Research workbench

NADH-dependent variant of tbadh

Analyse NADH-dependent variant of tbadh in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 6SDM
Type: protein
Length: 1,416 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: NADP-dependent isopropanol dehydrogenase
EC: 1.1.1.80
UniProt: P14941
Ligands: ZN
Pockets: 12 · best druggability 0.76

Structure

x-ray diffraction · 1 distinct chain · 29% helix, 27% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B, C, D	NADP-dependent isopropanol dehydrogenase (EC 1.1.1.80)	protein	354	29% helix, 27% strand	P14941

Ligands and binding sites

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

12 pockets found on a 1 Å grid, 9 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	674	0.76	0.82	63	empty
2	1062	0.76	0.78	79	empty
3	1005	0.75	0.78	66	empty
4	566	0.73	0.80	59	empty
5	634	0.72	0.79	64	empty

Interfaces

6 interfaces between chains.

C–D · 1917 Å² buried · 36 hydrogen bonds · protein-protein
A–B · 1897 Å² buried · 42 hydrogen bonds · protein-protein
A–D · 1178 Å² buried · 22 hydrogen bonds · protein-protein
B–C · 1170 Å² buried · 19 hydrogen bonds · protein-protein
A–C · 776 Å² buried · 9 hydrogen bonds · protein-protein

Compared structures

6SDM · NADH-dependent variant of TBADH · the same entry in another collection · chain D against D, TM-score 1.00
P14941 · AlphaFold monomer V2.0 prediction for NADP-dependent isopropanol dehydrogenase (P14941) · a predicted model of the same protein · chain A 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 P14941
Elsewhere: RCSB PDB 6SDM · PDBe 6SDM · UniProt P14941

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