MolNFT v1 · #103498 · protein

X-ray crystal structure of the K11S/K63S double mutant of ubiquitin

4PIJ: “X-ray crystal structure of the K11S/K63S double mutant of ubiquitin”. X-ray diffraction, 1 ligand (SO4), 2 pockets (best druggability 0.39). MolNFT v1 #103498 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 4PIJ
Type: protein
Length: 150 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Ubiquitin
UniProt: P62987
Ligands: SO4
Pockets: 2 · best druggability 0.39

Structure

x-ray diffraction · 1 distinct chain · 24% helix, 33% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B	Ubiquitin	protein	75	24% helix, 33% strand	P62987

Ligands and binding sites

SO4 · Sulfate ion · ion · 5 copies · chains B, A
GOL · Glycerol · additive · chains A, B

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

Pockets

2 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	103	0.39	0.76	25	GOL, SO4
2	58	0.30	0.76	15	SO4

Interfaces

1 interface between chains.

A–B · 553 Å² buried · 7 hydrogen bonds · protein-protein

Compared structures

4PIJ · X-ray crystal structure of the K11S/K63S double mutant of ubiquitin · the same entry in another collection · chain A against A, TM-score 1.00
P62987 · AlphaFold monomer V2.0 prediction for ubiquitin-60S ribosomal protein L40 (P62987) · a predicted model of the same protein · chain A against A, TM-score 0.96

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 P62987
Elsewhere: RCSB PDB 4PIJ · PDBe 4PIJ · UniProt P62987

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