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ALPHA/BETA foldamer in complex with BCL-xl

Analyse ALPHA/BETA 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: 3FDM
Type: protein
Length: 479 residues
Chains: 6
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Apoptosis regulator BCL-X; ALPHA/BETA-peptide foldamer
UniProt: Q07817
Ligands: ACE, NH2
Pockets: 6 · best druggability 0.56

Structure

x-ray diffraction · 4 distinct chains · 77% helix, 0% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Apoptosis regulator BCL-X	protein	147	78% helix, 0% strand	Q07817
B	Apoptosis regulator BCL-X	protein	146	76% helix, 0% strand	Q07817
C	Apoptosis regulator BCL-X	protein	141	77% helix, 0% strand	Q07817
D, E, F	ALPHA/BETA-peptide foldamer	protein	15	73% helix, 0% strand	—

Ligands and binding sites

ACE · Acetyl group · ligand · chains F
NH2 · Amino group · ion · 3 copies · chains A, D, B, E, C, F
EDO · 1,2-ethanediol · additive · 11 copies · chains A, D, B, E

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

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	267	0.56	0.77	22	empty
2	181	0.55	0.80	34	empty
3	69	0.48	0.84	20	EDO
4	162	0.41	0.72	21	empty
5	53	0.38	0.80	8	empty

Interfaces

6 interfaces between chains.

A–B · 2279 Å² buried · 23 hydrogen bonds · protein-protein
A–D · 866 Å² buried · 10 hydrogen bonds · protein-protein
B–E · 793 Å² buried · 9 hydrogen bonds · protein-protein
C–F · 784 Å² buried · 6 hydrogen bonds · protein-protein
C–D · 193 Å² buried · 4 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 15 modified, 1 covalent (nonstandard, covalent ligand).

Compared structures

3FDM · alpha/beta 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 0.81

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 3FDM · PDBe 3FDM · UniProt Q07817

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