4WVT: XIAP-BIR2 domain

Crystal structure of XIAP-BIR2 domain complexed with ligand bound. Determined by X-ray diffraction at 1.96 Å resolution. Released 4 Mar 2015.

Method: X-ray diffraction
Resolution: 1.96 Å
Organism: Homo sapiens
Chains: 4
Atoms: 1,571
Mol. weight: 24.41 kDa
Ligands: ZN
Released: 4 Mar 2015

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

Secondary structure: helices and β-sheets

4WVT contains 10 α-helices and 8 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.

Chains A and B: 5 helices, 3 β-strands

Element	Residues	Length	Sheet
α-helix	158-160	3
α-helix	163-169	7
α-helix	175-177	3
α-helix	181-186	6
β-strand	189-191	3	1
β-strand	198-200	3	1
β-strand	206-208	3	1
α-helix	216-223	8

Chains C and D: 0 helices, 1 β-strand

Element	Residues	Length	Sheet
β-strand	2-4	3	1

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
E3 ubiquitin-protein ligase XIAP	A, B	protein	98	Homo sapiens	P98170 (AlphaFold model)
3,11-difluoro-6,8,13-trimethyl-8H-QUINO[4,3,2-kl]acridin-13-ium	C, D	protein	6

Sequence of entity 1 (A, B), FASTA

>4WVT_1 E3 ubiquitin-protein ligase XIAP (chains A, B)
MGSSHHHHHHSSGETVRFQGHMRNPAMYSEEARLKSFQNWPDYAHLTPRELASAGLYYTG
IGDQVQCFACGGKLKNWEPGDRAWSEHRRHFPNCFFVL

Sequence of entity 2 (C, D), FASTA

>4WVT_2 3,11-DIFLUORO-6,8,13-TRIMETHYL-8H-QUINO[4,3,2-KL]ACRIDIN-13-IUM (chains C, D)
AFPFFX

Ligands and cofactors

ID	Name	Formula	Copies
ZN	Zinc ion	Zn	2

Primary citation

The Discovery of Macrocyclic XIAP Antagonists from a DNA-Programmed Chemistry Library, and Their Optimization To Give Lead Compounds with in Vivo Antitumor Activity. Seigal, B.A., Connors, W.H., Fraley, A. et al. J Med Chem (2015) 58:2855-2861. DOI 10.1021/jm501892g · 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
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

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