5O6T: BIRC4 RING

Name: PDB 5O6T: BIRC4 RING in complex with dimeric ubiquitin variant
Published: 2017-11-01
License: https://creativecommons.org/publicdomain/zero/1.0/
Keywords: ligase

BIRC4 RING in complex with dimeric ubiquitin variant. Determined by X-ray diffraction at 1.57 Å resolution. Released 1 Nov 2017.

Method: X-ray diffraction
Resolution: 1.57 Å
Organism: Homo sapiens
Chains: 4
Atoms: 2,532
Mol. weight: 33.61 kDa
Ligands: ZN
Released: 1 Nov 2017

Explore 5O6T in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

5O6T contains 21 α-helices and 32 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, 9 β-strands

Element	Residues	Length	Sheet
α-helix	437-447	11
β-strand	449	1	1
β-strand	457	1	1
α-helix	458	1
β-strand	460-463	4	2
β-strand	467	1	3
β-strand	470	1	2
α-helix	472-475	4
β-strand	480	1	4
α-helix	486	1
β-strand	487	1	4
α-helix	488	1
β-strand	490-493	4	2
α-helix	494	1
β-strand	495	1	5

Chain B: 5 helices, 9 β-strands

Element	Residues	Length	Sheet
α-helix	437-447	11
β-strand	449	1	6
β-strand	457	1	6
α-helix	458	1
β-strand	460-463	4	7
β-strand	467	1	5
β-strand	468-470	3	7
α-helix	472-475	4
β-strand	480	1	8
α-helix	486	1
β-strand	487	1	8
α-helix	488	1
β-strand	490-493	4	7
β-strand	495	1	3

Chains C and D: 5 helices, 7 β-strands

Element	Residues	Length	Sheet
β-strand	1-9	9	9
α-helix	12	1
β-strand	13-17	5	9
β-strand	22	1	10
α-helix	23-34	12
α-helix	38-40	3
β-strand	41-45	5	9
β-strand	48-49	2	9
α-helix	50-51	2
β-strand	55	1	10
α-helix	57-59	3
β-strand	66-71	6	9

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
E3 ubiquitin-protein ligase XIAP	A, B	protein	66	Homo sapiens	P98170 (AlphaFold model)
Polyubiquitin-B	C, D	protein	80	Homo sapiens	P0CG47 (AlphaFold model)

Sequence of entity 1 (A, B), FASTA

>5O6T_1 E3 ubiquitin-protein ligase XIAP (chains A, B)
GSEISTEEQLRRLQEEKLCKICMDRNIAIVFVPCGHLVTCKQCAEAVDKCPMCYTVITFK
QKIFMS

Sequence of entity 2 (C, D), FASTA

>5O6T_2 Polyubiquitin-B (chains C, D)
GSMQILVTTISAETIRLEVEPSDTIENVKAKIQDKEGIPPDQQRLFFEGKQLEDGRTLSD
YNINKKSTLLLVVKFHRVAS

Ligands and cofactors

ID	Name	Formula	Copies
ZN	Zinc ion	Zn	4

Water and common crystallization additives (EDO) are not listed.

Primary citation

A General Strategy for Discovery of Inhibitors and Activators of RING and U-box E3 Ligases with Ubiquitin Variants. Gabrielsen, M., Buetow, L., Nakasone, M.A. et al. Mol Cell (2017) 68:456-470.e10. DOI 10.1016/j.molcel.2017.09.027 · 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
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
4IC3 1.78 Å, Crystal structure of the F495L mutant XIAP RING domain

Browse structure collections

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