1D5F: E6AP: insights into ubiquitination pathway

Structure of E6AP: insights into ubiquitination pathway. Determined by X-ray diffraction at 2.8 Å resolution. Released 17 Nov 1999.

Method: X-ray diffraction
Resolution: 2.8 Å
Organism: Homo sapiens
Chains: 3
Atoms: 8,583
Mol. weight: 124.62 kDa
Released: 17 Nov 1999

Explore 1D5F in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

1D5F contains 55 α-helices and 42 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: 19 helices, 14 β-strands

Element	Residues	Length	Sheet
β-strand	502-504	3	1
α-helix	509-519	11
α-helix	525-529	5
β-strand	534-536	3	1
α-helix	546-559	14
α-helix	562-564	3
β-strand	567-569	3	2
β-strand	576-578	3	2
α-helix	588-601	14
α-helix	604-606	3
α-helix	613-618	6
α-helix	625-627	3
α-helix	628-631	4
α-helix	633-644	12
β-strand	656	1	3
β-strand	658-662	5	4
β-strand	668-672	5	4
β-strand	681	1	3
α-helix	687-699	13
α-helix	704-716	13
α-helix	729-737	9
β-strand	739	1	5
β-strand	752-754	3	6
α-helix	762-772	11
α-helix	776-786	11
β-strand	792	1	5
α-helix	797-800	4
β-strand	803-809	7	6
α-helix	813-815	3
β-strand	816-818	3	6
α-helix	819-821	3
β-strand	823-828	6	6
α-helix	832-845	14

Chain B: 18 helices, 14 β-strands

Element	Residues	Length	Sheet
β-strand	502-504	3	7
α-helix	509-522	14
α-helix	525-529	5
β-strand	534-536	3	7
α-helix	546-559	14
β-strand	567-570	4	8
β-strand	575-578	4	8
α-helix	586-599	14
α-helix	612-618	7
α-helix	625-631	7
α-helix	633-644	12
β-strand	656	1	9
β-strand	658-659	2	10
β-strand	671-672	2	10
α-helix	677-679	3
β-strand	681	1	9
α-helix	687-699	13
α-helix	701-703	3
α-helix	704-717	14
α-helix	730-737	8
β-strand	739	1	11
β-strand	752-754	3	12
α-helix	762-773	12
α-helix	778-786	9
β-strand	792	1	11
α-helix	797-800	4
β-strand	803-809	7	12
α-helix	814-815	2
β-strand	816-818	3	12
α-helix	819-821	3
β-strand	823-828	6	12
α-helix	832-843	12

Chain C: 18 helices, 14 β-strands

Element	Residues	Length	Sheet
β-strand	502-504	3	13
α-helix	509-523	15
α-helix	525-529	5
β-strand	534-536	3	13
α-helix	546-560	15
α-helix	562-564	3
β-strand	567-569	3	14
β-strand	576-578	3	14
α-helix	586-601	16
α-helix	612-618	7
α-helix	621-623	3
α-helix	628-631	4
α-helix	633-643	11
β-strand	656	1	15
β-strand	658-659	2	16
β-strand	671-672	2	16
β-strand	681	1	15
α-helix	686-699	14
α-helix	706-718	13
α-helix	722-725	4
α-helix	729-737	9
β-strand	739	1	17
β-strand	752-754	3	18
α-helix	762-773	12
α-helix	776-786	11
β-strand	792	1	17
α-helix	797-800	4
β-strand	803-806	4	18
α-helix	813-815	3
β-strand	816-818	3	18
β-strand	823-826	4	18
α-helix	832-844	13

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
E6AP hect catalytic domain, E3 ligase	A, B, C	protein	358	Homo sapiens	Q05086 (AlphaFold model)

Sequence of entity 1 (A, B, C), FASTA

>1D5F_1 E6AP HECT CATALYTIC DOMAIN, E3 LIGASE (chains A, B, C)
QLNPYLRLKVRRDHIIDDALVRLEMIAMENPADLKKQLYVEFEGEQGVDEGGVSKEFFQL
VVEEIFNPDIGMFTYDESTKLFWFNPSSFETEGQFTLIGIVLGLAIYNNCILDVHFPMVV
YRKLMGKKGTFRDLGDSHPVLYQSLKDLLEYEGNVEDDMMITFQISQTDLFGNPMMYDLK
ENGDKIPITNENRKEFVNLYSDYILNKSVEKQFKAFRRGFHMVTNESPLKYLFRPEEIEL
LICGSRNLDFQALEETTEYDGGYTRDSVLIREFWEIVHSFTDEQKRLFLQFTTGTDRAPV
GGLGKLKMIIAKNGPDTERLPTSHTCFNVLLLPEYSSKEKLKERLLKAITYAKGFGML

Primary citation

Structure of an E6AP-UbcH7 complex: insights into ubiquitination by the E2-E3 enzyme cascade. Huang, L., Kinnucan, E., Wang, G. et al. Science (1999) 286:1321-1326. DOI 10.1126/science.286.5443.1321 · PubMed

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…
9L3L 2.59 Å, Crystal structure of the C lobe of E6AP in complex with K48-linked diUb
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
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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