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Crystal structure of the apo-form of USP7 catalytic domain [V302K] mutant

Analyse Crystal structure of the apo-form of USP7 catalytic domain [V302K] mutant in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 5KYB
Type: protein
Length: 662 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Ubiquitin carboxyl-terminal hydrolase 7
EC: 3.4.19.12
UniProt: Q93009
Pockets: 8 · best druggability 0.59

Structure

x-ray diffraction · 2 distinct chains · 32% helix, 27% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Ubiquitin carboxyl-terminal hydrolase 7 (EC 3.4.19.12)	protein	330	33% helix, 28% strand	Q93009
B	Ubiquitin carboxyl-terminal hydrolase 7 (EC 3.4.19.12)	protein	332	32% helix, 27% strand	Q93009

Ligands and binding sites

GOL · Glycerol · additive · 2 copies · chains A, B

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

Pockets

8 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	252	0.59	0.79	38	GOL
2	200	0.56	0.80	38	GOL
3	90	0.45	0.80	19	empty
4	85	0.41	0.78	18	empty
5	70	0.35	0.76	16	empty

Compared structures

5KYB · Crystal structure of the apo-form of USP7 catalytic domain [V302K] mutant · the same entry in another collection · chain A against A, 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 Q93009
Elsewhere: RCSB PDB 5KYB · PDBe 5KYB · UniProt Q93009

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