MolNFT v1 · #175540 · protein

Crystal structure of arabidopsis thaliana SOBIR1 kinase domain D489A mutant in complex with AMP-pnp and magnesium

7CTV · Leucine-rich repeat receptor-like…: “Crystal structure of arabidopsis thaliana SOBIR1 kinase domain D489A mutant in complex with AMP-pnp and…”. X-ray diffraction, 2 ligands (ANP, MG), 7 pockets (best druggability 0.79). MolNFT v1…

PDB: 7CTV
Type: protein
Length: 592 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Leucine-rich repeat receptor-like SERINE/THREONINE/TYROSINE-protein kinase SOBIR1
EC: 2.7.10.1, 2.7.11.1
UniProt: Q9SKB2
Ligands: ANP, MG
Pockets: 7 · best druggability 0.79

Structure

x-ray diffraction · 2 distinct chains · 46% helix, 13% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Leucine-rich repeat receptor-like SERINE/THREONINE/TYROSINE-protein kinase SOBIR1 (EC 2.7.10.1, 2.7.11.1)	protein	299	45% helix, 15% strand	Q9SKB2
B	Leucine-rich repeat receptor-like SERINE/THREONINE/TYROSINE-protein kinase SOBIR1 (EC 2.7.10.1, 2.7.11.1)	protein	293	47% helix, 11% strand	Q9SKB2

Ligands and binding sites

ANP · Phosphoaminophosphonic acid-adenylate ester · ligand · 2 copies · chains A, B
MG · Magnesium ion · metal · 2 copies · chains A, B

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

Pockets

7 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	753	0.79	0.83	61	MG, ANP
2	630	0.75	0.81	43	MG, ANP
3	341	0.65	0.80	55	empty
4	106	0.45	0.78	22	empty
5	83	0.41	0.78	21	empty

Interfaces

1 interface between chains.

A–B · 572 Å² buried · 4 hydrogen bonds · protein-protein

Compared structures

7CTV · Crystal structure of Arabidopsis thaliana SOBIR1 kinase domain D489A mutant in complex… · the same entry in another collection · chain A against A, TM-score 1.00
Q9SKB2 · AlphaFold monomer V2.0 prediction for leucine-rich repeat receptor- like… · a predicted model of the same protein · chain B against A, TM-score 0.87

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 Q9SKB2
Elsewhere: RCSB PDB 7CTV · PDBe 7CTV · UniProt Q9SKB2

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