4KJU: E3 ubiquitin-protein ligase XIAP

Crystal structure of XIAP-Bir2 with a bound benzodiazepinone inhibitor. Determined by X-ray diffraction at 1.6 Å resolution. Released 27 Nov 2013.

Method: X-ray diffraction
Resolution: 1.6 Å
Organism: Homo sapiens
Chains: 2
Atoms: 1,435
Mol. weight: 20.55 kDa
Ligands: 1RH, ZN
Released: 27 Nov 2013

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

Secondary structure: helices and β-sheets

4KJU 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	159-161	3
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	228-231	4

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

>4KJU_1 E3 ubiquitin-protein ligase XIAP (chains A, C)
GTIYPRNPAMYSEEARLKSFQNWPDYAHLTPRELASAGLYYTGIGDQVQCFACGGKLKNW
EPGDRAWSEHRRHFPNCFFVLGRNLN

Ligands and cofactors

ID	Name	Formula	Copies
1RH	N-{(3S)-5-(4-aminobenzoyl)-1-[(2-methoxynaphthalen-1-yl)methyl]-2-oxo-2,3,4,5-t…	C32 H33 N5 O4	1
ZN	Zinc ion	Zn	2

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
8W5A 1.65 Å, Crystal structure of the RING domain of human XIAP
4KJV 1.7 Å, Crystal structure of XIAP-Bir2 with a bound spirocyclic benzoxazepinone inhibitor.
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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