MolNFT v1 · #161971 · protein
Structural signatures in EPR3 define a unique class of plant carbohydrate receptors
6QUP · Lysm type receptor kinase: “Structural signatures in EPR3 define a unique class of plant carbohydrate receptors”. X-ray diffraction, 1 ligand (NAG), 5 pockets (best druggability 0.63). MolNFT v1 #161971 on GenesisL1: 3D structure…
- PDB
- 6QUP
- Type
- protein
- Length
- 301 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Lysm type receptor kinase; Nanobody 186 (NB186)
- UniProt
- D3KU53
- Ligands
- NAG
- Pockets
- 5 · best druggability 0.63
Structure
x-ray diffraction · 2 distinct chains · 16% helix, 41% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Lysm type receptor kinase | protein | 182 | 21% helix, 34% strand | D3KU53 |
| B | Nanobody 186 (NB186) | protein | 119 | 8% helix, 52% strand | — |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · chains A
- EDO · 1,2-ethanediol · additive · 4 copies · chains A, B
- IPA · Isopropyl alcohol · additive · 3 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 151 | 0.63 | 0.85 | 21 | IPA, EDO |
| 2 | 207 | 0.60 | 0.81 | 31 | IPA |
| 3 | 78 | 0.41 | 0.79 | 14 | empty |
| 4 | 74 | 0.37 | 0.77 | 26 | EDO |
| 5 | 50 | 0.26 | 0.74 | 14 | empty |
Interfaces
1 interface between chains.
- A–B · 1015 Ų buried · 15 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 3 disulfide, 1 glycan (disulfide, N-glycosylation).
Compared structures
- 6QUP · Structural signatures in EPR3 define a unique class of plant carbohydrate receptors · the same entry in another collection · chain A against A, TM-score 1.00
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 D3KU53
- Elsewhere: RCSB PDB 6QUP · PDBe 6QUP · UniProt D3KU53
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