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Crystal structure of RNase T in complex with a Y structured DNA

Analyse Crystal structure of RNase T in complex with a Y structured DNA in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB
4KAZ
Type
protein + DNA
Length
221 residues
Chains
2
Method
x-ray diffraction
Collection
MolNFT v1 / PDB
Contract
0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner
0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule
Ribonuclease T; DNA (5'- D(*TP*TP*GP*GP*CP*CP*CP*TP*CP*TP*TP*TP*AP*GP*GP*GP*CP*CP*CP*C)-3'…
EC
3.1.13.-
UniProt
P30014
Ligands
MG
Pockets
2 · best druggability 0.45

Structure

x-ray diffraction · 2 distinct chains · 39% helix, 24% strand (DSSP).

ChainMoleculeTypeResiduesSecondary structureUniProt
ARibonuclease T (EC 3.1.13.-)protein20639% helix, 24% strandP30014
BDNA (5'- D(*TP*TP*GP*GP*CP*CP*CP*TP*CP*TP*TP*TP*AP*GP*GP*GP*CP*CP*CP*C)-3')dna15——

Ligands and binding sites

  • MG · Magnesium ion · metal · 2 copies · chains A, B

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

Pockets

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

PocketVolume (ų)DruggabilityBuriednessLining residuesInside
11570.450.7618empty
2870.350.7415empty

Interfaces

1 interface between chains.

  • A–B · 810 Ų buried · 14 hydrogen bonds · protein-nucleic

Compared structures

  • 4KAZ · Crystal structure of RNase T in complex with a Y structured DNA · the same entry in another collection · chain A against A, TM-score 1.00
  • P30014 · AlphaFold monomer V2.0 prediction for ribonuclease T (P30014) · a predicted model of the same protein · chain A against A, TM-score 0.98

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