MolNFT v1 · #113410 · protein

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

5AEK · Sentrin-specific protease 2: “Crystal structure of the human SENP2 C548S in complex with the human SUMO1 K48M F66W”. X-ray diffraction, 20 pockets (best druggability 0.69). MolNFT v1 #113410 on GenesisL1: 3D structure, binding sites…

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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