6NNQ: Non-covalent structure of SENP1

Non-covalent structure of SENP1 in complex with SUMO2. Determined by X-ray diffraction at 2.62 Å resolution. Released 8 May 2019.

Method: X-ray diffraction
Resolution: 2.62 Å
Organism: Homo sapiens
Chains: 2
Atoms: 2,540
Mol. weight: 35.55 kDa
Released: 8 May 2019

Explore 6NNQ in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

6NNQ contains 16 α-helices and 14 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: 14 helices, 8 β-strands

Element	Residues	Length	Sheet
α-helix	427-435	9
β-strand	443-447	5	1
β-strand	450-453	4	1
α-helix	454-457	4
α-helix	458-460	3
α-helix	464-465	2
β-strand	466-467	2	2
α-helix	468-481	14
β-strand	490-492	3	3
α-helix	497-504	8
α-helix	506-509	4
α-helix	510-513	4
α-helix	518-520	3
β-strand	523-529	7	3
β-strand	534-540	7	3
β-strand	545-549	5	3
α-helix	557-571	15
α-helix	578-580	3
β-strand	585-588	4	3
α-helix	602-614	13
α-helix	623-625	3
α-helix	626-639	14

Chain B: 2 helices, 6 β-strands

Element	Residues	Length	Sheet
β-strand	17-23	7	4
β-strand	31-35	5	4
α-helix	41-51	11
α-helix	55-57	3
β-strand	58-62	5	4
β-strand	65-66	2	4
β-strand	82-88	7	4
β-strand	91-92	2	2

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Sentrin-specific protease 1	A	protein	224	Homo sapiens	Q9P0U3 (AlphaFold model)
Small ubiquitin-related modifier 3	B	protein	78	Homo sapiens	P55854 (AlphaFold model)

Sequence of entity 1 (A), FASTA

>6NNQ_1 Sentrin-specific protease 1 (chains A)
APEITEEMEKEIKNVFRNGNQDEVLSEAFRLTITRKDIQTLNHLNWLNDEIINFYMNMLM
ERSKEKGLPSVHAFNTFFFTKLKTAGYQAVKRWTKKVDVFSVDILLVPIHLGVHWCLAVV
DFRKKNITYYDSMGGINNEACRILLQYLKQESIDKKRKEFDTNGWQLFSKKSQIPQQMNG
SDCGMFACKYADCITKDRPINFTQQHMPYFRKRMVWEILHRKLL

Sequence of entity 2 (B), FASTA

>6NNQ_2 Small ubiquitin-related modifier 3 (chains B)
DHINLKVAGQDGSVVQFKIKRHTPLSKLMKAYCERQGLSMRQIRFRFDGQPINETDTPAQ
LEMEDEDTIDVFQQQTGG

Primary citation

Noncovalent structure of SENP1 in complex with SUMO2. Ambaye, N.D. Acta Crystallogr F Struct Biol Commun (2019) 75:332-339. DOI 10.1107/S2053230X19004266 · PubMed

Other PDB entries of the same protein (UniProt Q9P0U3 (AlphaFold model), which also has an AlphaFold model), best resolution first:

2XPH 2.4 Å, Crystal structure of human SENP1 with the bound cobalt
2CKG 2.45 Å, The structure of SENP1 SUMO-2 co-complex suggests a structural basis for discrimination…
2IYC 2.45 Å, SENP1 native structure
2XRE 2.45 Å, Detection of cobalt in previously unassigned human SENP1 structure
2IY1 2.46 Å, SENP1 (mutant) full length SUMO1
2IY0 2.77 Å, SENP1 (mutant) SUMO1 RanGAP
2G4D 2.8 Å, Crystal structure of human SENP1 mutant (C603S) in complex with SUMO-1
2CKH 3.2 Å, SENP1-SUMO2 complex
2IYD 3.2 Å, SENP1 covalent complex with SUMO-2

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