4KJV: E3 ubiquitin-protein ligase XIAP

Crystal structure of XIAP-Bir2 with a bound spirocyclic benzoxazepinone inhibitor. Determined by X-ray diffraction at 1.7 Å resolution. Released 27 Nov 2013.

Method: X-ray diffraction
Resolution: 1.7 Å
Organism: Homo sapiens
Chains: 2
Atoms: 1,440
Mol. weight: 20.55 kDa
Ligands: ZN, 1RK
Released: 27 Nov 2013

Explore 4KJV in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

4KJV contains 9 α-helices and 6 β-strands across 2 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: 5 helices, 3 β-strands

Element	Residues	Length	Sheet
α-helix	158-161	4
α-helix	163-168	6
α-helix	181-186	6
β-strand	189-191	3	1
β-strand	198-200	3	1
β-strand	206-207	2	1
α-helix	216-223	8
α-helix	228-232	5

Chain C: 4 helices, 3 β-strands

Element	Residues	Length	Sheet
α-helix	163-168	6
α-helix	181-186	6
β-strand	189-191	3	2
β-strand	198-200	3	2
β-strand	206-207	2	2
α-helix	216-223	8
α-helix	228-233	6

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
E3 ubiquitin-protein ligase XIAP	A, C	protein	86	Homo sapiens	P98170 (AlphaFold model)

Sequence of entity 1 (A, C), FASTA

>4KJV_1 E3 ubiquitin-protein ligase XIAP (chains A, C)
GTIYPRNPAMYSEEARLKSFQNWPDYAHLTPRELASAGLYYTGIGDQVQCFACGGKLKNW
EPGDRAWSEHRRHFPNCFFVLGRNLN

Ligands and cofactors

ID	Name	Formula	Copies
ZN	Zinc ion	Zn	2
1RK	6-methoxy-5-({(3S)-3-[(N-methyl-L-alanyl)amino]-4-oxo-2',3,3',4,5',6'-hexahydro…	C30 H33 N3 O7	1

Primary citation

Optimization of Benzodiazepinones as Selective Inhibitors of the X-Linked Inhibitor of Apoptosis Protein (XIAP) Second Baculovirus IAP Repeat (BIR2) Domain. Kester, R.F., Donnell, A.F., Lou, Y. et al. J Med Chem (2013) 56:7788-7803. DOI 10.1021/jm400732v · PubMed

Other PDB entries of the same protein (UniProt P98170 (AlphaFold model), which also has an AlphaFold model), best resolution first:

4J44 1.3 Å, Crystal structure of XIAP-BIR2 domain with AIAV bound
8W59 1.34 Å, Crystal structure of the RING domain of human XIAP treated with arsenic trioxide
4J47 1.35 Å, Crystal structure of XIAP-BIR2 domain with SVPI bound
4J46 1.42 Å, Crystal structure of XIAP-BIR2 domain with AVPI bound
4J3Y 1.45 Å, Crystal structure of XIAP-BIR2 domain
4J45 1.48 Å, Crystal structure of XIAP-BIR2 domain with ATAA bound
5O6T 1.57 Å, BIRC4 RING in complex with dimeric ubiquitin variant
4KJU 1.6 Å, Crystal structure of XIAP-Bir2 with a bound benzodiazepinone inhibitor.
8W5A 1.65 Å, Crystal structure of the RING domain of human XIAP
3UW5 1.71 Å, Crystal structure of the BIR domain of MLIAP bound to GDC0152
8GH7 1.75 Å, 142D6 bound to BIR3-XIAP
4IC3 1.78 Å, Crystal structure of the F495L mutant XIAP RING domain

Browse structure collections

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