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MolNFT v1 · #94630 · protein + DNA

Binary complex of mouse tdt with ssdna

4I2F · DNA nucleotidylexotransferase: “Binary complex of mouse tdt with ssdna”. X-ray diffraction, 3 ligands (MG, NA, ZN), 3 pockets (best druggability 0.72). MolNFT v1 #94630 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB
4I2F
Type
protein + DNA
Length
362 residues
Chains
2
Method
x-ray diffraction
Collection
MolNFT v1 / PDB
Contract
0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner
0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule
DNA nucleotidylexotransferase; 5'-D(P*AP*AP*AP*AP*A)-3'
EC
2.7.7.31
UniProt
P09838
Ligands
MG, NA, ZN
Pockets
3 · best druggability 0.72

Structure

x-ray diffraction · 2 distinct chains · 49% helix, 15% strand (DSSP).

ChainMoleculeTypeResiduesSecondary structureUniProt
ADNA nucleotidylexotransferase (EC 2.7.7.31)protein35849% helix, 15% strandP09838
C5'-D(P*AP*AP*AP*AP*A)-3'dna4——

Ligands and binding sites

  • MG · Magnesium ion · metal · chains A, C
  • NA · Sodium ion · metal · chains A, C
  • ZN · Zinc ion · metal · chains A, C

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

Pockets

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

PocketVolume (ų)DruggabilityBuriednessLining residuesInside
110200.720.7676MG
2690.370.7712empty
3560.340.7814empty

Interfaces

1 interface between chains.

  • A–C · 593 Ų buried · 18 hydrogen bonds · protein-nucleic

Compared structures

  • 4I2F · Binary complex of mouse TdT with ssDNA · the same entry in another collection · chain A against A, TM-score 1.00
  • P09838 · AlphaFold monomer V2.0 prediction for DNA nucleotidylexotransferase (P09838) · a predicted model of the same protein · chain A against A, TM-score 1.00

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