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Crystal structure of ILVN.VAL-1A

Analyse Crystal structure of ILVN.VAL-1A in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 5YPP
Type: protein
Length: 541 residues
Chains: 6
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: P0ADF8
Ligands: VAL
Pockets: 3 · best druggability 0.82

Structure

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

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B, C, D, F	Acetolactate synthase isozyme 1 small subunit (EC 2.2.1.6)	protein	90	33% helix, 32% strand	P0ADF8
E	Acetolactate synthase isozyme 1 small subunit (EC 2.2.1.6)	protein	91	32% helix, 34% strand	P0ADF8

Ligands and binding sites

VAL · Valine · ligand · 6 copies · chains A, B, C, D, E, F
PEG · Di(hydroxyethyl)ether · additive · 9 copies · chains A, B, C, D, E, F
ACT · Acetate ion · additive · chains F

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

Pockets

3 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	1051	0.82	0.83	108	PEG
2	113	0.47	0.80	21	empty
3	70	0.39	0.79	11	empty

Interfaces

9 interfaces between chains.

A–B · 1288 Å² buried · 23 hydrogen bonds · protein-protein
C–D · 1260 Å² buried · 22 hydrogen bonds · protein-protein
E–F · 1257 Å² buried · 20 hydrogen bonds · protein-protein
B–D · 377 Å² buried · 8 hydrogen bonds · protein-protein
D–F · 376 Å² buried · 7 hydrogen bonds · protein-protein

Compared structures

5YPP · Crystal structure of IlvN.Val-1a · the same entry in another collection · chain D against D, TM-score 1.00
P0ADF8 · AlphaFold monomer V2.0 prediction for acetolactate synthase isozyme 1 small subunit… · a predicted model of the same protein · chain A 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 P0ADF8
Elsewhere: RCSB PDB 5YPP · PDBe 5YPP · UniProt P0ADF8

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