5VWZ: Bak

Bak in complex with Bim-h3Pc. Determined by X-ray diffraction at 1.62 Å resolution. Released 15 Nov 2017.

Method: X-ray diffraction
Resolution: 1.62 Å
Organism: Homo sapiens
Chains: 4
Atoms: 3,615
Mol. weight: 45.26 kDa
Ligands: 1PG
Released: 15 Nov 2017

Explore 5VWZ in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

5VWZ contains 23 α-helices and 0 β-strands across 4 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.

Chain A: 10 helices, 0 β-strands

Element	Residues	Length
α-helix	24-48	25
α-helix	58-61	4
α-helix	70-80	11
α-helix	83-87	5
α-helix	90-100	11
α-helix	107-119	13
α-helix	125-144	20
α-helix	151-164	14
α-helix	167-173	7
α-helix	177-180	4

Chain B: 1 helix, 0 β-strands

Element	Residues	Length	Sheet
α-helix	144-165	22

Chain C: 11 helices, 0 β-strands

Element	Residues	Length
α-helix	24-47	24
α-helix	55-56	2
α-helix	58-61	4
α-helix	70-81	12
α-helix	83-88	6
α-helix	90-100	11
α-helix	107-119	13
α-helix	125-144	20
α-helix	151-164	14
α-helix	167-173	7
α-helix	177-182	6

Chain D: 1 helix, 0 β-strands

Element	Residues	Length	Sheet
α-helix	144-162	19

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Bcl-2 homologous antagonist/killer	A, C	protein	170	Homo sapiens	Q16611 (AlphaFold model)
Bcl-2-like protein 11	B, D	protein	26	Homo sapiens	O43521 (AlphaFold model)

Sequence of entity 1 (A, C), FASTA

>5VWZ_1 Bcl-2 homologous antagonist/killer (chains A, C)
GPLGSMSEEQVAQDTEEVFRSYVFYRHQQEQEAEGVAAPADPEMVTLPLQPSSTMGQVGR
QLAIIGDDINRRYDSEFQTMLQHLQPTAENAYEYFTKIATSLFESGINWGRVVALLGFGY
RLALHVYQHGLTGFLGQVTRFVVDFMLHHSIARWIAQRGGWVAALNLGNG

Sequence of entity 2 (B, D), FASTA

>5VWZ_2 Bcl-2-like protein 11 (chains B, D)
DMRPEIWIAQELRRXGDEFNAYYARR

Ligands and cofactors

ID	Name	Formula	Copies
1PG	2-(2-{2-[2-(2-methoxy-ethoxy)-ethoxy]-ethoxy}-ethoxy)-ethanol	C11 H24 O6	2

Water and common crystallization additives (NH4) are not listed.

Primary citation

Conversion of Bim-BH3 from Activator to Inhibitor of Bak through Structure-Based Design. Brouwer, J.M., Lan, P., Cowan, A.D. et al. Mol Cell (2017) 68:659-672.e9. DOI 10.1016/j.molcel.2017.11.001 · 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
6UXQ 1.7 Å, Crystal structure of BAK core domain BH3-groove-dimer in complex with POPC and C8E4
8IGC 1.7 Å, Crystal structure of Bak bound to Bnip5 BH3

Browse structure collections

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