Research workbench

Beclin 2 ccd homodimer

Analyse Beclin 2 ccd homodimer in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 5K7B
Type: protein
Length: 352 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Beclin-2
UniProt: A8MW95
Pockets: 6 · best druggability 0.61

Structure

x-ray diffraction · 4 distinct chains · 97% helix, 0% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Beclin-2	protein	87	97% helix, 0% strand	A8MW95
B	Beclin-2	protein	91	97% helix, 0% strand	A8MW95
C	Beclin-2	protein	86	97% helix, 0% strand	A8MW95
D	Beclin-2	protein	88	98% helix, 0% strand	A8MW95

Pockets

6 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	154	0.61	0.84	25	empty
2	170	0.60	0.83	22	empty
3	64	0.46	0.83	11	empty
4	91	0.44	0.79	23	empty
5	181	0.42	0.73	31	empty

Interfaces

6 interfaces between chains.

A–B · 2236 Å² buried · 6 hydrogen bonds · protein-protein
C–D · 2170 Å² buried · 9 hydrogen bonds · protein-protein
A–C · 1145 Å² buried · 20 hydrogen bonds · protein-protein
B–D · 502 Å² buried · 10 hydrogen bonds · protein-protein
B–C · 495 Å² buried · 6 hydrogen bonds · protein-protein

Compared structures

5K7B · Beclin 2 CCD 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 A against A, TM-score 0.90

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 5K7B · PDBe 5K7B · UniProt A8MW95

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