MolNFT v1 · #124249 · protein

Beclin 2 ccd N187L mutant homodimer

5K9L · Beclin-2: “Beclin 2 ccd N187L mutant homodimer”. X-ray diffraction, 6 pockets (best druggability 0.60). MolNFT v1 #124249 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 5K9L
Type: protein
Length: 357 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Beclin-2
UniProt: A8MW95
Pockets: 6 · best druggability 0.60

Structure

x-ray diffraction · 4 distinct chains · 94% helix, 0% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Beclin-2	protein	89	94% helix, 0% strand	A8MW95
B	Beclin-2	protein	90	97% helix, 0% strand	A8MW95
C	Beclin-2	protein	89	94% helix, 0% strand	A8MW95
D	Beclin-2	protein	89	92% helix, 0% strand	A8MW95

Pockets

6 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	124	0.60	0.85	22	empty
2	149	0.58	0.83	22	empty
3	283	0.55	0.76	42	empty
4	76	0.50	0.84	13	empty
5	118	0.49	0.80	23	empty

Interfaces

6 interfaces between chains.

A–B · 2333 Å² buried · 2 hydrogen bonds · protein-protein
C–D · 2282 Å² buried · 3 hydrogen bonds · protein-protein
A–D · 1164 Å² buried · 14 hydrogen bonds · protein-protein
B–C · 517 Å² buried · 6 hydrogen bonds · protein-protein
B–D · 455 Å² buried · 5 hydrogen bonds · protein-protein

Compared structures

5K9L · Beclin 2 CCD N187L mutant homodimer · the same entry in another collection · chain D against D, TM-score 1.00
A8MW95 · AlphaFold monomer V2.0 prediction for beclin-2 (A8MW95) · a predicted model of the same protein · chain C against A, TM-score 0.89

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 A8MW95
Elsewhere: RCSB PDB 5K9L · PDBe 5K9L · UniProt A8MW95

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