MolNFT v1 · #105255 · protein + DNA

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

4QZA · DNA nucleotidylexotransferase: “Mouse tdt in complex with a dsb substrate, C-C base pair”. X-ray diffraction, 3 ligands (DCT, MG, NA), 3 pockets (best druggability 0.78). MolNFT v1 #105255 on GenesisL1: 3D structure, binding sites…

PDB: 4QZA
Type: protein + DNA
Length: 375 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*C)-3'
EC: 2.7.7.31
UniProt: P09838
Ligands: DCT, MG, NA
Pockets: 3 · best druggability 0.78

Structure

x-ray diffraction · 4 distinct chains · 49% helix, 15% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	DNA nucleotidylexotransferase (EC 2.7.7.31)	protein	357	49% helix, 15% strand	P09838
D	5'-D(APAPAPAPAPC)-3'	dna	5	—	—
T	5'-D(TPTPTPTPTPGP*C)-3'	dna	7	—	—
U	5'-D(APAPAPAPAPC)-3'	dna	6	—	—

Ligands and binding sites

DCT · 2',3'-dideoxycytidine 5'-triphosphate · ligand · 2 copies · 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	1066	0.78	0.80	95	MG, DCT
2	115	0.59	0.86	19	empty
3	75	0.33	0.75	17	empty

Interfaces

5 interfaces between chains.

A–T · 511 Å² buried · 11 hydrogen bonds · protein-nucleic
A–U · 496 Å² buried · 12 hydrogen bonds · protein-nucleic
A–D · 362 Å² buried · 10 hydrogen bonds · protein-nucleic
D–T · 206 Å² buried · 14 hydrogen bonds · nucleic-nucleic
T–U · 30 Å² buried · 1 hydrogen bond · nucleic-nucleic

Compared structures

4QZA · Mouse Tdt in complex with a DSB substrate, C-C 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 4QZA · PDBe 4QZA · UniProt P09838

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