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MolNFT v1 · #47502 · protein + DNA

Structure of restriction endonuclease bstyi bound to non-cognate DNA

2P0J · 5'-D(*AP*TP*GP*AP*AP*TP*CP*CP*AP*TP*A)-3': “Structure of restriction endonuclease bstyi bound to non-cognate DNA”. X-ray diffraction, 2 pockets (best druggability 0.80). MolNFT v1 #47502 on GenesisL1: 3D structure, binding sites and…

PDB
2P0J
Type
protein + DNA
Length
421 residues
Chains
4
Method
x-ray diffraction
Collection
MolNFT v1 / PDB
Contract
0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner
0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule
5'-D(*AP*TP*GP*AP*AP*TP*CP*CP*AP*TP*A)-3'; 5'-D(*TP*AP*TP*GP*GP*AP*TP*TP*CP*AP*T)-3'…
UniProt
Q84AF2
Pockets
2 · best druggability 0.80

Structure

x-ray diffraction · 4 distinct chains · 43% helix, 26% strand (DSSP).

ChainMoleculeTypeResiduesSecondary structureUniProt
C5'-D(*AP*TP*GP*AP*AP*TP*CP*CP*AP*TP*A)-3'dna11——
D5'-D(*TP*AP*TP*GP*GP*AP*TP*TP*CP*AP*T)-3'dna11——
ABstyiprotein20344% helix, 25% strandQ84AF2
BBstyiprotein19643% helix, 26% strandQ84AF2

Pockets

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

PocketVolume (ų)DruggabilityBuriednessLining residuesInside
110520.800.8190empty
21170.460.7920empty

Interfaces

6 interfaces between chains.

  • A–B · 1952 Ų buried · 9 hydrogen bonds · protein-protein
  • C–D · 498 Ų buried · 36 hydrogen bonds · nucleic-nucleic
  • C–A · 422 Ų buried · 6 hydrogen bonds · protein-nucleic
  • C–B · 332 Ų buried · 7 hydrogen bonds · protein-nucleic
  • D–B · 325 Ų buried · 8 hydrogen bonds · protein-nucleic

Compared structures

  • 2P0J · Structure of restriction endonuclease BstYI bound to non-cognate DNA · the same entry in another collection · chain C against C, TM-score 1.00

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