MolNFT v1 · #25250 · protein
X-ray structure of gene product from arabidopsis thaliana AT5G06450
1VK0 · Hypothetical protein: “X-ray structure of gene product from arabidopsis thaliana AT5G06450”. X-ray diffraction, 13 pockets (best druggability 0.70). MolNFT v1 #25250 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 1VK0
- Type
- protein
- Length
- 1,200 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Hypothetical protein
- UniProt
- Q9FNG3
- Pockets
- 13 · best druggability 0.70
Structure
x-ray diffraction · 1 distinct chain · 49% helix, 21% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D, E, F | Hypothetical protein | protein | 200 | 49% helix, 21% strand | Q9FNG3 |
Pockets
13 pockets found on a 1 Å grid, 9 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 686 | 0.70 | 0.77 | 74 | empty |
| 2 | 383 | 0.69 | 0.81 | 38 | empty |
| 3 | 375 | 0.66 | 0.80 | 34 | empty |
| 4 | 394 | 0.66 | 0.79 | 37 | empty |
| 5 | 396 | 0.66 | 0.79 | 36 | empty |
Interfaces
6 interfaces between chains.
- C–D · 1501 Ų buried · 20 hydrogen bonds · protein-protein
- A–B · 1485 Ų buried · 21 hydrogen bonds · protein-protein
- B–C · 1475 Ų buried · 22 hydrogen bonds · protein-protein
- E–F · 1444 Ų buried · 21 hydrogen bonds · protein-protein
- A–F · 1439 Ų buried · 20 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 6 modified (engineered).
Compared structures
- 1VK0 · X-ray Structure of Gene Product from Arabidopsis Thaliana At5g06450 · the same entry in another collection · chain D against D, TM-score 1.00
- Q9FNG3 · AlphaFold monomer V2.0 prediction for protein risc-interacting clearing 3'-5'… · a predicted model of the same protein · chain A against A, TM-score 0.98
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 Q9FNG3
- Elsewhere: RCSB PDB 1VK0 · PDBe 1VK0 · UniProt Q9FNG3
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