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Exonuclease domain-containing 1 (EXD1) in the native conformation

Analyse Exonuclease domain-containing 1 (EXD1) in the native conformation in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 5FIQ
Type: protein
Length: 1,202 residues
Chains: 5
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: EXD1
Pockets: 17 · best druggability 0.72

Structure

x-ray diffraction · 2 distinct chains · 54% helix, 10% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	EXD1	protein	242	53% helix, 9% strand	—
C, E, G, I	EXD1	protein	240	54% helix, 10% strand	—

Pockets

17 pockets found on a 1 Å grid, 9 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	185	0.72	0.88	30	empty
2	291	0.70	0.84	54	empty
3	265	0.66	0.83	30	empty
4	257	0.64	0.82	29	empty
5	306	0.64	0.81	29	empty

Interfaces

5 interfaces between chains.

G–I · 2578 Å² buried · 35 hydrogen bonds · protein-protein
C–E · 2561 Å² buried · 34 hydrogen bonds · protein-protein
A–C · 359 Å² buried · 6 hydrogen bonds · protein-protein
C–G · 210 Å² buried · 0 hydrogen bonds · protein-protein
E–G · 39 Å² buried · 0 hydrogen bonds · protein-protein

Compared structures

5FIQ · Exonuclease domain-containing 1 (Exd1) in the native conformation · the same entry in another collection · chain A against A, TM-score 1.00

Analyse

Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
Elsewhere: RCSB PDB 5FIQ · PDBe 5FIQ

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