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Structure of escherichia COLI adhp (ethanol-inducible dehydrogenase) with bound NAD

Analyse Structure of escherichia COLI adhp (ethanol-inducible dehydrogenase) with bound… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 4GKV
Type: protein
Length: 1,354 residues
Chains: 5
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Alcohol dehydrogenase, propanol-preferring; Cleaved peptide fragment corresponding to the…
EC: 1.1.1.1
UniProt: P39451
Ligands: NAD, ZN
Pockets: 14 · best druggability 0.80

Structure

x-ray diffraction · 2 distinct chains · 31% helix, 28% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B, C, D	Alcohol dehydrogenase, propanol-preferring (EC 1.1.1.1)	protein	336	32% helix, 29% strand	P39451
P	Cleaved peptide fragment corresponding to the C-terminal his tag	protein	10	0% helix, 0% strand	—

Ligands and binding sites

NAD · Nicotinamide-adenine-dinucleotide · ligand · 4 copies · chains A, D, B, C
ZN · Zinc ion · metal · 8 copies · chains A, B, C, D
GOL · Glycerol · additive · 2 copies · chains B, C

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

Pockets

14 pockets found on a 1 Å grid, 10 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	913	0.80	0.82	98	empty
2	291	0.77	0.88	48	NAD
3	321	0.75	0.87	51	NAD
4	334	0.75	0.86	52	NAD
5	389	0.74	0.85	57	NAD

Interfaces

8 interfaces between chains.

A–D · 1540 Å² buried · 25 hydrogen bonds · protein-protein
B–C · 1532 Å² buried · 25 hydrogen bonds · protein-protein
A–C · 588 Å² buried · 8 hydrogen bonds · protein-protein
B–D · 579 Å² buried · 7 hydrogen bonds · protein-protein
C–D · 544 Å² buried · 9 hydrogen bonds · protein-protein

Compared structures

4GKV · Structure of Escherichia coli AdhP (ethanol-inducible dehydrogenase) with bound NAD · the same entry in another collection · chain P against P, TM-score 1.00
P39451 · AlphaFold monomer V2.0 prediction for alcohol dehydrogenase, propanol-preferring (P39451) · a predicted model of the same protein · chain C against A, TM-score 0.98

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 P39451
Elsewhere: RCSB PDB 4GKV · PDBe 4GKV · UniProt P39451

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