8GH7: 142D6

142D6 bound to BIR3-XIAP. Determined by X-ray diffraction at 1.75 Å resolution. Released 5 Jul 2023.

Method: X-ray diffraction
Resolution: 1.75 Å
Organisms: Homo sapiens, synthetic construct
Chains: 4
Atoms: 1,709
Mol. weight: 24.6 kDa
Ligands: ZN, 7PE
Released: 5 Jul 2023

Explore 8GH7 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

8GH7 contains 12 α-helices and 10 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: 6 helices, 4 β-strands

Element	Residues	Length	Sheet
α-helix	260-262	3
α-helix	265-271	7
α-helix	281-286	6
β-strand	289-291	3	1
β-strand	298-300	3	1
β-strand	306-307	2	1
β-strand	308	1	2
α-helix	310-311	2
α-helix	316-323	8
α-helix	328-342	15

Chain B: 6 helices, 4 β-strands

Element	Residues	Length	Sheet
α-helix	260-262	3
α-helix	265-270	6
α-helix	281-286	6
β-strand	289-291	3	3
β-strand	298-300	3	3
β-strand	306-307	2	3
β-strand	308	1	4
α-helix	310-311	2
α-helix	316-323	8
α-helix	328-344	17

Chains D and H: 0 helices, 1 β-strand

Element	Residues	Length	Sheet
β-strand	2	1	2

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
E3 ubiquitin-protein ligase XIAP	A, B	protein	99	Homo sapiens	P98170 (AlphaFold model)
BIR3 inhibitor MAA-CHG-PRO-ZHW	D, H	protein	4	synthetic construct

Sequence of entity 1 (A, B), FASTA

>8GH7_1 E3 ubiquitin-protein ligase XIAP (chains A, B)
GSHMSTNLPRNPSMADYEARIFTFGTWIYSVNKEQLARAGFYALGEGDKVKCFHCGGGLT
DWKPSEDPWEQHAKWYPGCKYLLEQKGQEYINNIHLTHS

Sequence of entity 2 (D, H), FASTA

>8GH7_2 BIR3 inhibitor MAA-CHG-PRO-ZHW (chains D, H)
AXPX

Ligands and cofactors

ID	Name	Formula	Copies
ZN	Zinc ion	Zn	2
7PE	2-(2-(2-(2-(2-(2-ethoxyethoxy)ethoxy)ethoxy)ethoxy)ethoxy)ethanol	C14 H30 O7	2

Primary citation

Characterization of a Potent and Orally Bioavailable Lys-Covalent Inhibitor of Apoptosis Protein (IAP) Antagonist. Udompholkul, P., Garza-Granados, A., Alboreggia, G. et al. J Med Chem (2023) 66:8159-8169. DOI 10.1021/acs.jmedchem.3c00467 · 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
4IC3 1.78 Å, Crystal structure of the F495L mutant XIAP RING domain

Browse structure collections

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