MolNFT v1 · #105254 · protein + DNA

Mouse tdt in complex with a dsb substrate, C-a base pair

4QZ9 · DNA nucleotidylexotransferase: “Mouse tdt in complex with a dsb substrate, C-a base pair”. X-ray diffraction, 3 ligands (DCT, MG, NA), 3 pockets (best druggability 0.72). MolNFT v1 #105254 on GenesisL1: 3D structure, binding sites…

PDB: 4QZ9
Type: protein + DNA
Length: 369 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: DNA nucleotidylexotransferase; 5'-D(*AP*AP*AP*AP*AP*C)-3'; 5'-D(*TP*TP*TP*TP*TP*GP*A)-3'
EC: 2.7.7.31
UniProt: P09838
Ligands: DCT, MG, NA
Pockets: 3 · best druggability 0.72

Structure

x-ray diffraction · 4 distinct chains · 50% helix, 15% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	DNA nucleotidylexotransferase (EC 2.7.7.31)	protein	351	50% helix, 15% strand	P09838
D	5'-D(APAPAPAPAPC)-3'	dna	5	—	—
T	5'-D(TPTPTPTPTPGP*A)-3'	dna	7	—	—
U	5'-D(APAPAPAPAPC)-3'	dna	6	—	—

Ligands and binding sites

DCT · 2',3'-dideoxycytidine 5'-triphosphate · ligand · chains A, T, U
MG · Magnesium ion · metal · 2 copies · chains A, U
NA · Sodium ion · metal · chains A, U

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

Pockets

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

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	1068	0.72	0.76	73	MG, DCT
2	80	0.54	0.86	13	empty
3	71	0.35	0.76	19	empty

Interfaces

5 interfaces between chains.

A–U · 465 Å² buried · 12 hydrogen bonds · protein-nucleic
A–T · 462 Å² buried · 9 hydrogen bonds · protein-nucleic
A–D · 364 Å² buried · 10 hydrogen bonds · protein-nucleic
D–T · 208 Å² buried · 15 hydrogen bonds · nucleic-nucleic
T–U · 46 Å² buried · 2 hydrogen bonds · nucleic-nucleic

Compared structures

4QZ9 · Mouse Tdt in complex with a DSB substrate, C-A base pair · 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 0.99

Analyse

Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
Every structure of UniProt P09838
Elsewhere: RCSB PDB 4QZ9 · PDBe 4QZ9 · UniProt P09838

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