MolNFT v1 · #170870 · protein

Crystal structure of human BCL-xl bound to trichoplax adhaerens trbak BH3

6YLI · BCL-2-like protein 1: “Crystal structure of human BCL-xl bound to trichoplax adhaerens trbak BH3”. X-ray diffraction, 1 ligand (SO4), 2 pockets (best druggability 0.60). MolNFT v1 #170870 on GenesisL1: 3D structure, binding sites…

PDB: 6YLI
Type: protein
Length: 355 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: BCL-2-like protein 1; BCL-2 homologous ANTAGONIST/KILLER
UniProt: Q07817, A0A369S334
Ligands: SO4
Pockets: 2 · best druggability 0.60

Structure

x-ray diffraction · 4 distinct chains · 76% helix, 0% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	BCL-2-like protein 1	protein	155	76% helix, 0% strand	Q07817
B	BCL-2 homologous ANTAGONIST/KILLER	protein	24	79% helix, 0% strand	A0A369S334
C	BCL-2-like protein 1	protein	153	76% helix, 0% strand	Q07817
D	BCL-2 homologous ANTAGONIST/KILLER	protein	23	78% helix, 0% strand	A0A369S334

Ligands and binding sites

SO4 · Sulfate ion · ion · 9 copies · chains A, B, D, C

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

Pockets

2 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	422	0.60	0.76	44	empty
2	59	0.33	0.77	16	empty

Interfaces

6 interfaces between chains.

A–B · 1115 Å² buried · 13 hydrogen bonds · protein-protein
C–D · 1094 Å² buried · 12 hydrogen bonds · protein-protein
A–C · 702 Å² buried · 14 hydrogen bonds · protein-protein
B–D · 196 Å² buried · 7 hydrogen bonds · protein-protein
B–C · 97 Å² buried · 0 hydrogen bonds · protein-protein

Compared structures

6YLI · Crystal structure of human bcl-xL bound to trichoplax adhaerens trBak BH3 · 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 0.94

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 A0A369S334
Elsewhere: RCSB PDB 6YLI · PDBe 6YLI · UniProt Q07817 · UniProt A0A369S334

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