7L9X: VPS4B

Structure of VPS4B in complex with an allele-specific covalent inhibitor. Determined by X-ray diffraction at 2.81 Å resolution. Released 14 Apr 2021.

Method: X-ray diffraction
Resolution: 2.81 Å
Organism: Homo sapiens
Chains: 1
Atoms: 2,326
Mol. weight: 50.04 kDa
Ligands: XQV
Released: 14 Apr 2021

Explore 7L9X in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

7L9X contains 19 α-helices and 11 β-strands across 1 chain. 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: 19 helices, 11 β-strands

Element	Residues	Length	Sheet
α-helix	133-135	3
α-helix	140-146	7
α-helix	147-151	5
α-helix	152-155	4
β-strand	169-173	5	1
α-helix	180-191	12
β-strand	196-199	4	1
α-helix	214-225	12
β-strand	229-233	5	1
α-helix	236-238	3
α-helix	251-254	4
α-helix	257-262	6
β-strand	272-278	7	1
α-helix	286-289	4
β-strand	294-297	4	1
α-helix	299-302	4
α-helix	303-312	10
β-strand	319	1	2
α-helix	323-332	10
α-helix	338-358	21
β-strand	361-368	8	3
β-strand	376-383	8	3
β-strand	392-393	2	3
α-helix	396-398	3
α-helix	401-403	3
β-strand	404	1	3
α-helix	406-408	3
β-strand	409	1	2
α-helix	411-418	8
α-helix	427-439	13

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Vacuolar protein sorting-associated protein 4B	A	protein	446	Homo sapiens	O75351 (AlphaFold model)

Sequence of entity 1 (A), FASTA

>7L9X_1 Vacuolar protein sorting-associated protein 4B (chains A)
SHMSSTSPNLQKAIDLASKAAQEDKAGNYEEALQLYQHAVQYFLHVVKYEAQGDKAKQSI
RAKCTEYLDRAEKLKEYLKNKEKKAQKPVKEGQPSPADEKGNDSDGEGESDDPEKKKLQN
QLQGAIVIERPNVKWSCVAGLEGAKEALKEAVILPIKFPHLFTGKRTPWRGILLFGPPGT
GKSYLAKAVATEANNSTFFSISSSDLVSKWLGESEKLVKNLFQLARENKPSIIFIDEIDS
LCGSRSENESEAARRIKTEFLVQMQGVGVDNDGILVLGATNIPWVLDSAIRRRFEKRIYI
PLPEPHARAAMFKLHLGTTQNSLTEADFRELGRKTDGYSGADISIIVRDALMQPVRKVQS
ATHFKKVRGPSRADPNHLVDDLLTPCSPGDPGAIEMTWMDVPGDKLLEPVVSMSDMLRSL
SNTKPTVNEHDLLKLKKFTEDFGQEG

Ligands and cofactors

ID	Name	Formula	Copies
XQV	N-{3-[(8-phenyl[1,2,4]triazolo[1,5-a]pyridin-2-yl)amino]phenyl}propanamide	C21 H19 N5 O	1

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

Primary citation

A chemical genetics approach to examine the functions of AAA proteins. Cupido, T., Jones, N.H., Grasso, M.J. et al. Nat Struct Mol Biol (2021) 28:388-397. DOI 10.1038/s41594-021-00575-9 · PubMed

Other PDB entries of the same protein (UniProt O75351 (AlphaFold model), which also has an AlphaFold model), best resolution first:

4U7Y 2.5 Å, Structure of the complex of VPS4B MIT and IST1 MIM
1XWI 2.8 Å, Crystal Structure of VPS4B
1WR0 Structural characterization of the MIT domain from human Vps4b
2CPT Solution structure of MIT domain from human SKD1
2JQH VPS4B mit
2JQK VPS4B MIT-CHMP2B Complex

Browse structure collections

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