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Crystal structure of the UAF1-USP12 complex in C2 space group

Analyse Crystal structure of the UAF1-USP12 complex in C2 space group in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 5K1A
Type: protein
Length: 3,307 residues
Chains: 8
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Ubiquitin carboxyl-terminal hydrolase 12; Wd repeat-containing protein 48
EC: 3.4.19.12
UniProt: O75317, Q8TAF3
Ligands: ZN
Pockets: 20 · best druggability 0.81

Structure

x-ray diffraction · 8 distinct chains · 18% helix, 41% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Ubiquitin carboxyl-terminal hydrolase 12 (EC 3.4.19.12)	protein	239	33% helix, 38% strand	O75317
B	Wd repeat-containing protein 48	protein	595	13% helix, 42% strand	Q8TAF3
C	Ubiquitin carboxyl-terminal hydrolase 12 (EC 3.4.19.12)	protein	236	30% helix, 38% strand	O75317
D	Wd repeat-containing protein 48	protein	597	13% helix, 42% strand	Q8TAF3
E	Ubiquitin carboxyl-terminal hydrolase 12 (EC 3.4.19.12)	protein	222	31% helix, 38% strand	O75317
F	Wd repeat-containing protein 48	protein	600	12% helix, 42% strand	Q8TAF3
G	Ubiquitin carboxyl-terminal hydrolase 12 (EC 3.4.19.12)	protein	224	31% helix, 40% strand	O75317
H	Wd repeat-containing protein 48	protein	594	13% helix, 42% strand	Q8TAF3

Ligands and binding sites

ZN · Zinc ion · metal · 4 copies · chains A, C, E, G

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

Pockets

20 pockets found on a 1 Å grid, 17 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	755	0.81	0.85	63	empty
2	759	0.81	0.84	64	empty
3	750	0.80	0.84	66	empty
4	760	0.80	0.84	61	empty
5	890	0.72	0.77	74	empty

Interfaces

11 interfaces between chains.

B–H · 1176 Å² buried · 17 hydrogen bonds · protein-protein
D–F · 1166 Å² buried · 17 hydrogen bonds · protein-protein
G–H · 799 Å² buried · 15 hydrogen bonds · protein-protein
E–F · 783 Å² buried · 16 hydrogen bonds · protein-protein
A–B · 770 Å² buried · 14 hydrogen bonds · protein-protein

Compared structures

5K1A · Crystal structure of the UAF1-USP12 complex in C2 space group · the same entry in another collection · chain H against H, TM-score 1.00
Q8TAF3 · AlphaFold monomer V2.0 prediction for wd repeat-containing protein 48 (Q8TAF3) · 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 O75317
Every structure of UniProt Q8TAF3
Elsewhere: RCSB PDB 5K1A · PDBe 5K1A · UniProt O75317 · UniProt Q8TAF3

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