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Exonuclease domain-containing 1 (EXD1) in the gd bound conformation

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

PDB: 5FIS
Type: protein
Length: 482 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: EXD1
Ligands: GD
Pockets: 5 · best druggability 0.74

Structure

x-ray diffraction · 2 distinct chains · 55% helix, 9% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	EXD1	protein	241	55% helix, 9% strand	—
B	EXD1	protein	241	55% helix, 9% strand	—

Ligands and binding sites

GD · Gadolinium atom · metal · 3 copies · chains A, B

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

Pockets

5 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	609	0.74	0.81	74	empty
2	380	0.68	0.81	43	empty
3	256	0.64	0.82	27	empty
4	296	0.60	0.78	31	empty
5	106	0.43	0.78	17	empty

Interfaces

1 interface between chains.

A–B · 2884 Å² buried · 45 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 2 modified (oxidation).

Compared structures

5FIS · Exonuclease domain-containing 1 (Exd1) in the Gd bound 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 5FIS · PDBe 5FIS

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