Research workbench

Leucine-bound SESTRIN2 from homo sapiens

Analyse Leucine-bound SESTRIN2 from homo sapiens in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 5DJ4
Type: protein
Length: 1,824 residues
Chains: 5
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Sestrin-2
UniProt: P58004
Ligands: LEU
Pockets: 20 · best druggability 0.70

Structure

x-ray diffraction · 5 distinct chains · 64% helix, 3% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Sestrin-2	protein	366	64% helix, 2% strand	P58004
B	Sestrin-2	protein	365	64% helix, 3% strand	P58004
C	Sestrin-2	protein	364	65% helix, 3% strand	P58004
D	Sestrin-2	protein	364	63% helix, 3% strand	P58004
E	Sestrin-2	protein	365	63% helix, 3% strand	P58004

Ligands and binding sites

LEU · Leucine · ligand · 5 copies · chains A, B, C, D, E

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

Pockets

20 pockets found on a 1 Å grid, 14 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	61	0.70	0.97	19	LEU
2	62	0.69	0.96	20	LEU
3	65	0.69	0.95	19	LEU
4	61	0.68	0.96	19	LEU
5	58	0.68	0.96	19	LEU

Interfaces

5 interfaces between chains.

A–E · 355 Å² buried · 3 hydrogen bonds · protein-protein
C–D · 340 Å² buried · 5 hydrogen bonds · protein-protein
A–C · 340 Å² buried · 2 hydrogen bonds · protein-protein
B–D · 329 Å² buried · 2 hydrogen bonds · protein-protein
B–E · 303 Å² buried · 3 hydrogen bonds · protein-protein

Compared structures

5DJ4 · Leucine-bound Sestrin2 from Homo sapiens · the same entry in another collection · chain E against E, TM-score 1.00
P58004 · AlphaFold monomer V2.0 prediction for sestrin-2 (P58004) · a predicted model of the same protein · chain B against A, TM-score 0.94

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 P58004
Elsewhere: RCSB PDB 5DJ4 · PDBe 5DJ4 · UniProt P58004

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