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Puma BH3 foldamer in complex with BCL-xl

Analyse Puma BH3 foldamer in complex with BCL-xl in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 2YJ1
Type: protein
Length: 333 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: BCL-2-like protein 1; Alpha-beta-puma BH3 foldamer
UniProt: Q07817
Ligands: NH2, ACE
Pockets: 3 · best druggability 0.54

Structure

x-ray diffraction · 3 distinct chains · 76% helix, 0% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	BCL-2-like protein 1	protein	151	74% helix, 0% strand	Q07817
B, D	Alpha-beta-puma BH3 foldamer	protein	21	90% helix, 0% strand	—
C	BCL-2-like protein 1	protein	140	76% helix, 0% strand	Q07817

Ligands and binding sites

NH2 · Amino group · ion · chains B
ACE · Acetyl group · ion · chains D

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

Pockets

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

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	162	0.54	0.80	25	empty
2	95	0.40	0.77	17	empty
3	96	0.38	0.76	16	empty

Interfaces

3 interfaces between chains.

A–C · 2333 Å² buried · 41 hydrogen bonds · protein-protein
A–B · 1264 Å² buried · 17 hydrogen bonds · protein-protein
C–D · 1098 Å² buried · 17 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 12 modified (nonstandard).

Compared structures

2YJ1 · Puma BH3 foldamer in complex with Bcl-xL · the same entry in another collection · chain A against A, TM-score 1.00
Q07817 · AlphaFold monomer V2.0 prediction for BCL-2-like protein 1 (Q07817) · a predicted model of the same protein · chain C against A, TM-score 0.80

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 Q07817
Elsewhere: RCSB PDB 2YJ1 · PDBe 2YJ1 · UniProt Q07817

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