MolNFT v1 · #152015 · protein

Crystal structure of the disease-causing P453L mutant of the human dihydrolipoamide dehydrogenase

6I4Z · Dihydrolipoyl dehydrogenase, mitochondrial: “Crystal structure of the disease-causing P453L mutant of the human dihydrolipoamide dehydrogenase”. X-ray diffraction, 2 ligands (FAD, SO4), 20 pockets (best druggability 0.84). MolNFT v1…

PDB: 6I4Z
Type: protein
Length: 3,776 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, SO4
Pockets: 20 · best druggability 0.84

Structure

x-ray diffraction · 1 distinct chain · 36% helix, 27% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B, C, D, E, F, G, H	Dihydrolipoyl dehydrogenase, mitochondrial (EC 1.8.1.4)	protein	472	36% helix, 27% strand	P09622

Ligands and binding sites

FAD · Flavin-adenine dinucleotide · ligand · 8 copies · chains A, B, C, D, E, F, G, H
SO4 · Sulfate ion · ion · 27 copies · chains A, B, C, F, D, E, G, H

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	912	0.84	0.86	72	empty
2	881	0.84	0.86	77	empty
3	973	0.84	0.85	77	SO4
4	932	0.83	0.85	77	empty
5	915	0.81	0.83	99	FAD

Interfaces

12 interfaces between chains.

C–D · 4057 Å² buried · 60 hydrogen bonds · protein-protein
E–F · 4001 Å² buried · 52 hydrogen bonds · protein-protein
A–B · 3998 Å² buried · 60 hydrogen bonds · protein-protein
G–H · 3957 Å² buried · 54 hydrogen bonds · protein-protein
C–E · 654 Å² buried · 13 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 8 disulfide (disulfide).

Compared structures

6I4Z · Crystal structure of the disease-causing P453L mutant of the human dihydrolipoamide… · 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 D 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 6I4Z · PDBe 6I4Z · UniProt P09622

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