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Structure of TREX2 in complex with a Y structured dsdna

Analyse Structure of TREX2 in complex with a Y structured dsdna in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 6A47
Type: protein + DNA
Length: 479 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Three prime repair exonuclease 2; DNA (5'- D(P*CP*CP*AP*GP*GP*CP*CP*CP*TP*CP*TP*AP*GP*GP*G…
EC: 3.1.11.2
UniProt: Q9R1A9
Ligands: MG, NA
Pockets: 7 · best druggability 0.55

Structure

x-ray diffraction · 4 distinct chains · 41% helix, 18% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Three prime repair exonuclease 2 (EC 3.1.11.2)	protein	224	41% helix, 17% strand	Q9R1A9
B	Three prime repair exonuclease 2 (EC 3.1.11.2)	protein	217	42% helix, 18% strand	Q9R1A9
C	DNA (5'- D(PCPCPAPGPGPCPCPCPTPCPTPAPGPGPGPCPCPTP*T)-3')	dna	19	—	—
D	DNA (5'- D(PCPCPAPGPGPCPCPCPTPCPTPAPGPGPGPCPCPTP*T)-3')	dna	19	—	—

Ligands and binding sites

MG · Magnesium ion · metal · 4 copies · chains A, C, B, D
NA · Sodium ion · metal · chains A, B

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

Pockets

7 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	205	0.55	0.79	33	empty
2	175	0.54	0.80	30	empty
3	246	0.49	0.74	28	empty
4	97	0.45	0.80	14	empty
5	72	0.36	0.77	22	empty

Interfaces

3 interfaces between chains.

A–B · 1539 Å² buried · 37 hydrogen bonds · protein-protein
B–D · 1015 Å² buried · 15 hydrogen bonds · protein-nucleic
A–C · 930 Å² buried · 12 hydrogen bonds · protein-nucleic

Compared structures

6A47 · Structure of TREX2 in complex with a Y structured dsDNA · the same entry in another collection · chain A against A, TM-score 1.00
Q9R1A9 · AlphaFold monomer V2.0 prediction for three prime repair exonuclease 2 (Q9R1A9) · 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 Q9R1A9
Elsewhere: RCSB PDB 6A47 · PDBe 6A47 · UniProt Q9R1A9

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