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Villin headpiece subdomain with a LYS30 to apc substitution

Analyse Villin headpiece subdomain with a LYS30 to apc substitution in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 5I1S
Type: protein
Length: 140 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Villin-1; D-villin headpiece subdomain
UniProt: P02640
Pockets: 1 · best druggability 0.49

Structure

x-ray diffraction · 2 distinct chains · 67% helix, 0% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B	Villin-1	protein	35	66% helix, 0% strand	P02640
C, D	D-villin headpiece subdomain	protein	35	69% helix, 0% strand	—

Pockets

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

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	190	0.49	0.76	38	empty

Interfaces

5 interfaces between chains.

B–D · 214 Å² buried · 6 hydrogen bonds · protein-protein
C–D · 211 Å² buried · 4 hydrogen bonds · protein-protein
A–C · 209 Å² buried · 6 hydrogen bonds · protein-protein
A–B · 209 Å² buried · 2 hydrogen bonds · protein-protein
A–D · 94 Å² buried · 2 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 66 d-amino, 2 modified (D-amino acid, nonstandard).

Compared structures

5I1S · Villin headpiece subdomain with a Lys30 to APC substitution · the same entry in another collection · chain A against A, 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 0.84

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 5I1S · PDBe 5I1S · UniProt P02640

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