Research workbench

Villin headpiece subdomain with a GLN26 to beta-3-homoglutamine substitution

Analyse Villin headpiece subdomain with a GLN26 to beta-3-homoglutamine substitution in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 5I1N
Type: protein
Length: 280 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: 5 · best druggability 0.60

Structure

x-ray diffraction · 2 distinct chains · 64% helix, 0% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B, C, D	Villin-1	protein	35	63% helix, 0% strand	P02640
E, F, G, H	D-villin headpiece subdomain	protein	35	66% helix, 0% strand	—

Pockets

5 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	377	0.60	0.76	42	empty
2	396	0.59	0.75	55	empty
3	113	0.39	0.74	19	empty
4	97	0.34	0.73	19	empty
5	56	0.31	0.76	16	empty

Interfaces

16 interfaces between chains.

C–F · 380 Å² buried · 4 hydrogen bonds · protein-protein
A–H · 362 Å² buried · 3 hydrogen bonds · protein-protein
D–E · 329 Å² buried · 4 hydrogen bonds · protein-protein
B–G · 324 Å² buried · 4 hydrogen bonds · protein-protein
E–G · 274 Å² buried · 0 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 132 d-amino, 4 modified (D-amino acid, nonstandard).

Compared structures

5I1N · Villin headpiece subdomain with a Gln26 to beta-3-homoglutamine substitution · the same entry in another collection · chain H against H, 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 0.89

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 5I1N · PDBe 5I1N · UniProt P02640

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