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3-isopropylmalate dehydrogenase from shewanella oneidensis mr-1 at atmospheric pressure

Analyse 3-isopropylmalate dehydrogenase from shewanella oneidensis mr-1 at atmospheric… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 3VKZ
Type: protein
Length: 364 residues
Chains: 1
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: 3-isopropylmalate dehydrogenase
EC: 1.1.1.85
UniProt: Q8E9N3
Ligands: IPM, CA, CL
Pockets: 3 · best druggability 0.57

Structure

x-ray diffraction · 1 distinct chain · 47% helix, 18% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	3-isopropylmalate dehydrogenase (EC 1.1.1.85)	protein	364	47% helix, 18% strand	Q8E9N3

Ligands and binding sites

IPM · 3-isopropylmalic acid · ligand · chains A
CA · Calcium ion · metal · chains A
CL · Chloride ion · ion · chains A

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

Pockets

3 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	306	0.57	0.76	38	empty
2	233	0.53	0.77	23	IPM, CA
3	119	0.48	0.79	22	empty

Compared structures

3VKZ · 3-isopropylmalate dehydrogenase from Shewanella oneidensis MR-1 at atmospheric pressure · the same entry in another collection · chain A against A, TM-score 1.00
Q8E9N3 · AlphaFold monomer V2.0 prediction for 3-isopropylmalate dehydrogenase (Q8E9N3) · a predicted model of the same protein · chain A against A, TM-score 0.99

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 Q8E9N3
Elsewhere: RCSB PDB 3VKZ · PDBe 3VKZ · UniProt Q8E9N3

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