Research workbench

BCL-xl in complex with bim-H3PC-rt

Analyse BCL-xl in complex with bim-H3PC-rt in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 5VX3
Type: protein
Length: 661 residues
Chains: 8
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: BCL-2-like protein 1; BCL-2-like protein 11
UniProt: Q07817, O43521
Pockets: 10 · best druggability 0.64

Structure

x-ray diffraction · 6 distinct chains · 78% helix, 0% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	BCL-2-like protein 1	protein	140	78% helix, 0% strand	Q07817
B	BCL-2-like protein 11	protein	21	86% helix, 0% strand	O43521
C	BCL-2-like protein 1	protein	141	77% helix, 0% strand	Q07817
D, F	BCL-2-like protein 11	protein	22	86% helix, 0% strand	O43521
E, G	BCL-2-like protein 1	protein	146	76% helix, 0% strand	Q07817
H	BCL-2-like protein 11	protein	23	87% helix, 0% strand	O43521

Ligands and binding sites

EDO · 1,2-ethanediol · additive · 13 copies · chains A, E, C, D, G, F, H

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

Pockets

10 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	351	0.64	0.79	39	EDO
2	310	0.62	0.79	35	EDO
3	191	0.57	0.80	24	empty
4	177	0.56	0.80	33	EDO
5	190	0.55	0.79	23	empty

Interfaces

9 interfaces between chains.

C–G · 2083 Å² buried · 23 hydrogen bonds · protein-protein
A–E · 2077 Å² buried · 19 hydrogen bonds · protein-protein
G–H · 1160 Å² buried · 12 hydrogen bonds · protein-protein
C–D · 1142 Å² buried · 15 hydrogen bonds · protein-protein
E–F · 1130 Å² buried · 14 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 4 modified (nonstandard).

Compared structures

5VX3 · Bcl-xL in complex with Bim-h3Pc-RT · the same entry in another collection · chain H against H, 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
Every structure of UniProt O43521
Elsewhere: RCSB PDB 5VX3 · PDBe 5VX3 · UniProt Q07817 · UniProt O43521

GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.