9L3L: C lobe of E6AP

Crystal structure of the C lobe of E6AP in complex with K48-linked diUb. Determined by X-ray diffraction at 2.59 Å resolution. Released 24 Dec 2025.

Method: X-ray diffraction
Resolution: 2.59 Å
Organism: Homo sapiens
Chains: 3
Atoms: 2,075
Mol. weight: 29.29 kDa
Released: 24 Dec 2025

Explore 9L3L in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

9L3L contains 14 α-helices and 20 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, 5 β-strands

Element	Residues	Length	Sheet
α-helix	767-772	6
β-strand	775-777	3	1
α-helix	785-795	11
α-helix	799-810	12
α-helix	815-816	2
α-helix	820-823	4
β-strand	826-829	4	1
α-helix	836-838	3
β-strand	839-841	3	1
β-strand	846-849	4	1
α-helix	855-868	14
β-strand	869	1	2

Chain B: 3 helices, 8 β-strands

Element	Residues	Length	Sheet
β-strand	2-6	5	2
β-strand	12-16	5	2
β-strand	22	1	3
α-helix	23-34	12
α-helix	38-40	3
β-strand	41-45	5	2
β-strand	48-49	2	2
α-helix	50-51	2
β-strand	55	1	3
β-strand	66-71	6	2
β-strand	74	1	1

Chain C: 4 helices, 7 β-strands

Element	Residues	Length	Sheet
β-strand	2-7	6	4
β-strand	12-16	5	4
β-strand	22	1	5
α-helix	23-34	12
α-helix	38-40	3
β-strand	41-45	5	4
β-strand	48-49	2	4
α-helix	50-51	2
β-strand	55	1	5
α-helix	57-59	3
β-strand	66-71	6	4

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Ubiquitin-protein ligase E3A	A	protein	108	Homo sapiens	Q05086 (AlphaFold model)
Donor Ubiquitin	B	protein	76	Homo sapiens	P62979 (AlphaFold model)
Acceptor Ubiquitin	C	protein	73	Homo sapiens	P62979 (AlphaFold model)

Sequence of entity 1 (A), FASTA

>9L3L_1 Ubiquitin-protein ligase E3A (chains A)
LDFQALEETTEYDGGYTRDSVLIREFWEIVHSFTDEQKRLFLQFTTGTDRAPVGGLGKLK
MIIAKNGPDTERLPTSHTCFNVLLLPEYSSKEKLKERLLKAITYAKGF

Sequence of entity 2 (B), FASTA

>9L3L_2 Donor Ubiquitin (chains B)
MQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLSDYN
IQKESTLHLVLRLRGG

Sequence of entity 3 (C), FASTA

>9L3L_3 Acceptor Ubiquitin (chains C)
MQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLSDYN
IQKESTLHLVLRL

Primary citation

Structural Insights into the Role of the C-Lobe of E6AP in Catalyzing K48-Linked Ubiquitin Chain Formation. Wu, X.W., Cai, H.Y., Du, Y.X. et al. To be published.

Other PDB entries of the same protein (UniProt Q05086 (AlphaFold model), which also has an AlphaFold model), best resolution first:

6TGK 1.3 Å, Domain swapped E6AP C-lobe dimer
6SJV 2.03 Å, Structure of HPV18 E6 oncoprotein in complex with mutant E6AP LxxLL motif
4XR8 2.25 Å, Crystal structure of the HPV16 E6/E6AP/p53 ternary complex at 2.25 A resolution
7QPB 2.34 Å, Catalytic C-lobe of the HECT-type ubiquitin ligase E6AP in complex with a hybrid…
4GIZ 2.55 Å, Crystal structure of full-length human papillomavirus oncoprotein E6 in complex with…
1C4Z 2.6 Å, Structure of an E6AP-UBCH7 complex: insights into the ubiquitination pathway
8JRN 2.6 Å, Structure of E6AP-E6 complex in Att1 state
1D5F 2.8 Å, Structure of E6AP: insights into ubiquitination pathway
6SLM 2.8 Å, Crystal structure of full-length HPV31 E6 oncoprotein in complex with LXXLL peptide of…
8JRO 3.01 Å, Structure of E6AP-E6 complex in Att2 state
7Q41 3.01 Å, Crystal structure of RCC1-Like domain 2 of ubiquitin ligase HERC2 in complex with…
9U4A 3.3 Å, Structure of UBE3A T485E tetramer

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