Research workbench

BCL-xl bound to alpha beta puma BH3 peptide 5

Analyse BCL-xl bound to alpha beta puma BH3 peptide 5 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 4BPK
Type: protein
Length: 317 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: BCL-2-like protein 1; Alpha beta BH3-peptide
UniProt: Q07817
Ligands: ACE, CD, NH2
Pockets: 3 · best druggability 0.58

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	139	77% helix, 0% strand	Q07817
B	BCL-2-like protein 1	protein	138	78% helix, 0% strand	Q07817
C, D	Alpha beta BH3-peptide	protein	20	60% helix, 0% strand	—

Ligands and binding sites

ACE · Acetyl group · ligand · chains D
CD · Cadmium ion · metal · 15 copies · chains A, C, B, D
NH2 · Amino group · ion · 2 copies · chains C, D
EDO · 1,2-ethanediol · additive · 2 copies · chains A, B

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	263	0.58	0.79	41	EDO
2	77	0.40	0.79	15	empty
3	68	0.36	0.77	16	empty

Interfaces

3 interfaces between chains.

A–B · 2168 Å² buried · 25 hydrogen bonds · protein-protein
A–C · 1121 Å² buried · 14 hydrogen bonds · protein-protein
B–D · 1066 Å² buried · 12 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 14 modified, 1 covalent (nonstandard, covalent ligand).

Compared structures

4BPK · Bcl-xL bound to alpha beta Puma BH3 peptide 5 · 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 B 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 4BPK · PDBe 4BPK · UniProt Q07817

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