Research workbench

Eqadh-NADH-heptafluorobutanol, P21

Analyse Eqadh-NADH-heptafluorobutanol, P21 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 6XT2
Type: protein
Length: 1,496 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Alcohol dehydrogenase E chain
EC: 1.1.1.1
UniProt: P00327
Ligands: NAI, B7F, ZN
Pockets: 9 · best druggability 0.77

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 E chain (EC 1.1.1.1)	protein	374	30% helix, 25% strand	P00327

Ligands and binding sites

NAI · 1,4-dihydronicotinamide adenine dinucleotide · ligand · 4 copies · chains A, B, C, D
B7F · 2,2,3,3,4,4,4-heptafluorobutan-1-ol · ligand · 4 copies · chains A, B, C, D
ZN · Zinc ion · metal · 8 copies · chains A, B, C, D
MRD · (4R)-2-methylpentane-2,4-diol · additive · 2 copies · chains B, C

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

Pockets

9 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	536	0.77	0.84	65	NAI, B7F
2	609	0.77	0.83	68	NAI, B7F
3	559	0.76	0.83	66	NAI, B7F
4	658	0.75	0.81	81	NAI, B7F
5	389	0.68	0.81	45	empty

Interfaces

5 interfaces between chains.

A–B · 1753 Å² buried · 30 hydrogen bonds · protein-protein
C–D · 1722 Å² buried · 33 hydrogen bonds · protein-protein
B–D · 231 Å² buried · 2 hydrogen bonds · protein-protein
A–C · 163 Å² buried · 2 hydrogen bonds · protein-protein
B–C · 58 Å² buried · 0 hydrogen bonds · protein-protein

Compared structures

6XT2 · Eqadh-NADH-heptafluorobutanol, P21 · the same entry in another collection · chain D against D, TM-score 1.00
P00327 · AlphaFold monomer V2.0 prediction for alcohol dehydrogenase E chain (P00327) · a predicted model of the same protein · chain C 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 P00327
Elsewhere: RCSB PDB 6XT2 · PDBe 6XT2 · UniProt P00327

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