6UXO: BAK core domain BH3-groove-dimer

Crystal structure of BAK core domain BH3-groove-dimer in complex with DDM. Determined by X-ray diffraction at 1.8 Å resolution. Released 2 Sept 2020.

Method: X-ray diffraction
Resolution: 1.8 Å
Organism: Homo sapiens
Chains: 12
Atoms: 9,090
Mol. weight: 131.53 kDa
Ligands: LMT
Released: 2 Sept 2020

Explore 6UXO in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

6UXO contains 36 α-helices and 0 β-strands across 12 chains. Residue ranges use author residue numbering, as in the PDB file, from PDBe. To see them in 3D, choose the Cartoon representation with Secondary structure coloring: helices, sheets and coils get different colors.

Chains A and I: 3 helices, 0 β-strands

Element	Residues	Length
α-helix	70-100	31
α-helix	107-119	13
α-helix	125-146	22

Chains B, C, D, F and L: 3 helices, 0 β-strands

Element	Residues	Length
α-helix	70-100	31
α-helix	107-119	13
α-helix	125-144	20

Chain E: 3 helices, 0 β-strands

Element	Residues	Length
α-helix	69-100	32
α-helix	107-119	13
α-helix	125-145	21

Chains G, H, J and K: 3 helices, 0 β-strands

Element	Residues	Length
α-helix	70-100	31
α-helix	107-119	13
α-helix	125-145	21

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Bcl-2 homologous antagonist/killer	A, B, C, D, E, F, G, H, I, J, K, L	protein	85	Homo sapiens	Q16611 (AlphaFold model)

Sequence of entity 1 (A, B, C, D, E, F, G, H, I, J, K, L), FASTA

>6UXO_1 Bcl-2 homologous antagonist/killer (chains A, B, C, D, E, F, G, H, I, J, K, L)
GPLGSSTMGQVGRQLAIIGDDINRRYDSEFQTMLQHLQPTAENAYEYFTKIATSLFESGI
NWGRVVALLGFGYRLALHVYQHGLT

Ligands and cofactors

ID	Name	Formula	Copies
LMT	Dodecyl-beta-D-maltoside	C24 H46 O11	24

Water and common crystallization additives (SO4, ACT, EDO) are not listed.

Primary citation

BAK core dimers bind lipids and can be bridged by them. Cowan, A.D., Smith, N.A., Sandow, J.J. et al. Nat Struct Mol Biol (2020) 27:1024-1031. DOI 10.1038/s41594-020-0494-5 · PubMed

Other PDB entries of the same protein (UniProt Q16611 (AlphaFold model), which also has an AlphaFold model), best resolution first:

5VX1 1.22 Å, Bak L100A
8CZF 1.3 Å, Human BAK in complex with the dF2 peptide
8CZH 1.3 Å, Human BAK in complex with the dM2 peptide
2IMS 1.48 Å, The X-ray Structure of a Bak Homodimer Reveals an Inhibitory Zinc Binding Site
2IMT 1.49 Å, The X-ray Structure of a Bak Homodimer Reveals an Inhibitory Zinc Binding Site
9CPE 1.49 Å, Structural basis of BAK sequestration by MCL-1 and consequences for apoptosis initiation
5FMI 1.49 Å, Human Bak Q77L
7M5A 1.5 Å, Crystal Structure of human BAK in complex with W3W5_BID
5VWY 1.55 Å, Bak core latch dimer in complex with Bim-h3Pc-RT
5VX0 1.6 Å, Bak in complex with Bim-h3Glg
5VWZ 1.62 Å, Bak in complex with Bim-h3Pc
6UXQ 1.7 Å, Crystal structure of BAK core domain BH3-groove-dimer in complex with POPC and C8E4

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