Research workbench

Human SDH/NADH/INHIBITOR complex

Analyse Human SDH/NADH/INHIBITOR complex in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 1PL6
Type: protein
Length: 1,424 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Sorbitol dehydrogenase
EC: 1.1.1.14
UniProt: Q00796
Ligands: NAD, 572, ZN
Pockets: 17 · best druggability 0.71

Structure

x-ray diffraction · 1 distinct chain · 31% helix, 26% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B, C, D	Sorbitol dehydrogenase (EC 1.1.1.14)	protein	356	31% helix, 26% strand	Q00796

Ligands and binding sites

NAD · Nicotinamide-adenine-dinucleotide · ligand · 4 copies · chains A, B, C, D
572 · 4-[2-(hydroxymethyl)pyrimidin-4-yl]-N,N-dimethylpiperazine-1-sulfonamide · ligand · 4 copies · chains A, B, C, D
ZN · Zinc ion · metal · 4 copies · chains A, B, C, D

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

Pockets

17 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	689	0.71	0.78	69	ZN, NAD, 572
2	633	0.70	0.78	69	ZN, NAD, 572
3	557	0.68	0.78	54	ZN, NAD, 572
4	562	0.68	0.78	51	ZN, NAD, 572
5	302	0.62	0.79	49	empty

Interfaces

5 interfaces between chains.

A–B · 653 Å² buried · 2 hydrogen bonds · protein-protein
C–D · 650 Å² buried · 2 hydrogen bonds · protein-protein
A–D · 460 Å² buried · 6 hydrogen bonds · protein-protein
A–C · 18 Å² buried · 0 hydrogen bonds · protein-protein
B–D · 18 Å² buried · 0 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 32 modified (engineered).

Compared structures

1PL6 · Human SDH/NADH/inhibitor complex · the same entry in another collection · chain C against C, TM-score 1.00
Q00796 · AlphaFold monomer V2.0 prediction for sorbitol dehydrogenase (Q00796) · a predicted model of the same protein · chain B 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 Q00796
Elsewhere: RCSB PDB 1PL6 · PDBe 1PL6 · UniProt Q00796

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