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Structure of IDH2 mutant R140Q

Analyse Structure of IDH2 mutant R140Q in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 5SVO
Type: protein
Length: 799 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Isocitrate dehydrogenase [NADP], mitochondrial
EC: 1.1.1.42
UniProt: P48735
Ligands: NAP
Pockets: 8 · best druggability 0.56

Structure

x-ray diffraction · 2 distinct chains · 47% helix, 22% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Isocitrate dehydrogenase [NADP], mitochondrial (EC 1.1.1.42)	protein	410	47% helix, 21% strand	P48735
B	Isocitrate dehydrogenase [NADP], mitochondrial (EC 1.1.1.42)	protein	389	48% helix, 23% strand	P48735

Ligands and binding sites

NAP · Nadp nicotinamide-adenine-dinucleotide phosphate · ligand · 2 copies · chains A, B
EPE · 4-(2-hydroxyethyl)-1-piperazine ethanesulfonic acid · additive · chains A

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

Pockets

8 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	269	0.56	0.77	32	empty
2	335	0.56	0.75	42	empty
3	309	0.55	0.76	38	empty
4	285	0.54	0.75	42	NAP
5	198	0.54	0.78	24	empty

Interfaces

1 interface between chains.

A–B · 3200 Å² buried · 47 hydrogen bonds · protein-protein

Compared structures

5SVO · Structure of IDH2 mutant R140Q · the same entry in another collection · chain A against A, TM-score 1.00
P48735 · AlphaFold monomer V2.0 prediction for isocitrate dehydrogenase [NADP], mitochondrial… · a predicted model of the same protein · chain B against A, TM-score 0.93

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 P48735
Elsewhere: RCSB PDB 5SVO · PDBe 5SVO · UniProt P48735

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