MolNFT v1 · #121651 · protein

Villin headpiece subdomain with a LYS30 to beta-3-homolysine substitution

5I1P · Villin-1: “Villin headpiece subdomain with a LYS30 to beta-3-homolysine substitution”. X-ray diffraction, 4 pockets (best druggability 0.82). MolNFT v1 #121651 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 5I1P
Type: protein
Length: 277 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 0.82

Structure

x-ray diffraction · 4 distinct chains · 66% helix, 0% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, C	Villin-1	protein	34	71% helix, 0% strand	P02640
B, D	Villin-1	protein	35	63% helix, 0% strand	P02640
E, F, G	D-villin headpiece subdomain	protein	35	63% helix, 0% strand	—
H	D-villin headpiece subdomain	protein	34	68% helix, 0% strand	—

Ligands and binding sites

EOH · Ethanol · additive · 3 copies · chains A, H, B, C

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

Pockets

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

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	606	0.82	0.87	47	empty
2	115	0.43	0.77	16	empty
3	61	0.35	0.77	19	empty
4	59	0.29	0.73	17	empty

Interfaces

11 interfaces between chains.

A–F · 404 Å² buried · 4 hydrogen bonds · protein-protein
B–G · 395 Å² buried · 3 hydrogen bonds · protein-protein
D–G · 361 Å² buried · 5 hydrogen bonds · protein-protein
A–E · 353 Å² buried · 3 hydrogen bonds · protein-protein
A–H · 296 Å² buried · 4 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 131 d-amino, 4 modified (D-amino acid, nonstandard).

Compared structures

5I1P · Villin headpiece subdomain with a Lys30 to beta-3-homolysine substitution · the same entry in another collection · chain E against E, 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 0.90

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 5I1P · PDBe 5I1P · UniProt P02640

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