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Crystal structure of a tdif-tdr complex

Analyse Crystal structure of a tdif-tdr complex in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 5JFI
Type: protein
Length: 1,178 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Leucine-rich repeat receptor-like protein kinase tdr; CLE41
EC: 2.7.11.1
UniProt: Q9FII5, A0A178VDH8
Ligands: NAG
Pockets: 2 · best druggability 0.69

Structure

x-ray diffraction · 2 distinct chains · 15% helix, 20% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B	Leucine-rich repeat receptor-like protein kinase tdr (EC 2.7.11.1)	protein	577	15% helix, 20% strand	Q9FII5
C, D	CLE41	protein	12	0% helix, 0% strand	A0A178VDH8

Ligands and binding sites

NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 10 copies · chains A, B

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

Pockets

2 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	132	0.69	0.89	35	empty
2	103	0.67	0.91	25	empty

Interfaces

2 interfaces between chains.

B–D · 804 Å² buried · 13 hydrogen bonds · protein-protein
A–C · 803 Å² buried · 12 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 10 glycan, 4 disulfide, 4 modified (N-glycosylation, disulfide, hydroxylation).

Compared structures

5JFI · Crystal structure of a TDIF-TDR complex · the same entry in another collection · chain A against A, TM-score 1.00
Q9FII5 · AlphaFold monomer V2.0 prediction for leucine-rich repeat receptor- like protein kinase… · a predicted model of the same protein · chain A against A, TM-score 0.95

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 Q9FII5
Every structure of UniProt A0A178VDH8
Elsewhere: RCSB PDB 5JFI · PDBe 5JFI · UniProt Q9FII5 · UniProt A0A178VDH8

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