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MolNFT v1 · #182927 · protein

Crystal structure of ERI2 nuclease bound to ramp

7N8W · ERI1 exoribonuclease 2: “Crystal structure of ERI2 nuclease bound to ramp”. X-ray diffraction, 3 ligands (AMP, MN, SO4), 1 pocket (best druggability 0.85). MolNFT v1 #182927 on GenesisL1: 3D structure, binding sites and pockets in…

PDB
7N8W
Type
protein
Length
427 residues
Chains
2
Method
x-ray diffraction
Collection
MolNFT v1 / PDB
Contract
0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner
0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule
ERI1 exoribonuclease 2
EC
3.1.-.-
UniProt
A8K979
Ligands
AMP, MN, SO4
Pockets
1 · best druggability 0.85

Structure

x-ray diffraction · 2 distinct chains · 38% helix, 20% strand (DSSP).

ChainMoleculeTypeResiduesSecondary structureUniProt
AERI1 exoribonuclease 2 (EC 3.1.-.-)protein21437% helix, 20% strandA8K979
BERI1 exoribonuclease 2 (EC 3.1.-.-)protein21338% helix, 20% strandA8K979

Ligands and binding sites

  • AMP · Adenosine monophosphate · ligand · chains A, B
  • MN · Manganese (II) ion · metal · chains A, B
  • SO4 · Sulfate ion · ion · 4 copies · chains A, B
  • EDO · 1,2-ethanediol · additive · chains B

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

Pockets

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

PocketVolume (ų)DruggabilityBuriednessLining residuesInside
111370.850.86124AMP, SO4, MN

Interfaces

1 interface between chains.

  • A–B · 991 Ų buried · 6 hydrogen bonds · protein-protein

Compared structures

  • 7N8W · Crystal structure of ERI2 nuclease bound to rAMP · the same entry in another collection · chain A against A, TM-score 1.00
  • A8K979 · AlphaFold monomer V2.0 prediction for ERI1 exoribonuclease 2 (A8K979) · a predicted model of the same protein · chain A against A, TM-score 0.96

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