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Crystal structure of the human SENP2 C548S in complex with the human SUMO1 K48M F66W

Analyse Crystal structure of the human SENP2 C548S in complex with the human SUMO1 K48M… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 5AEK
Type: protein
Length: 3,612 residues
Chains: 24
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Sentrin-specific protease 2; Small ubiquitin-related modifier 1
EC: 3.4.22.68
UniProt: Q9HC62, P63165
Pockets: 20 · best druggability 0.69

Structure

x-ray diffraction · 5 distinct chains · 40% helix, 19% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, G, I, K, O, U	Sentrin-specific protease 2 (EC 3.4.22.68)	protein	223	45% helix, 16% strand	Q9HC62
B, D, F, J, N, P, R, T, V, X	Small ubiquitin-related modifier 1	protein	78	19% helix, 36% strand	P63165
C, E, Q, S	Sentrin-specific protease 2 (EC 3.4.22.68)	protein	224	46% helix, 16% strand	Q9HC62
H, L	Small ubiquitin-related modifier 1	protein	77	23% helix, 29% strand	P63165
M, W	Sentrin-specific protease 2 (EC 3.4.22.68)	protein	222	43% helix, 18% strand	Q9HC62

Pockets

20 pockets found on a 1 Å grid, 20 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	585	0.69	0.78	65	empty
2	457	0.64	0.77	49	empty
3	281	0.62	0.80	28	empty
4	444	0.62	0.76	48	empty
5	300	0.62	0.79	30	empty

Interfaces

25 interfaces between chains.

Q–R · 1085 Å² buried · 18 hydrogen bonds · protein-protein
K–L · 1084 Å² buried · 27 hydrogen bonds · protein-protein
C–D · 1032 Å² buried · 26 hydrogen bonds · protein-protein
I–J · 1021 Å² buried · 16 hydrogen bonds · protein-protein
W–X · 996 Å² buried · 25 hydrogen bonds · protein-protein

Compared structures

5AEK · Crystal structure of the human SENP2 C548S in complex with the human SUMO1 K48M F66W · the same entry in another collection · chain K against K, TM-score 1.00

Analyse

Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
Every structure of UniProt Q9HC62
Every structure of UniProt P63165
Elsewhere: RCSB PDB 5AEK · PDBe 5AEK · UniProt Q9HC62 · UniProt P63165

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