MolNFT v1 · #93325 · protein + DNA

Mus musculus TDP2 excluded ssdna complex

4GZ2 · Tyrosyl-DNA phosphodiesterase 2: “Mus musculus TDP2 excluded ssdna complex”. X-ray diffraction, 1 ligand (MG), 2 pockets (best druggability 0.59). MolNFT v1 #93325 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 4GZ2
Type: protein + DNA
Length: 518 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Tyrosyl-DNA phosphodiesterase 2; DNA (5'-D(*CP*AP*TP*CP*CP*GP*AP*AP*TP*TP*CP*G)-3')
EC: 3.1.4.-
UniProt: Q9JJX7
Ligands: MG
Pockets: 2 · best druggability 0.59

Structure

x-ray diffraction · 3 distinct chains · 22% helix, 37% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Tyrosyl-DNA phosphodiesterase 2 (EC 3.1.4.-)	protein	248	22% helix, 37% strand	Q9JJX7
D, C	DNA (5'-D(CPAPTPCPCPGPAPAPTPTPCPG)-3')	dna	12	—	—
B	Tyrosyl-DNA phosphodiesterase 2 (EC 3.1.4.-)	protein	246	23% helix, 37% strand	Q9JJX7

Ligands and binding sites

MG · Magnesium ion · metal · 4 copies · chains A, D, C, B
FMT · Formic acid · additive · 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, 1 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	491	0.59	0.74	35	MG
2	86	0.33	0.74	20	empty

Interfaces

5 interfaces between chains.

A–D · 636 Å² buried · 11 hydrogen bonds · protein-nucleic
B–C · 589 Å² buried · 8 hydrogen bonds · protein-nucleic
D–C · 381 Å² buried · 36 hydrogen bonds · nucleic-nucleic
A–C · 105 Å² buried · 0 hydrogen bonds · protein-nucleic
D–B · 96 Å² buried · 0 hydrogen bonds · protein-nucleic

Compared structures

4GZ2 · Mus Musculus Tdp2 excluded ssDNA complex · the same entry in another collection · chain A against A, TM-score 1.00
Q9JJX7 · AlphaFold monomer V2.0 prediction for tyrosyl-DNA phosphodiesterase 2 (Q9JJX7) · a predicted model of the same protein · chain B 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 Q9JJX7
Elsewhere: RCSB PDB 4GZ2 · PDBe 4GZ2 · UniProt Q9JJX7

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