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Mutant of human sigma alcohol dehydrogenase with leucine at position 141

Analyse Mutant of human sigma alcohol dehydrogenase with leucine at position 141 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 1D1T
Type: protein
Length: 1,492 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Alcohol dehydrogenase class IV sigma chain
EC: 1.1.1.1
UniProt: P40394
Ligands: NAD, ZN
Pockets: 9 · best druggability 0.79

Structure

x-ray diffraction · 1 distinct chain · 30% helix, 25% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B, C, D	Alcohol dehydrogenase class IV sigma chain (EC 1.1.1.1)	protein	373	30% helix, 25% strand	P40394

Ligands and binding sites

NAD · Nicotinamide-adenine-dinucleotide · ligand · 4 copies · chains A, B, C, D
ZN · Zinc ion · metal · 19 copies · chains A, B, D, C
ACT · Acetate ion · additive · 13 copies · chains A, B, C, D
CAC · Cacodylate ion · additive · 5 copies · chains A, B

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

Pockets

9 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	565	0.79	0.85	70	ACT, NAD
2	595	0.78	0.84	67	ACT, NAD
3	624	0.77	0.83	86	ACT, NAD
4	1166	0.76	0.79	102	empty
5	522	0.76	0.84	75	ZN, ACT, NAD

Interfaces

4 interfaces between chains.

A–B · 1707 Å² buried · 26 hydrogen bonds · protein-protein
C–D · 1672 Å² buried · 26 hydrogen bonds · protein-protein
B–D · 287 Å² buried · 6 hydrogen bonds · protein-protein
B–C · 106 Å² buried · 1 hydrogen bond · protein-protein

Compared structures

1D1T · Mutant of human sigma alcohol dehydrogenase with leucine at position 141 · the same entry in another collection · chain D against D, TM-score 1.00
P40394 · AlphaFold monomer V2.0 prediction for all-trans-retinol dehydrogenase [NAD(+)] ADH7… · a predicted model of the same protein · chain D 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 P40394
Elsewhere: RCSB PDB 1D1T · PDBe 1D1T · UniProt P40394

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