MolNFT v1 · #120074 · protein

LYS27-linked di-ubiquitin

5GOD: “LYS27-linked di-ubiquitin”. X-ray diffraction, 1 ligand (MG), 1 pocket (best druggability 0.65). MolNFT v1 #120074 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 5GOD
Type: protein
Length: 304 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Ubiquitin; D-ubiquitin
UniProt: P0CG47
Ligands: MG
Pockets: 1 · best druggability 0.65

Structure

x-ray diffraction · 2 distinct chains · 24% helix, 34% strand (DSSP).

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

Ligands and binding sites

MG · Magnesium ion · metal · chains B

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

Pockets

1 pocket found on a 1 Å grid, 1 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	444	0.65	0.78	50	empty

Interfaces

5 interfaces between chains.

B–D · 744 Å² buried · 4 hydrogen bonds · protein-protein
A–C · 725 Å² buried · 4 hydrogen bonds · protein-protein
A–B · 567 Å² buried · 13 hydrogen bonds · protein-protein
C–D · 67 Å² buried · 3 hydrogen bonds · protein-protein
A–D · 23 Å² buried · 0 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 138 d-amino, 2 modified (D-amino acid, nonstandard).

Compared structures

5GOD · Lys27-linked di-ubiquitin · 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 5GOD · PDBe 5GOD · UniProt P0CG47

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