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MolNFT v1 · #94632 · protein + DNA

Ternary complex of mouse tdt with ssdna and ampcpp

4I2H · DNA nucleotidylexotransferase: “Ternary complex of mouse tdt with ssdna and ampcpp”. X-ray diffraction, 4 ligands (APC, ZN, MG), 2 pockets (best druggability 0.50). MolNFT v1 #94632 on GenesisL1: 3D structure, binding sites and…

PDB
4I2H
Type
protein + DNA
Length
341 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
APC, ZN, MG, NA
Pockets
2 · best druggability 0.50

Structure

x-ray diffraction · 2 distinct chains · 52% helix, 14% strand (DSSP).

ChainMoleculeTypeResiduesSecondary structureUniProt
ADNA nucleotidylexotransferase (EC 2.7.7.31)protein34052% helix, 14% strandP09838
C5'-D(P*AP*AP*AP*AP*A)-3'dna1——

Ligands and binding sites

  • APC · Diphosphomethylphosphonic acid adenosyl ester · ligand · chains A
  • ZN · Zinc ion · metal · 2 copies · chains A
  • MG · Magnesium ion · metal · chains A
  • NA · Sodium ion · metal · chains A

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
12800.500.7436MG, APC
21550.420.7421empty

Interfaces

1 interface between chains.

  • A–C · 133 Ų buried · 4 hydrogen bonds · protein-nucleic

Compared structures

  • 4I2H · Ternary complex of mouse TdT with ssDNA and AMPcPP · 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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