MolNFT v1 · #140896 · protein

Crystal structure of ILVN.VAL-1B

5YPW · Acetolactate synthase isozyme 1 small subunit: “Crystal structure of ILVN.VAL-1B”. X-ray diffraction, 1 ligand (VAL), 7 pockets (best druggability 0.72). MolNFT v1 #140896 on GenesisL1: 3D structure, binding sites and pockets in…

PDB: 5YPW
Type: protein
Length: 721 residues
Chains: 8
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Acetolactate synthase isozyme 1 small subunit
EC: 2.2.1.6
UniProt: P0ADG0
Ligands: VAL
Pockets: 7 · best druggability 0.72

Structure

x-ray diffraction · 2 distinct chains · 33% helix, 33% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B, C, D, E, G, H	Acetolactate synthase isozyme 1 small subunit (EC 2.2.1.6)	protein	90	33% helix, 33% strand	P0ADG0
F	Acetolactate synthase isozyme 1 small subunit (EC 2.2.1.6)	protein	91	33% helix, 33% strand	P0ADG0

Ligands and binding sites

VAL · Valine · ligand · 8 copies · chains A, B, C, D, E, F, G, H

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

Pockets

7 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	55	0.72	0.98	19	VAL
2	497	0.64	0.77	55	empty
3	366	0.57	0.75	34	empty
4	214	0.46	0.74	36	empty
5	66	0.40	0.80	12	empty

Interfaces

13 interfaces between chains.

G–H · 1276 Å² buried · 20 hydrogen bonds · protein-protein
C–D · 1264 Å² buried · 18 hydrogen bonds · protein-protein
A–B · 1248 Å² buried · 17 hydrogen bonds · protein-protein
E–F · 1217 Å² buried · 18 hydrogen bonds · protein-protein
E–H · 324 Å² buried · 4 hydrogen bonds · protein-protein

Compared structures

5YPW · Crystal structure of IlvN.Val-1b · the same entry in another collection · chain H against H, TM-score 1.00
P0ADG0 · AlphaFold monomer V2.0 prediction for acetolactate synthase isozyme 1 small subunit… · a predicted model of the same protein · chain H against A, TM-score 0.88

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 P0ADG0
Elsewhere: RCSB PDB 5YPW · PDBe 5YPW · UniProt P0ADG0

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