MolNFT v1 · #134151 · protein

Structure of IDH2 mutant R172K

5SVN · Isocitrate dehydrogenase [NADP], mitochondrial: “Structure of IDH2 mutant R172K”. X-ray diffraction, 1 ligand (NDP), 7 pockets (best druggability 0.80). MolNFT v1 #134151 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 5SVN
Type: protein
Length: 806 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: NDP
Pockets: 7 · best druggability 0.80

Structure

x-ray diffraction · 2 distinct chains · 47% helix, 21% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Isocitrate dehydrogenase [NADP], mitochondrial (EC 1.1.1.42)	protein	399	47% helix, 21% strand	P48735
B	Isocitrate dehydrogenase [NADP], mitochondrial (EC 1.1.1.42)	protein	407	47% helix, 21% strand	P48735

Ligands and binding sites

NDP · Nadph dihydro-nicotinamide-adenine-dinucleotide phosphate · ligand · 2 copies · chains A, B
PEG · Di(hydroxyethyl)ether · additive · 2 copies · chains A, B

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

Pockets

7 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	887	0.80	0.82	77	PEG, NDP
2	742	0.79	0.83	69	NDP
3	201	0.50	0.76	23	empty
4	220	0.47	0.74	21	empty
5	82	0.40	0.78	19	empty

Interfaces

1 interface between chains.

A–B · 3995 Å² buried · 59 hydrogen bonds · protein-protein

Compared structures

5SVN · Structure of IDH2 mutant R172K · 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 0.96

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 5SVN · PDBe 5SVN · UniProt P48735

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