2G4D: Human SENP1 mutant

Crystal structure of human SENP1 mutant (C603S) in complex with SUMO-1. Determined by X-ray diffraction at 2.8 Å resolution. Released 17 Oct 2006.

Method: X-ray diffraction
Resolution: 2.8 Å
Organism: Homo sapiens
Chains: 4
Atoms: 4,716
Mol. weight: 66.95 kDa
Released: 17 Oct 2006

Explore 2G4D in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

2G4D contains 32 α-helices and 30 β-strands across 4 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.

Chains A and C: 12 helices, 9 β-strands

Element	Residues	Length	Sheet
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	484	1	3
β-strand	490-492	3	4
α-helix	497-504	8
α-helix	506-508	3
α-helix	518-520	3
β-strand	523-529	7	4
β-strand	534-540	7	4
β-strand	545-549	5	4
α-helix	557-573	17
β-strand	585-588	4	4
α-helix	595-597	3
α-helix	603-615	13
α-helix	624-626	3
α-helix	627-640	14

Chains B and D: 4 helices, 6 β-strands

Element	Residues	Length	Sheet
β-strand	21-27	7	5
β-strand	33-39	7	5
α-helix	45-55	11
α-helix	59-61	3
β-strand	62-66	5	5
β-strand	69-70	2	5
α-helix	71-72	2
α-helix	77-80	4
β-strand	86-92	7	5
β-strand	95-96	2	2

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
SENP1 protein	A, C	protein	205	Homo sapiens	Q9P0U3 (AlphaFold model)
Small ubiquitin-related modifier 1	B, D	protein	78	Homo sapiens	P63165 (AlphaFold model)

Sequence of entity 1 (A, C), FASTA

>2G4D_1 SENP1 protein (chains A, C)
QDEVLSEAFRLTITRKDIQTLNHLNWLNDEIINFYMNMLMERSKEKGLPSVHAFNTFFFT
KLKTAGYQAVKRWTKKVDVFSVDILLVPIHLGVHWCLAVVDFRKKNITYYDSMGGINNEA
CRILLQYLKQESIDKKRKEFDTNGWQLFSKKSQEIPQQMNGSDSGMFACKYADCITKDRP
INFTQQHMPYFRKRMVWEILHRKLL

Sequence of entity 2 (B, D), FASTA

>2G4D_2 Small ubiquitin-related modifier 1 (chains B, D)
EYIKLKVIGQDSSEIHFKVKMTTHLKKLKESYCQRQGVPMNSLRFLFEGQRIADNHTPKE
LGMEEEDVIEVYQEQTGG

Primary citation

Crystal structure of the SENP1 mutant C603S-SUMO complex reveals the hydrolytic mechanism of SUMO-specific protease. Xu, Z., Chau, S.F., Lam, K.H. et al. Biochem J (2006) 398:345-352. DOI 10.1042/BJ20060526 · 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
6NNQ 2.62 Å, Non-covalent structure of SENP1 in complex with SUMO2
2IY0 2.77 Å, SENP1 (mutant) SUMO1 RanGAP
2CKH 3.2 Å, SENP1-SUMO2 complex
2IYD 3.2 Å, SENP1 covalent complex with SUMO-2

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