MolNFT v1 · #166684 · protein

Crystal structure of bak core domain BH3-groove-dimer in complex with phosphatidylglycerol

6UXP · BCL-2 homologous ANTAGONIST/KILLER: “Crystal structure of bak core domain BH3-groove-dimer in complex with phosphatidylglycerol”. X-ray diffraction, 1 ligand (PG8), 5 pockets (best druggability 0.77). MolNFT v1 #166684 on GenesisL1…

PDB: 6UXP
Type: protein
Length: 626 residues
Chains: 8
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: BCL-2 homologous ANTAGONIST/KILLER
UniProt: Q16611
Ligands: PG8
Pockets: 5 · best druggability 0.77

Structure

x-ray diffraction · 7 distinct chains · 82% helix, 0% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	BCL-2 homologous ANTAGONIST/KILLER	protein	79	81% helix, 0% strand	Q16611
B	BCL-2 homologous ANTAGONIST/KILLER	protein	75	87% helix, 0% strand	Q16611
C	BCL-2 homologous ANTAGONIST/KILLER	protein	76	83% helix, 0% strand	Q16611
D	BCL-2 homologous ANTAGONIST/KILLER	protein	79	82% helix, 0% strand	Q16611
E	BCL-2 homologous ANTAGONIST/KILLER	protein	76	83% helix, 0% strand	Q16611
F, H	BCL-2 homologous ANTAGONIST/KILLER	protein	80	81% helix, 0% strand	Q16611
G	BCL-2 homologous ANTAGONIST/KILLER	protein	81	79% helix, 0% strand	Q16611

Ligands and binding sites

PG8 · 1,2-dioctanoyl-sn-glycero-3-[phospho-rac-(1-glycerol) · ligand · 8 copies · chains A, B, D, C, E, F, H, G
GOL · Glycerol · additive · 4 copies · chains C, D, G, H

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

Pockets

5 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	842	0.77	0.80	66	PG8
2	672	0.74	0.80	49	PG8
3	535	0.70	0.79	37	PG8
4	195	0.55	0.78	30	PG8
5	67	0.50	0.85	22	GOL

Interfaces

15 interfaces between chains.

G–H · 2057 Å² buried · 21 hydrogen bonds · protein-protein
C–D · 1891 Å² buried · 17 hydrogen bonds · protein-protein
A–B · 1854 Å² buried · 15 hydrogen bonds · protein-protein
E–F · 1850 Å² buried · 16 hydrogen bonds · protein-protein
D–G · 583 Å² buried · 10 hydrogen bonds · protein-protein

Compared structures

6UXP · Crystal structure of BAK core domain BH3-groove-dimer in complex with phosphatidylglycerol · the same entry in another collection · chain H against H, TM-score 1.00
Q16611 · AlphaFold monomer V2.0 prediction for BCL-2 homologous ANTAGONIST/KILLER (Q16611) · a predicted model of the same protein · chain B against A, TM-score 0.72

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 Q16611
Elsewhere: RCSB PDB 6UXP · PDBe 6UXP · UniProt Q16611

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