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USP14 catalytic domain mutant C114S

Analyse USP14 catalytic domain mutant C114S in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 6LVS
Type: protein
Length: 1,982 residues
Chains: 6
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Ubiquitin carboxyl-terminal hydrolase 14
EC: 3.4.19.12
UniProt: P54578
Ligands: NA
Pockets: 20 · best druggability 0.82

Structure

x-ray diffraction · 6 distinct chains · 29% helix, 32% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Ubiquitin carboxyl-terminal hydrolase 14 (EC 3.4.19.12)	protein	331	29% helix, 34% strand	P54578
B	Ubiquitin carboxyl-terminal hydrolase 14 (EC 3.4.19.12)	protein	330	29% helix, 33% strand	P54578
C	Ubiquitin carboxyl-terminal hydrolase 14 (EC 3.4.19.12)	protein	333	31% helix, 32% strand	P54578
D	Ubiquitin carboxyl-terminal hydrolase 14 (EC 3.4.19.12)	protein	329	31% helix, 32% strand	P54578
E	Ubiquitin carboxyl-terminal hydrolase 14 (EC 3.4.19.12)	protein	328	28% helix, 31% strand	P54578
F	Ubiquitin carboxyl-terminal hydrolase 14 (EC 3.4.19.12)	protein	331	28% helix, 30% strand	P54578

Ligands and binding sites

NA · Sodium ion · metal · 41 copies · chains A, B, C, D, E, F
FMT · Formic acid · additive · 26 copies · chains A, B, C, D, E, F
GOL · Glycerol · additive · 12 copies · chains A, C, B, D, E
BME · Beta-mercaptoethanol · additive · 9 copies · chains A, B, C, E, F
EDO · 1,2-ethanediol · additive · chains E

Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.

Pockets

20 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	1004	0.82	0.83	98	BME
2	745	0.78	0.82	71	GOL, NA, FMT
3	475	0.62	0.76	48	FMT
4	480	0.62	0.75	48	empty
5	298	0.56	0.76	35	empty

Interfaces

9 interfaces between chains.

A–C · 1184 Å² buried · 16 hydrogen bonds · protein-protein
A–F · 536 Å² buried · 6 hydrogen bonds · protein-protein
E–F · 381 Å² buried · 1 hydrogen bond · protein-protein
C–E · 377 Å² buried · 3 hydrogen bonds · protein-protein
B–C · 315 Å² buried · 4 hydrogen bonds · protein-protein

Compared structures

6LVS · USP14 catalytic domain mutant C114S · the same entry in another collection · chain F against F, TM-score 1.00
P54578 · AlphaFold monomer V2.0 prediction for ubiquitin carboxyl-terminal hydrolase 14 (P54578) · a predicted model of the same protein · chain B against A, TM-score 0.99

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 P54578
Elsewhere: RCSB PDB 6LVS · PDBe 6LVS · UniProt P54578

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