MolNFT v1 · #165181 · protein
Monomeric LRX8 in complex with RALF4
6TME · Pollen-specific leucine-rich repeat extensin-like protein 1: “Monomeric LRX8 in complex with RALF4”. X-ray diffraction, 2 ligands (NAG, SO4), 3 pockets (best druggability 0.36). MolNFT v1 #165181 on GenesisL1: 3D structure, binding…
- PDB
- 6TME
- Type
- protein
- Length
- 741 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Pollen-specific leucine-rich repeat extensin-like protein 1; Protein ralf-like 4
- UniProt
- Q9LJ64, Q9FZA0
- Ligands
- NAG, SO4
- Pockets
- 3 · best druggability 0.36
Structure
x-ray diffraction · 4 distinct chains · 21% helix, 24% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Pollen-specific leucine-rich repeat extensin-like protein 1 | protein | 324 | 22% helix, 27% strand | Q9LJ64 |
| B | Pollen-specific leucine-rich repeat extensin-like protein 1 | protein | 324 | 21% helix, 27% strand | Q9LJ64 |
| C | Protein ralf-like 4 | protein | 47 | 19% helix, 0% strand | Q9FZA0 |
| D | Protein ralf-like 4 | protein | 46 | 17% helix, 0% strand | Q9FZA0 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 6 copies · chains A, C, B, D
- SO4 · Sulfate ion · ion · 12 copies · chains A, B, C, D
- GOL · Glycerol · additive · 4 copies · chains A, B, C
- EDO · 1,2-ethanediol · additive · 4 copies · chains A, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 90 | 0.36 | 0.75 | 21 | GOL |
| 2 | 91 | 0.35 | 0.74 | 21 | empty |
| 3 | 66 | 0.30 | 0.74 | 16 | empty |
Interfaces
3 interfaces between chains.
- A–C · 1610 Ų buried · 26 hydrogen bonds · protein-protein
- B–D · 1545 Ų buried · 23 hydrogen bonds · protein-protein
- A–B · 876 Ų buried · 15 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 11 disulfide, 4 glycan (disulfide, N-glycosylation).
Compared structures
- 6TME · Monomeric LRX8 in complex with RALF4. · the same entry in another collection · chain D against D, TM-score 1.00
- Q9LJ64 · AlphaFold monomer V2.0 prediction for pollen-specific leucine-rich repeat extensin-like… · a predicted model of the same protein · chain A against A, TM-score 1.00
- Q9FZA0 · AlphaFold monomer V2.0 prediction for protein ralf-like 4 (Q9FZA0) · a predicted model of the same protein · chain D 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 Q9LJ64
- Every structure of UniProt Q9FZA0
- Elsewhere: RCSB PDB 6TME · PDBe 6TME · UniProt Q9LJ64 · UniProt Q9FZA0
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