Research workbench

Isopropylmalate dehydrogenase K232M mutant

Analyse Isopropylmalate dehydrogenase K232M mutant in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 5J34
Type: protein
Length: 1,436 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: 3-isopropylmalate dehydrogenase 2, chloroplastic
EC: 1.1.1.85
UniProt: P93832
Ligands: MG, SO4
Pockets: 13 · best druggability 0.69

Structure

x-ray diffraction · 1 distinct chain · 48% helix, 21% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B, C, D	3-isopropylmalate dehydrogenase 2, chloroplastic (EC 1.1.1.85)	protein	359	48% helix, 21% strand	P93832

Ligands and binding sites

MG · Magnesium ion · metal · 4 copies · chains A, C, B, D
SO4 · Sulfate ion · ion · 6 copies · chains A, B, C, D

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

Pockets

13 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	671	0.69	0.77	52	MG, SO4
2	617	0.69	0.78	52	MG, SO4
3	574	0.68	0.78	50	empty
4	552	0.67	0.77	40	MG, SO4
5	550	0.67	0.77	39	MG, SO4

Interfaces

3 interfaces between chains.

A–C · 2297 Å² buried · 49 hydrogen bonds · protein-protein
B–D · 2284 Å² buried · 49 hydrogen bonds · protein-protein
A–B · 398 Å² buried · 7 hydrogen bonds · protein-protein

Compared structures

5J34 · Isopropylmalate dehydrogenase K232M mutant · the same entry in another collection · chain A against A, TM-score 1.00
P93832 · AlphaFold monomer V2.0 prediction for 3-isopropylmalate dehydrogenase 2, chloroplastic… · a predicted model of the same protein · chain A against A, TM-score 0.98

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 P93832
Elsewhere: RCSB PDB 5J34 · PDBe 5J34 · UniProt P93832

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