5D0M: UbE2D2:RNF165:Ub complex

Name: PDB 5D0M: Structure of UbE2D2:RNF165:Ub complex
Published: 2015-12-09
License: https://creativecommons.org/publicdomain/zero/1.0/
Keywords: ligase

Structure of UbE2D2:RNF165:Ub complex. Determined by X-ray diffraction at 1.91 Å resolution. Released 9 Dec 2015.

Method: X-ray diffraction
Resolution: 1.91 Å
Organism: Homo sapiens
Chains: 3
Atoms: 2,307
Mol. weight: 35.82 kDa
Ligands: ZN, PO4
Released: 9 Dec 2015

Explore 5D0M in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

5D0M contains 12 α-helices and 22 β-strands across 3 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: 7 helices, 8 β-strands

Element	Residues	Length	Sheet
α-helix	2-15	14
β-strand	21-26	6	1
β-strand	29-38	10	1
α-helix	39-40	2
β-strand	49-55	7	1
α-helix	64-65	2
β-strand	66-69	4	1
β-strand	75	1	2
β-strand	78	1	2
β-strand	83	1	1
β-strand	84	1	2
α-helix	87-89	3
α-helix	99-111	13
α-helix	121-129	9
α-helix	131-145	15

Chain B: 3 helices, 7 β-strands

Element	Residues	Length	Sheet
β-strand	2-6	5	6
β-strand	12-16	5	6
β-strand	22	1	7
α-helix	23-34	12
α-helix	38-40	3
β-strand	41-45	5	6
β-strand	48-49	2	6
α-helix	50-51	2
β-strand	55	1	7
β-strand	66-71	6	6

Chain C: 2 helices, 7 β-strands

Element	Residues	Length	Sheet
α-helix	259-263	5
β-strand	266-269	4	3
β-strand	293	1	4
β-strand	300	1	4
β-strand	306-309	4	3
β-strand	315-317	3	3
α-helix	318-325	8
β-strand	330	1	5
β-strand	337	1	5

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Ubiquitin-conjugating enzyme E2 D2	A	protein	152	Homo sapiens	P62837 (AlphaFold model)
RING finger protein 165	C	protein	87	Homo sapiens	Q6ZSG1 (AlphaFold model)
Polyubiquitin-B	B	protein	76	Homo sapiens	P0CG47 (AlphaFold model)

Sequence of entity 1 (A), FASTA

>5D0M_1 Ubiquitin-conjugating enzyme E2 D2 (chains A)
GPLGSMALKRIHKELNDLARDPPAQSRAGPVGDDMFHWQATIMGPNDSPYQGGVFFLTIH
FPTDYPFKPPKVAFTTRIYHPNINSNGSIKLDILRSQWSPALTISKVLLSISSLLSDPNP
DDPLVPEIARIYKTDREKYNRIAREWTQKYAM

Sequence of entity 2 (C), FASTA

>5D0M_2 RING finger protein 165 (chains C)
GPLGSGAVQNTIERFTFPHKYKKDEGEESDTDEKCTICLSMLEDGEDVRRLPCAHLFHQL
CVDQWLAMSKKCPICRVDIETQLGADS

Sequence of entity 3 (B), FASTA

>5D0M_3 Polyubiquitin-B (chains B)
MQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLSDYN
IQKESTLHLVLRLRGG

Ligands and cofactors

ID	Name	Formula	Copies
ZN	Zinc ion	Zn	2
PO4	Phosphate ion	O4 P	1

Primary citation

Secondary ubiquitin-RING docking enhances Arkadia and Ark2C E3 ligase activity. Wright, J.D., Mace, P.D., Day, C.L. Nat Struct Mol Biol (2016) 23:45-52. DOI 10.1038/nsmb.3142 · PubMed

Other PDB entries of the same protein (UniProt P62837 (AlphaFold model), which also has an AlphaFold model), best resolution first:

9GLS 1.25 Å, Crystal Structure of Human UBCH5B C85E
2ESK 1.36 Å, Human Ubiquitin-Conjugating Enzyme (E2) UbcH5b, wild-type
6SQO 1.41 Å, Crystal structure of human MDM2 RING domain homodimer bound to UbcH5B-Ub
2ESQ 1.44 Å, Human Ubiquitin-Conjugating Enzyme (E2) UbcH5b mutant Ser94Gly
2ESO 1.5 Å, Human Ubiquitin-Conjugating Enzyme (E2) UbcH5b mutant Ile37Ala
2ESP 1.52 Å, Human ubiquitin-conjugating enzyme (E2) UbcH5b mutant Ile88Ala
4V3L 1.53 Å, RNF38-UB-UbcH5B-Ub complex
7AI0 1.56 Å, Crystal structure of human MDM2-G443T RING domain homodimer bound to UbcH5B-Ub (Crystal…
5D1M 1.58 Å, Crystal Structure of UbcH5B in Complex with the RING-U5BR Fragment of AO7 (P199A)
3L1Y 1.6 Å, Crystal structure of human UBC4 E2 conjugating enzyme
5D1L 1.62 Å, Crystal Structure of UbcH5B in Complex with the RING-U5BR Fragment of AO7 (Y165A)
6HPR 1.7 Å, Crystal structure of cIAP1 RING domain bound to UbcH5B-Ub and a non-covalent Ub

Browse structure collections

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