4IC3: F495L mutant XIAP RING domain

Name: PDB 4IC3: Crystal structure of the F495L mutant XIAP RING domain
Published: 2012-12-19
License: https://creativecommons.org/publicdomain/zero/1.0/
Keywords: ligase

Crystal structure of the F495L mutant XIAP RING domain. Determined by X-ray diffraction at 1.78 Å resolution. Released 19 Dec 2012.

Method: X-ray diffraction
Resolution: 1.78 Å
Organism: Homo sapiens
Chains: 2
Atoms: 1,118
Mol. weight: 17.1 kDa
Ligands: NI, ZN
Released: 19 Dec 2012

Explore 4IC3 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

4IC3 contains 9 α-helices and 16 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, 8 β-strands

Element	Residues	Length	Sheet
α-helix	437-447	11
β-strand	449	1	1
β-strand	457	1	1
β-strand	460-463	4	2
β-strand	468	1	2
α-helix	472-475	4
β-strand	480	1	3
α-helix	486	1
β-strand	487	1	3
α-helix	488	1
β-strand	490-493	4	2
α-helix	494	1
β-strand	495	1	4

Chain B: 4 helices, 8 β-strands

Element	Residues	Length	Sheet
α-helix	437-447	11
β-strand	449	1	5
β-strand	457	1	5
β-strand	460-463	4	6
β-strand	467	1	4
β-strand	468	1	6
α-helix	472-475	4
β-strand	480	1	7
α-helix	486	1
β-strand	487	1	7
α-helix	488	1
β-strand	490-493	4	6

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
E3 ubiquitin-protein ligase XIAP	A, B	protein	74	Homo sapiens	P98170 (AlphaFold model)

Sequence of entity 1 (A, B), FASTA

>4IC3_1 E3 ubiquitin-protein ligase XIAP (chains A, B)
GPLGSTSLQKEISTEEQLRRLQEEKLCKICMDRNIAIVFVPCGHLVTCKQCAEAVDKCPM
CYTVITFKQKILMS

Ligands and cofactors

ID	Name	Formula	Copies
NI	Nickel (II) ion	Ni	2
ZN	Zinc ion	Zn	4

Primary citation

Regulation of ubiquitin transfer by XIAP, a dimeric RING E3 ligase. Nakatani, Y., Kleffmann, T., Linke, K. et al. Biochem J (2013) 450:629-638. DOI 10.1042/BJ20121702 · 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

Browse structure collections

About this viewer

MolViewer shows 4IC3 directly in your browser with nothing to install. Switch between cartoon, ball-and-stick, spacefill and surface views, color by chain, secondary structure or B-factor, measure distances, angles and dihedrals, and share or embed the view.