MolNFT v1 · #128132 · protein

Crystal structure of the human dihydrolipoamide dehydrogenase

5NHG · Dihydrolipoyl dehydrogenase, mitochondrial: “Crystal structure of the human dihydrolipoamide dehydrogenase”. X-ray diffraction, 1 ligand (FAD), 20 pockets (best druggability 0.86). MolNFT v1 #128132 on GenesisL1: 3D structure…

PDB: 5NHG
Type: protein
Length: 3,771 residues
Chains: 8
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Dihydrolipoyl dehydrogenase, mitochondrial
EC: 1.8.1.4
UniProt: P09622
Ligands: FAD
Pockets: 20 · best druggability 0.86

Structure

x-ray diffraction · 2 distinct chains · 35% helix, 27% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, E, F, G, H	Dihydrolipoyl dehydrogenase, mitochondrial (EC 1.8.1.4)	protein	471	35% helix, 27% strand	P09622
B, C, D	Dihydrolipoyl dehydrogenase, mitochondrial (EC 1.8.1.4)	protein	472	35% helix, 27% strand	P09622

Ligands and binding sites

FAD · Flavin-adenine dinucleotide · ligand · 8 copies · chains A, B, C, D, E, F, G, H
TRS · 2-amino-2-hydroxymethyl-propane-1,3-diol · additive · 7 copies · chains A, E, C, F, G
BTB · 2-[bis-(2-hydroxy-ethyl)-amino]-2-hydroxymethyl-propane-1,3-diol · additive · chains C

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

Pockets

20 pockets found on a 1 Å grid, 20 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	855	0.86	0.88	112	TRS
2	928	0.84	0.86	75	empty
3	758	0.84	0.87	71	empty
4	869	0.84	0.86	73	empty
5	805	0.83	0.86	70	empty

Interfaces

10 interfaces between chains.

G–H · 4101 Å² buried · 61 hydrogen bonds · protein-protein
A–B · 4049 Å² buried · 57 hydrogen bonds · protein-protein
C–D · 4043 Å² buried · 59 hydrogen bonds · protein-protein
E–F · 3979 Å² buried · 61 hydrogen bonds · protein-protein
B–F · 701 Å² buried · 2 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 8 disulfide (disulfide).

Compared structures

5NHG · Crystal structure of the human dihydrolipoamide dehydrogenase · the same entry in another collection · chain H against H, TM-score 1.00
P09622 · AlphaFold monomer V2.0 prediction for dihydrolipoyl dehydrogenase, mitochondrial (P09622) · a predicted model of the same protein · chain C against A, TM-score 1.00

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 P09622
Elsewhere: RCSB PDB 5NHG · PDBe 5NHG · UniProt P09622

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