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Cryo-EM structure of activated and oligomeric restriction endonuclease sgrai

Analyse Cryo-EM structure of activated and oligomeric restriction endonuclease sgrai in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB
4C3G
Type
protein + DNA
Length
746 residues
Chains
6
Method
electron microscopy
Collection
MolNFT v1 / PDB
Contract
0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner
0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule
Sgrair restriction enzyme; 5'-D(*GP*AP*TP*GP*CP*GP*TP*GP*GP*GP*TP*CP*TP*TP…
UniProt
Q9F6L0
Pockets
1 · best druggability 0.26

Structure

electron microscopy · 3 distinct chains · 0% helix, 0% strand (DSSP).

ChainMoleculeTypeResiduesSecondary structureUniProt
A, BSgrair restriction enzymeprotein3330% helix, 0% strandQ9F6L0
C, D5'-D(*GP*AP*TP*GP*CP*GP*TP*GP*GP*GP*TP*CP*TP*TP *CP*AP*CP*AP)-3'dna18——
E, F5'-D(*CP*CP*GP*GP*TP*GP*TP*GP*AP*AP*GP*AP*CP*CP *CP*AP*CP*GP*CP*AP*TP*CP)-3'dna22——

Pockets

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

PocketVolume (ų)DruggabilityBuriednessLining residuesInside
1510.260.7314empty

Interfaces

10 interfaces between chains.

  • A–E · 345 Ų buried · 0 hydrogen bonds · protein-nucleic
  • B–F · 329 Ų buried · 0 hydrogen bonds · protein-nucleic
  • B–E · 194 Ų buried · 0 hydrogen bonds · protein-nucleic
  • A–F · 186 Ų buried · 0 hydrogen bonds · protein-nucleic
  • A–B · 105 Ų buried · 0 hydrogen bonds · protein-protein

Compared structures

  • 4C3G · cryo-EM structure of activated and oligomeric restriction endonuclease SgrAI · the same entry in another collection · chain A against A, TM-score 1.00

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