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Complex of BCL-xl with its BH3 domain

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

PDB: 4CIN
Type: protein
Length: 316 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: BCL-2-like protein 1
UniProt: Q07817
Ligands: CA
Pockets: 4 · best druggability 0.63

Structure

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

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	BCL-2-like protein 1	protein	140	76% helix, 0% strand	Q07817
B	BCL-2-like protein 1	protein	134	78% helix, 0% strand	Q07817
C	BCL-2-like protein 1	protein	23	83% helix, 0% strand	Q07817
D	BCL-2-like protein 1	protein	19	74% helix, 0% strand	Q07817

Ligands and binding sites

CA · Calcium ion · metal · 2 copies · chains A, B
EDO · 1,2-ethanediol · additive · 6 copies · chains A, B
EPE · 4-(2-hydroxyethyl)-1-piperazine ethanesulfonic acid · additive · 2 copies · chains A, B

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

Pockets

4 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	310	0.63	0.80	48	EPE
2	57	0.58	0.90	13	empty
3	171	0.51	0.77	21	empty
4	150	0.44	0.75	16	empty

Interfaces

3 interfaces between chains.

A–B · 2133 Å² buried · 27 hydrogen bonds · protein-protein
A–C · 1054 Å² buried · 16 hydrogen bonds · protein-protein
B–D · 1018 Å² buried · 15 hydrogen bonds · protein-protein

Compared structures

4CIN · Complex of Bcl-xL with its BH3 domain · the same entry in another collection · chain D against D, 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 A 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 4CIN · PDBe 4CIN · UniProt Q07817

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