MolNFT v1 · #180024 · protein

Structure of mtb lpd bound to 010705

7KMY · Dihydrolipoyl dehydrogenase: “Structure of mtb lpd bound to 010705”. X-ray diffraction, 2 ligands (FAD, WPM), 20 pockets (best druggability 0.84). MolNFT v1 #180024 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 7KMY
Type: protein
Length: 3,720 residues
Chains: 8
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Dihydrolipoyl dehydrogenase
EC: 1.8.1.4
UniProt: P9WHH9
Ligands: FAD, WPM
Pockets: 20 · best druggability 0.84

Structure

x-ray diffraction · 1 distinct chain · 35% helix, 28% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B, C, D, I, J, M, N	Dihydrolipoyl dehydrogenase (EC 1.8.1.4)	protein	465	35% helix, 28% strand	P9WHH9

Ligands and binding sites

FAD · Flavin-adenine dinucleotide · ligand · 8 copies · chains A, B, C, D, I, J, M, N
WPM · N~2~-methyl-N~2~-[(5-methyl-1H-indazol-7-yl)sulfonyl]-N-(1-methyl-2-oxo-1,2-dihydropyridin-4-yl)glycinamide · ligand · 8 copies · chains A, B, C, D, N, I, J, M
GOL · Glycerol · additive · 37 copies · chains A, B, C, D, I, J, M, N

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	1111	0.84	0.85	119	GOL, WPM
2	184	0.82	0.97	36	empty
3	162	0.82	0.97	39	empty
4	1002	0.81	0.82	93	FAD, GOL
5	983	0.81	0.83	96	FAD, GOL

Interfaces

13 interfaces between chains.

C–D · 3785 Å² buried · 53 hydrogen bonds · protein-protein
I–J · 3748 Å² buried · 59 hydrogen bonds · protein-protein
M–N · 3724 Å² buried · 55 hydrogen bonds · protein-protein
A–B · 3706 Å² buried · 55 hydrogen bonds · protein-protein
C–I · 407 Å² buried · 3 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 8 disulfide (disulfide).

Compared structures

7KMY · Structure of Mtb Lpd bound to 010705 · the same entry in another collection · chain N against N, TM-score 1.00
P9WHH9 · AlphaFold monomer V2.0 prediction for dihydrolipoyl dehydrogenase (P9WHH9) · a predicted model of the same protein · chain C against A, TM-score 0.99

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 P9WHH9
Elsewhere: RCSB PDB 7KMY · PDBe 7KMY · UniProt P9WHH9

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