MolNFT v1 · #121650 · protein

Villin headpiece subdomain with a GLN26 to acpc substitution

5I1O · Villin-1: “Villin headpiece subdomain with a GLN26 to acpc substitution”. X-ray diffraction, 4 pockets (best druggability 0.64). MolNFT v1 #121650 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 5I1O
Type: protein
Length: 278 residues
Chains: 8
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Villin-1; D-villin headpiece subdomain
UniProt: P02640
Pockets: 4 · best druggability 0.64

Structure

x-ray diffraction · 3 distinct chains · 67% helix, 0% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B, C, D	Villin-1	protein	35	66% helix, 0% strand	P02640
E, H	D-villin headpiece subdomain	protein	35	66% helix, 0% strand	—
F, G	D-villin headpiece subdomain	protein	34	71% helix, 0% strand	—

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	493	0.64	0.76	51	empty
2	440	0.61	0.75	51	empty
3	134	0.44	0.76	21	empty
4	94	0.41	0.77	21	empty

Interfaces

17 interfaces between chains.

B–G · 364 Å² buried · 4 hydrogen bonds · protein-protein
A–H · 358 Å² buried · 4 hydrogen bonds · protein-protein
C–F · 353 Å² buried · 4 hydrogen bonds · protein-protein
D–E · 330 Å² buried · 3 hydrogen bonds · protein-protein
A–G · 235 Å² buried · 4 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 130 d-amino, 4 modified (D-amino acid, nonstandard).

Compared structures

5I1O · Villin headpiece subdomain with a Gln26 to ACPC substitution · the same entry in another collection · chain F against F, TM-score 1.00
P02640 · AlphaFold monomer V2.0 prediction for villin-1 (P02640) · a predicted model of the same protein · chain A against A, TM-score 0.93

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 P02640
Elsewhere: RCSB PDB 5I1O · PDBe 5I1O · UniProt P02640

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