5D1K: UbcH5B

Crystal Structure of UbcH5B in Complex with the RING-U5BR Fragment of AO7. Determined by X-ray diffraction at 1.78 Å resolution. Released 28 Oct 2015.

Method: X-ray diffraction
Resolution: 1.78 Å
Organism: Homo sapiens
Chains: 2
Atoms: 2,494
Mol. weight: 32.86 kDa
Ligands: ZN, OXL
Released: 28 Oct 2015

Explore 5D1K in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

5D1K contains 15 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: 9 helices, 9 β-strands

Element	Residues	Length	Sheet
α-helix	3-15	13
α-helix	17-18	2
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	71	1	2
β-strand	75	1	3
β-strand	78	1	3
β-strand	83	1	1
β-strand	84	1	3
α-helix	87-89	3
α-helix	99-111	13
α-helix	121-129	9
α-helix	131-141	11
α-helix	142-146	5

Chain B: 6 helices, 7 β-strands

Element	Residues	Length	Sheet
β-strand	134	1	4
β-strand	141	1	4
β-strand	148-150	3	5
β-strand	156-158	3	5
α-helix	159-174	16
β-strand	197	1	6
α-helix	203	1
β-strand	204	1	6
α-helix	205-206	2
α-helix	209-214	6
α-helix	216-218	3
α-helix	229-247	19
β-strand	251	1	2

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Ubiquitin-conjugating enzyme E2 D2	A	protein	147	Homo sapiens	P62837 (AlphaFold model)
E3 ubiquitin-protein ligase RNF25	B	protein	133	Homo sapiens	Q96BH1 (AlphaFold model)

Sequence of entity 1 (A), FASTA

>5D1K_1 Ubiquitin-conjugating enzyme E2 D2 (chains A)
MALKRIHKELNDLARDPPAQCSAGPVGDDMFHWQATIMGPNDSPYQGGVFFLTIHFPTDY
PFKPPKVAFTTRIYHPNINSNGSICLDILRSQWSPALTISKVLLSICSLLCDPNPDDPLV
PEIARIYKTDREKYNRIAREWTQKYAM

Sequence of entity 2 (B), FASTA

>5D1K_2 E3 ubiquitin-protein ligase RNF25 (chains B)
TDNNIPHGQCVICLYGFQEKEAFTKTPCYHYFHCHCLARYIQHMEQELKAQGQEQEQERQ
HATTKQKAVGVQCPVCREPLVYDLASLKAAPEPQQPMELYQPSAESLRQQEERKRLYQRQ
QERGGIIDLEAER

Ligands and cofactors

ID	Name	Formula	Copies
ZN	Zinc ion	Zn	2
OXL	Oxalate ion	C2 O4	1

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

Primary citation

Insights into Ubiquitination from the Unique Clamp-like Binding of the RING E3 AO7 to the E2 UbcH5B. Li, S., Liang, Y.H., Mariano, J. et al. J Biol Chem (2015) 290:30225-30239. DOI 10.1074/jbc.M115.685867 · 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

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