MolNFT v1 · #159225 · protein

Redox regulation of FN3K from arabidopsis thaliana

6OID · Protein-ribulosamine 3-kinase, chloroplastic: “Redox regulation of FN3K from arabidopsis thaliana”. X-ray diffraction, 3 ligands (ADP, SO4, CL), 4 pockets (best druggability 0.80). MolNFT v1 #159225 on GenesisL1: 3D structure…

PDB: 6OID
Type: protein
Length: 578 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Protein-ribulosamine 3-kinase, chloroplastic
EC: 2.7.1.172
UniProt: Q9LEW8
Ligands: ADP, SO4, CL
Pockets: 4 · best druggability 0.80

Structure

x-ray diffraction · 1 distinct chain · 44% helix, 20% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B	Protein-ribulosamine 3-kinase, chloroplastic (EC 2.7.1.172)	protein	289	44% helix, 20% strand	Q9LEW8

Ligands and binding sites

ADP · Adenosine-5'-diphosphate · ligand · 2 copies · chains A, B
SO4 · Sulfate ion · ion · 14 copies · chains A, B
CL · Chloride ion · ion · 2 copies · chains A, B
EDO · 1,2-ethanediol · additive · 5 copies · chains A, B
DMS · Dimethyl sulfoxide · additive · 2 copies · chains A, B

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

Pockets

4 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	1189	0.80	0.82	110	ADP, CL, EDO, DMS
2	240	0.61	0.81	33	empty
3	276	0.61	0.80	37	empty
4	56	0.27	0.74	19	empty

Interfaces

1 interface between chains.

A–B · 2674 Å² buried · 39 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 2 disulfide (disulfide).

Compared structures

6OID · Redox Regulation of FN3K from Arabidopsis thaliana · the same entry in another collection · chain A against A, TM-score 1.00
Q9LEW8 · AlphaFold monomer V2.0 prediction for protein-ribulosamine 3-kinase, chloroplastic… · a predicted model of the same protein · chain A against A, TM-score 0.90

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 Q9LEW8
Elsewhere: RCSB PDB 6OID · PDBe 6OID · UniProt Q9LEW8

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