MolNFT v1 · #103495 · protein

Crystal structure of the ubiquitin K11S mutant

4PIG: “Crystal structure of the ubiquitin K11S mutant”. X-ray diffraction, 3 ligands (CA, NA, CL), 4 pockets (best druggability 0.58). MolNFT v1 #103495 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 4PIG
Type: protein
Length: 302 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Ubiquitin
UniProt: P62987
Ligands: CA, NA, CL
Pockets: 4 · best druggability 0.58

Structure

x-ray diffraction · 2 distinct chains · 22% helix, 34% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, C	Ubiquitin	protein	75	24% helix, 35% strand	P62987
B, D	Ubiquitin	protein	76	20% helix, 34% strand	P62987

Ligands and binding sites

CA · Calcium ion · metal · 4 copies · chains B, D
NA · Sodium ion · metal · chains B
CL · Chloride ion · ion · 8 copies · chains A, C, D

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

Pockets

4 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	203	0.58	0.80	36	CL
2	157	0.50	0.79	30	empty
3	118	0.47	0.79	28	empty
4	108	0.42	0.77	20	CL

Interfaces

6 interfaces between chains.

A–C · 845 Å² buried · 13 hydrogen bonds · protein-protein
A–D · 311 Å² buried · 1 hydrogen bond · protein-protein
B–D · 309 Å² buried · 3 hydrogen bonds · protein-protein
C–D · 289 Å² buried · 2 hydrogen bonds · protein-protein
A–B · 228 Å² buried · 5 hydrogen bonds · protein-protein

Compared structures

4PIG · Crystal structure of the ubiquitin K11S mutant · 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 4PIG · PDBe 4PIG · UniProt P62987

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