MolNFT v1 · #25878 · protein

Binary structure of human decr.

1W8D · 2,4-dienoyl-CoA reductase, mitochondrial precursor: “Binary structure of human decr.”. X-ray diffraction, 1 ligand (NAP), 15 pockets (best druggability 0.87). MolNFT v1 #25878 on GenesisL1: 3D structure, binding sites and pockets in…

PDB: 1W8D
Type: protein
Length: 1,134 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: 2,4-dienoyl-CoA reductase, mitochondrial precursor
EC: 1.3.1.34
UniProt: Q16698
Ligands: NAP
Pockets: 15 · best druggability 0.87

Structure

x-ray diffraction · 4 distinct chains · 52% helix, 14% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	2,4-dienoyl-CoA reductase, mitochondrial precursor (EC 1.3.1.34)	protein	288	52% helix, 14% strand	Q16698
B	2,4-dienoyl-CoA reductase, mitochondrial precursor (EC 1.3.1.34)	protein	282	52% helix, 14% strand	Q16698
C	2,4-dienoyl-CoA reductase, mitochondrial precursor (EC 1.3.1.34)	protein	284	51% helix, 14% strand	Q16698
D	2,4-dienoyl-CoA reductase, mitochondrial precursor (EC 1.3.1.34)	protein	280	52% helix, 15% strand	Q16698

Ligands and binding sites

NAP · Nadp nicotinamide-adenine-dinucleotide phosphate · ligand · 4 copies · chains A, B, C, D
GOL · Glycerol · additive · 2 copies · chains A, B, 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, 11 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	764	0.87	0.90	65	empty
2	540	0.67	0.77	51	NAP
3	530	0.66	0.77	50	NAP
4	375	0.62	0.78	40	NAP
5	420	0.62	0.77	46	NAP

Interfaces

6 interfaces between chains.

C–D · 2396 Å² buried · 21 hydrogen bonds · protein-protein
A–B · 2367 Å² buried · 21 hydrogen bonds · protein-protein
B–D · 1539 Å² buried · 29 hydrogen bonds · protein-protein
A–C · 1531 Å² buried · 28 hydrogen bonds · protein-protein
A–D · 1432 Å² buried · 15 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 30 modified (engineered).

Compared structures

1W8D · Binary structure of human DECR. · the same entry in another collection · chain D against D, TM-score 1.00
Q16698 · AlphaFold monomer V2.0 prediction for 2,4-dienoyl-CoA reductase… · a predicted model of the same protein · chain B 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 Q16698
Elsewhere: RCSB PDB 1W8D · PDBe 1W8D · UniProt Q16698

GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.