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Crystalstructure of the ubiquitin protease

Analyse Crystalstructure of the ubiquitin protease in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 3VON
Type: protein
Length: 6,411 residues
Chains: 42
Method: x-ray diffraction
Collection: MolNFT v2 / PDB Bank
Contract: 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
Owner: 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
Resolution: 3.15
Source: Homo sapiens
Molecule: Ubiquitin thioesterase OTUB1; Ubiquitin-conjugating enzyme E2 variant 2…
EC: 3.4.19.12, 6.3.2.19
UniProt: Q96FW1, Q15819, P61088
Pockets: 20 · best druggability 0.85

Structure

x-ray diffraction · resolution 3.15 · 10 distinct chains · 47% helix, 15% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Ubiquitin thioesterase OTUB1 (EC 3.4.19.12)	protein	210	57% helix, 12% strand	Q96FW1
B, F, I, K, M, P, T, a, d, h, k, o	Ubiquitin-conjugating enzyme E2 variant 2	protein	138	21% helix, 19% strand	Q15819
C, E, G, J, L, N, Q, U, X, b, e, l, n	Ubiquitin-conjugating enzyme E2 N (EC 6.3.2.19)	protein	147	35% helix, 18% strand	P61088
D, R, W, Y, f, m	Ubiquitin-conjugating enzyme E2 variant 2	protein	137	23% helix, 20% strand	Q15819
H	Ubiquitin thioesterase OTUB1 (EC 3.4.19.12)	protein	214	55% helix, 12% strand	Q96FW1
O	Ubiquitin thioesterase OTUB1 (EC 3.4.19.12)	protein	216	56% helix, 13% strand	Q96FW1
S, Z, g, i, p	Ubiquitin-conjugating enzyme E2 N (EC 6.3.2.19)	protein	148	34% helix, 20% strand	P61088
V	Ubiquitin thioesterase OTUB1 (EC 3.4.19.12)	protein	215	54% helix, 13% strand	Q96FW1
c	Ubiquitin thioesterase OTUB1 (EC 3.4.19.12)	protein	217	55% helix, 13% strand	Q96FW1
j	Ubiquitin thioesterase OTUB1 (EC 3.4.19.12)	protein	210	51% helix, 11% strand	Q96FW1

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	1082	0.85	0.85	99	empty
2	1086	0.83	0.84	100	empty
3	840	0.83	0.86	90	empty
4	1001	0.83	0.84	109	empty
5	738	0.77	0.82	68	empty

Interfaces

98 interfaces between chains.

m–n · 841 Å² buried · 5 hydrogen bonds · protein-protein
D–E · 834 Å² buried · 4 hydrogen bonds · protein-protein
Y–Z · 813 Å² buried · 5 hydrogen bonds · protein-protein
f–g · 809 Å² buried · 5 hydrogen bonds · protein-protein
K–L · 805 Å² buried · 6 hydrogen bonds · protein-protein

Compared structures

3VON · Crystalstructure of the ubiquitin protease · the same entry in another collection · chain J against J, 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 Q96FW1
Every structure of UniProt Q15819
Every structure of UniProt P61088
Elsewhere: RCSB PDB 3VON · PDBe 3VON · UniProt Q96FW1 · UniProt Q15819 · UniProt P61088

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