2IO3: Human Senp2

Crystal structure of human Senp2 in complex with RanGAP1-SUMO-2. Determined by X-ray diffraction at 3.2 Å resolution. Released 14 Nov 2006.

Method: X-ray diffraction
Resolution: 3.2 Å
Organism: Homo sapiens
Chains: 3
Atoms: 3,664
Mol. weight: 55.28 kDa
Released: 14 Nov 2006

Explore 2IO3 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

2IO3 contains 24 α-helices and 18 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: 11 helices, 11 β-strands

Element	Residues	Length	Sheet
α-helix	370-373	4
β-strand	388	1	1
β-strand	392	1	2
β-strand	395	1	2
β-strand	398	1	1
α-helix	402-405	4
α-helix	409-410	2
β-strand	411	1	3
α-helix	413-419	7
α-helix	422-429	8
β-strand	435-437	3	4
α-helix	442-449	8
α-helix	455-458	4
β-strand	468-475	8	4
β-strand	477	1	3
β-strand	478-485	8	4
β-strand	490-494	5	4
α-helix	503-520	18
α-helix	526-528	3
β-strand	530-532	3	4
α-helix	548-558	11
α-helix	572-584	13

Chain B: 1 helix, 7 β-strands

Element	Residues	Length	Sheet
β-strand	21-23	3	5
β-strand	30-31	2	5
α-helix	41-49	9
β-strand	58-61	4	5
β-strand	62	1	6
β-strand	65	1	6
β-strand	83-88	6	5
β-strand	92	1	3

Chain C: 12 helices, 0 β-strands

Element	Residues	Length
α-helix	433-439	7
α-helix	443-447	5
α-helix	450-452	3
α-helix	453-459	7
α-helix	467-477	11
α-helix	484-502	19
α-helix	509-516	8
α-helix	528-536	9
α-helix	538-545	8
α-helix	556-560	5
α-helix	566-569	4
α-helix	573-584	12

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Sentrin-specific protease 2	A	protein	232	Homo sapiens	Q9HC62 (AlphaFold model)
Small ubiquitin-related modifier 2	B	protein	81	Homo sapiens	P61956 (AlphaFold model)
Ran GTPase-activating protein 1	C	protein	172	Homo sapiens	P46060 (AlphaFold model)

Sequence of entity 1 (A), FASTA

>2IO3_1 Sentrin-specific protease 2 (chains A)
GSHMASDLLELTEDMEKEISNALGHGPQDEILSSAFKLRITRGDIQTLKNYHWLNDEVIN
FYMNLLVERNKKQGYPALHVFSTFFYPKLKSGGYQAVKRWTKGVNLFEQEIILVPIHRKV
HWSLVVIDLRKKCLKYLDSMGQKGHRICEILLQYLQDESKTKRNSDLNLLEWTHHSMKPH
EIPQQLNGSDSGMFTCKYADYISRDKPITFTQHQMPLFRKKMVWEILHQQLL

Sequence of entity 2 (B), FASTA

>2IO3_2 Small ubiquitin-related modifier 2 (chains B)
MANDHINLKVAGQDGSVVQFKIKRHTPLSKLMKAYCERQGLSMRQIRFRFDGQPINETDT
PAQLEMEDEDTIDVFQQQTGG

Sequence of entity 3 (C), FASTA

>2IO3_3 Ran GTPase-activating protein 1 (chains C)
SLNTGEPAPVLSSPPPADVSTFLAFPSPEKLLRLGPKSSVLIAQQTDTSDPEKVVSAFLK
VSSVFKDEATVRMAVQDAVDALMQKAFNSSSFNSNTFLTRLLVHMGLLKSEDKVKAIANL
YGPLMALNHMVQQDYFPKALAPLLLAFVTKPNSALESSSFARHSLLQTLYKV

Primary citation

Structural basis for SENP2 protease interactions with SUMO precursors and conjugated substrates. Reverter, D., Lima, C.D. Nat Struct Mol Biol (2006) 13:1060-1068. DOI 10.1038/nsmb1168 · PubMed

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
5AEK 3.0 Å, Crystal structure of the human SENP2 C548S in complex with the human SUMO1 K48M F66W

Browse structure collections

About this viewer

MolViewer shows 2IO3 directly in your browser with nothing to install. Switch between cartoon, ball-and-stick, spacefill and surface views, color by chain, secondary structure or B-factor, measure distances, angles and dihedrals, and share or embed the view.