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NADH-dependent variant of cbadh

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

PDB: 6SCH
Type: protein
Length: 1,413 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: P25984
Ligands: NAD, ZN, MG
Pockets: 15 · best druggability 0.78

Structure

x-ray diffraction · 3 distinct chains · 32% helix, 26% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B	NADP-dependent isopropanol dehydrogenase (EC 1.1.1.80)	protein	352	32% helix, 26% strand	P25984
C	NADP-dependent isopropanol dehydrogenase (EC 1.1.1.80)	protein	355	32% helix, 26% strand	P25984
D	NADP-dependent isopropanol dehydrogenase (EC 1.1.1.80)	protein	354	32% helix, 26% strand	P25984

Ligands and binding sites

NAD · Nicotinamide-adenine-dinucleotide · ligand · 4 copies · chains A, B, C, D
ZN · Zinc ion · metal · 4 copies · chains A, B, C, D
MG · Magnesium ion · metal · 2 copies · chains A
2PE · Nonaethylene glycol · additive · 8 copies · chains A, B, C, D

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

Pockets

15 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	806	0.78	0.81	75	2PE
2	456	0.75	0.84	53	NAD, MG
3	447	0.75	0.84	52	NAD
4	452	0.74	0.83	55	NAD
5	573	0.73	0.81	55	empty

Interfaces

6 interfaces between chains.

A–B · 1748 Å² buried · 28 hydrogen bonds · protein-protein
C–D · 1735 Å² buried · 28 hydrogen bonds · protein-protein
A–D · 1104 Å² buried · 22 hydrogen bonds · protein-protein
B–C · 1094 Å² buried · 20 hydrogen bonds · protein-protein
B–D · 795 Å² buried · 12 hydrogen bonds · protein-protein

Compared structures

6SCH · NADH-dependent variant of CBADH · the same entry in another collection · chain D against D, TM-score 1.00
P25984 · AlphaFold monomer V2.0 prediction for NADP-dependent isopropanol dehydrogenase (P25984) · a predicted model of the same protein · chain B 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 P25984
Elsewhere: RCSB PDB 6SCH · PDBe 6SCH · UniProt P25984

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