5AEK: Human SENP2 C548S

Crystal structure of the human SENP2 C548S in complex with the human SUMO1 K48M F66W. Determined by X-ray diffraction at 3.0 Å resolution. Released 20 Jan 2016.

Method: X-ray diffraction
Resolution: 3.0 Å
Organism: HOMO SAPIENS
Chains: 24
Atoms: 29,972
Mol. weight: 428.2 kDa
Released: 20 Jan 2016

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

Secondary structure: helices and β-sheets

5AEK contains 204 α-helices and 179 β-strands across 24 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: 15 helices, 8 β-strands

Element	Residues	Length	Sheet
α-helix	370-380	11
β-strand	388-392	5	1
β-strand	395-398	4	1
α-helix	399-402	4
α-helix	403-405	3
α-helix	409-410	2
β-strand	411-412	2	2
α-helix	413-429	17
β-strand	435-437	3	3
α-helix	442-454	13
α-helix	456-458	3
α-helix	463-465	3
β-strand	468-473	6	3
β-strand	480-485	6	3
β-strand	490-494	5	3
α-helix	502-515	14
α-helix	516-520	5
β-strand	530-533	4	3
α-helix	534-535	2
α-helix	540-542	3
α-helix	548-559	12
α-helix	569-571	3
α-helix	572-584	13

Chain B: 3 helices, 6 β-strands

Element	Residues	Length	Sheet
β-strand	22-28	7	4
β-strand	34-38	5	4
α-helix	45-55	11
β-strand	62-66	5	4
β-strand	69-70	2	4
α-helix	71	1
α-helix	77-80	4
β-strand	86-92	7	4
β-strand	95-96	2	2

Chain C: 16 helices, 8 β-strands

Element	Residues	Length	Sheet
α-helix	370-380	11
β-strand	388-391	4	5
β-strand	396-398	3	5
α-helix	399-403	5
α-helix	409-410	2
β-strand	411-412	2	6
α-helix	413-427	15
α-helix	432-434	3
β-strand	435-437	3	7
α-helix	442-448	7
α-helix	450-454	5
α-helix	455-458	4
α-helix	463-465	3
β-strand	468-475	8	7
β-strand	478-485	8	7
α-helix	486-488	3
β-strand	490-493	4	7
α-helix	502-519	18
α-helix	526-528	3
β-strand	530-533	4	7
α-helix	534-535	2
α-helix	548-559	12
α-helix	569-571	3
α-helix	572-584	13

Chain D: 4 helices, 7 β-strands

Element	Residues	Length	Sheet
β-strand	24-28	5	8
β-strand	34-36	3	8
α-helix	44-53	10
α-helix	59-61	3
β-strand	62-64	3	8
β-strand	65-66	2	9
β-strand	69-70	2	9
α-helix	71	1
α-helix	86-87	2
β-strand	88-92	5	8
β-strand	95-96	2	6

Chain E: 14 helices, 11 β-strands

Element	Residues	Length	Sheet
α-helix	370-380	11
β-strand	388-390	3	10
β-strand	397-398	2	10
α-helix	399-402	4
α-helix	403-405	3
α-helix	409-410	2
β-strand	411-412	2	11
α-helix	413-430	18
β-strand	435-437	3	12
α-helix	442-449	8
α-helix	451-454	4
α-helix	455-458	4
β-strand	468-475	8	12
β-strand	478-483	6	12
β-strand	485	1	13
β-strand	490	1	13
β-strand	493-494	2	12
α-helix	502-520	19
β-strand	530	1	13
α-helix	532	1
β-strand	533	1	12
α-helix	534-535	2
α-helix	536-538	3
α-helix	548-561	14
α-helix	571-585	15

Chain F: 2 helices, 6 β-strands

Element	Residues	Length	Sheet
β-strand	22-28	7	14
β-strand	34-38	5	14
α-helix	45-53	9
β-strand	62-66	5	14
β-strand	69-70	2	14
α-helix	77-80	4
β-strand	87-92	6	14
β-strand	95-96	2	11

Chain G: 15 helices, 8 β-strands

Element	Residues	Length	Sheet
α-helix	370-380	11
β-strand	388-392	5	15
β-strand	395-398	4	15
α-helix	399-403	5
α-helix	409-410	2
β-strand	411-412	2	16
α-helix	413-430	18
α-helix	432-434	3
β-strand	435-437	3	17
α-helix	442-449	8
α-helix	451-453	3
α-helix	455-458	4
α-helix	463-465	3
β-strand	468-475	8	17
β-strand	478-485	8	17
β-strand	490-494	5	17
α-helix	502-520	19
β-strand	530-533	4	17
α-helix	534-535	2
α-helix	540-542	3
α-helix	548-559	12
α-helix	569-571	3
α-helix	572-585	14

Chain H: 4 helices, 7 β-strands

Element	Residues	Length	Sheet
β-strand	24-26	3	18
β-strand	34-36	3	18
α-helix	45-55	11
α-helix	59-61	3
β-strand	62-66	5	19
β-strand	69-70	2	19
α-helix	71-72	2
α-helix	77-80	4
β-strand	86-88	3	18
β-strand	89-92	4	19
β-strand	95-96	2	16

16 more chain groups are not listed. Open the entry in the viewer and use the sequence panel to see them.

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Sentrin-specific protease 2	A, C, E, G, I, K, M, O, Q, S, U, W	protein	224	HOMO SAPIENS	Q9HC62 (AlphaFold model)
Small ubiquitin-related modifier 1	B, D, F, H, J, L, N, P, R, T, V, X	protein	78	HOMO SAPIENS	P63165 (AlphaFold model)

Sequence of entity 1 (A, C, E, G, I, K, M, O, Q, S, U, W), FASTA

>5AEK_1 SENTRIN-SPECIFIC PROTEASE 2 (chains A, C, E, G, I, K, M, O, Q, S, U, W)
LELTEDMEKEISNALGHGPQDEILSSAFKLRITRGDIQTLKNYHWLNDEVINFYMNLLVE
RNKKQGYPALHVFSTFFYPKLKSGGYQAVKRWTKGVNLFEQEIILVPIHRKVHWSLVVID
LRKKCLKYLDSMGQKGHRICEILLQYLQDESKTKRNSDLNLLEWTHHSMKPHEIPQQLNG
SDSGMFTCKYADYISRDKPITFTQHQMPLFRKKMVWEILHQQLL

Sequence of entity 2 (B, D, F, H, J, L, N, P, R, T, V, X), FASTA

>5AEK_2 SMALL UBIQUITIN-RELATED MODIFIER 1 (chains B, D, F, H, J, L, N, P, R, T, V, X)
EYIKLKVIGQDSSEIHFKVKMTTHLKKLMESYCQRQGVPMNSLRFLWEGQRIADNHTPKE
LGMEEEDVIEVYQEQTGG

Primary citation

Stepping Back and Forward on Sumo Folding Evolution. Grana-Montes, R., Gallego, P., Espargaro, A. et al. To be published.

Other PDB entries of the same protein (UniProt Q9HC62 (AlphaFold model), which also has an AlphaFold model), best resolution first:

3ZO5 2.15 Å, Structure of SENP2-Loop1 in complex with preSUMO-2
1TH0 2.2 Å, Structure of human Senp2
2IO0 2.3 Å, Crystal structure of human Senp2 in complex with preSUMO-2
2IO1 2.6 Å, Crystal structure of human Senp2 in complex with preSUMO-3
1TGZ 2.8 Å, Structure of human Senp2 in complex with SUMO-1
2IO2 2.9 Å, Crystal structure of human Senp2 in complex with RanGAP1-SUMO-1
2IO3 3.2 Å, Crystal structure of human Senp2 in complex with RanGAP1-SUMO-2

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