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Crystal structure of BAK core domain BH3-groove-dimer in complex with phosphatidylserine

Analyse Crystal structure of BAK core domain BH3-groove-dimer in complex with… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 6UXN
Type: protein
Length: 953 residues
Chains: 12
Method: x-ray diffraction
Collection: MolNFT v2 / PDB Bank
Contract: 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
Owner: 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
Resolution: 2.49
Source: Homo sapiens
Molecule: Bcl-2 homologous antagonist/killer
UniProt: Q16611
Ligands: 8SP, SO4
Pockets: 12 · best druggability 0.81

Structure

x-ray diffraction · resolution 2.49 · 7 distinct chains · 81% helix, 0% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, I	Bcl-2 homologous antagonist/killer	protein	82	78% helix, 0% strand	Q16611
B, L	Bcl-2 homologous antagonist/killer	protein	78	82% helix, 0% strand	Q16611
C, K	Bcl-2 homologous antagonist/killer	protein	81	81% helix, 0% strand	Q16611
D, H	Bcl-2 homologous antagonist/killer	protein	77	82% helix, 0% strand	Q16611
E, F	Bcl-2 homologous antagonist/killer	protein	79	82% helix, 0% strand	Q16611
G	Bcl-2 homologous antagonist/killer	protein	80	80% helix, 0% strand	Q16611
J	Bcl-2 homologous antagonist/killer	protein	79	82% helix, 0% strand	Q16611

Ligands and binding sites

8SP · O-[(R)-{[(2R)-2,3-bis(octanoyloxy)propyl]oxy}(hydroxy) phosphoryl]-L-serine · ligand · 18 copies · chains A, B, C, D, E, F, G, H, K, I, J, L
SO4 · Sulfate ion · ion · 19 copies · chains A, B, C, D, E, F, G, L, H, I, J, K
GOL · Glycerol · additive · chains C, D, F

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

Pockets

12 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	1149	0.81	0.82	95	SO4
2	809	0.80	0.83	76	SO4
3	139	0.58	0.84	22	SO4
4	101	0.57	0.86	18	empty
5	124	0.54	0.83	17	empty

Interfaces

30 interfaces between chains.

K–L · 1979 Å² buried · 20 hydrogen bonds · protein-protein
C–D · 1961 Å² buried · 22 hydrogen bonds · protein-protein
E–F · 1949 Å² buried · 20 hydrogen bonds · protein-protein
G–H · 1943 Å² buried · 22 hydrogen bonds · protein-protein
A–B · 1942 Å² buried · 20 hydrogen bonds · protein-protein

Compared structures

6UXN · Crystal structure of bak core domain BH3-groove-dimer in complex with phosphatidylserine · the same entry in another collection · chain L against L, TM-score 1.00

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 6UXN · PDBe 6UXN · UniProt Q16611

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