MolNFT v1 · #119887 · protein
Crystal structure of tdr-tdif complex
5GIJ · Leucine-rich repeat receptor-like protein kinase tdr: “Crystal structure of tdr-tdif complex”. X-ray diffraction, 3 ligands (NAG, MAN, FUC). MolNFT v1 #119887 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 5GIJ
- Type
- protein
- Length
- 615 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Leucine-rich repeat receptor-like protein kinase tdr; Peptide from CLAVATA3/ESR…
- EC
- 2.7.11.1
- UniProt
- Q9FII5, Q84W98
- Ligands
- NAG, MAN, FUC
Structure
x-ray diffraction · 2 distinct chains · 19% helix, 19% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| B | Leucine-rich repeat receptor-like protein kinase tdr (EC 2.7.11.1) | protein | 603 | 20% helix, 20% strand | Q9FII5 |
| D | Peptide from CLAVATA3/ESR (cle)-related protein 41 | protein | 12 | 0% helix, 0% strand | Q84W98 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 18 copies · chains B
- MAN · alpha-D-mannopyranose · sugar · 5 copies
- FUC · alpha-L-fucopyranose · sugar · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Interfaces
1 interface between chains.
- B–D · 772 Ų buried · 11 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 11 glycan, 4 disulfide, 2 modified (N-glycosylation, disulfide, hydroxylation).
Compared structures
- 5GIJ · Crystal structure of TDR-TDIF complex · the same entry in another collection · chain B against B, 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 B against A, TM-score 0.98
- Q84W98 · AlphaFold monomer V2.0 prediction for CLAVATA3/ESR (cle)-related protein 41 (Q84W98) · a predicted model of the same protein · chain D against A, TM-score 0.21
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 Q84W98
- Elsewhere: RCSB PDB 5GIJ · PDBe 5GIJ · UniProt Q9FII5 · UniProt Q84W98
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