protein-nucleic
  • B–C · 545 Ų buried · 43 hydrogen bonds · nucleic-nucleic

Compared structures

  • 1VAS · Atomic model of a pyrimidine dimer specific excision repair enzyme complexed with a DNA… · the same entry in another collection · chain B against B, TM-score 1.00

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