MolNFT v1 · #134894 · protein

Comprehensive analysis of a novel ketoreductase for pentangular polyphenol biosynthesis

5TII · 3-oxoacyl-acp reductase: “Comprehensive analysis of a novel ketoreductase for pentangular polyphenol biosynthesis”. X-ray diffraction, 1 ligand (NDP), 16 pockets (best druggability 0.85). MolNFT v1 #134894 on GenesisL1: 3D…

PDB: 5TII
Type: protein
Length: 1,915 residues
Chains: 8
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: 3-oxoacyl-acp reductase
UniProt: A0A023PKG5
Ligands: NDP
Pockets: 16 · best druggability 0.85

Structure

x-ray diffraction · 8 distinct chains · 48% helix, 17% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	3-oxoacyl-acp reductase	protein	241	49% helix, 17% strand	A0A023PKG5
D	3-oxoacyl-acp reductase	protein	244	45% helix, 16% strand	A0A023PKG5
E	3-oxoacyl-acp reductase	protein	238	49% helix, 17% strand	A0A023PKG5
G	3-oxoacyl-acp reductase	protein	232	48% helix, 16% strand	A0A023PKG5
H	3-oxoacyl-acp reductase	protein	233	46% helix, 17% strand	A0A023PKG5
B	3-oxoacyl-acp reductase	protein	241	49% helix, 17% strand	A0A023PKG5
C	3-oxoacyl-acp reductase	protein	236	49% helix, 17% strand	A0A023PKG5
F	3-oxoacyl-acp reductase	protein	250	50% helix, 16% strand	A0A023PKG5

Ligands and binding sites

NDP · Nadph dihydro-nicotinamide-adenine-dinucleotide phosphate · ligand · 3 copies · chains E, B, F

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

Pockets

16 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	974	0.85	0.86	70	empty
2	997	0.85	0.86	69	empty
3	1045	0.76	0.78	103	NDP
4	536	0.75	0.82	57	empty
5	1152	0.75	0.77	102	empty

Interfaces

13 interfaces between chains.

G–H · 1917 Å² buried · 34 hydrogen bonds · protein-protein
D–E · 1850 Å² buried · 29 hydrogen bonds · protein-protein
A–C · 1850 Å² buried · 29 hydrogen bonds · protein-protein
B–F · 1740 Å² buried · 36 hydrogen bonds · protein-protein
A–F · 1593 Å² buried · 30 hydrogen bonds · protein-protein

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 A0A023PKG5
Elsewhere: RCSB PDB 5TII · PDBe 5TII · UniProt A0A023PKG5

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