MolNFT v1 · #137007 · protein

BCL-2 complex with beclin 1 BH3 domain

5VAX · Apoptosis regulator BCL-2 -- BCL-2-like protein 1 chimera: “BCL-2 complex with beclin 1 BH3 domain”. X-ray diffraction, 9 pockets (best druggability 0.75). MolNFT v1 #137007 on GenesisL1: 3D structure, binding sites and pockets in…

PDB: 5VAX
Type: protein
Length: 650 residues
Chains: 8
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Apoptosis regulator BCL-2 -- BCL-2-like protein 1 chimera; Beclin-1
UniProt: P10415, Q14457
Pockets: 9 · best druggability 0.75

Structure

x-ray diffraction · 7 distinct chains · 76% helix, 0% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Apoptosis regulator BCL-2 -- BCL-2-like protein 1 chimera	protein	143	76% helix, 0% strand	P10415
E	Beclin-1	protein	22	86% helix, 0% strand	Q14457
B	Apoptosis regulator BCL-2 -- BCL-2-like protein 1 chimera	protein	147	76% helix, 0% strand	P10415
F, H	Beclin-1	protein	21	90% helix, 0% strand	Q14457
C	Apoptosis regulator BCL-2 -- BCL-2-like protein 1 chimera	protein	136	74% helix, 0% strand	P10415
G	Beclin-1	protein	23	83% helix, 0% strand	Q14457
D	Apoptosis regulator BCL-2 -- BCL-2-like protein 1 chimera	protein	137	76% helix, 0% strand	P10415

Pockets

9 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	816	0.75	0.79	66	empty
2	241	0.59	0.80	29	empty
3	280	0.51	0.74	29	empty
4	71	0.48	0.84	15	empty
5	117	0.48	0.79	18	empty

Interfaces

9 interfaces between chains.

C–G · 1051 Å² buried · 10 hydrogen bonds · protein-protein
D–H · 1044 Å² buried · 11 hydrogen bonds · protein-protein
A–E · 1041 Å² buried · 10 hydrogen bonds · protein-protein
B–F · 1035 Å² buried · 10 hydrogen bonds · protein-protein
A–D · 619 Å² buried · 10 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 4 modified (phosphorylation).

Compared structures

5VAX · Bcl-2 complex with Beclin 1 BH3 domain · the same entry in another collection · chain H against H, TM-score 1.00
P10415 · AlphaFold monomer V2.0 prediction for apoptosis regulator BCL-2 (P10415) · a predicted model of the same protein · chain C against A, TM-score 0.96

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 P10415
Every structure of UniProt Q14457
Elsewhere: RCSB PDB 5VAX · PDBe 5VAX · UniProt P10415 · UniProt Q14457

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