MolNFT v1 · #174921 · protein

Cyclic LYS48-linked triubiquitin

7CAP: “Cyclic LYS48-linked triubiquitin”. X-ray diffraction, 1 ligand (ZN), 2 pockets (best druggability 0.76). MolNFT v1 #174921 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 7CAP
Type: protein
Length: 228 residues
Chains: 3
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Ubiquitin
UniProt: P0CG47
Ligands: ZN
Pockets: 2 · best druggability 0.76

Structure

x-ray diffraction · 1 distinct chain · 24% helix, 34% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B, C	Ubiquitin	protein	76	24% helix, 34% strand	P0CG47

Ligands and binding sites

ZN · Zinc ion · metal · 6 copies · chains A, B, C

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

Pockets

2 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	603	0.76	0.82	57	ZN
2	171	0.53	0.79	29	ZN

Interfaces

3 interfaces between chains.

B–C · 398 Å² buried · 4 hydrogen bonds · protein-protein
A–B · 334 Å² buried · 2 hydrogen bonds · protein-protein
A–C · 304 Å² buried · 5 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 3 isopeptide (isopeptide).

Compared structures

7CAP · Cyclic Lys48-linked triubiquitin · 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 P0CG47
Elsewhere: RCSB PDB 7CAP · PDBe 7CAP · UniProt P0CG47

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