MolNFT v1 · #60402 · protein
Crystal structure of the lipocalin domain of violaxanthin de-epoxidase (vde) at PH7
3CQN · Violaxanthin de-epoxidase, chloroplast: “Crystal structure of the lipocalin domain of violaxanthin de-epoxidase (vde) at PH7”. X-ray diffraction, 4 pockets (best druggability 0.56). MolNFT v1 #60402 on GenesisL1: 3D structure…
- PDB
- 3CQN
- Type
- protein
- Length
- 323 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Violaxanthin de-epoxidase, chloroplast
- EC
- 1.10.99.3
- UniProt
- Q39249
- Pockets
- 4 · best druggability 0.56
Structure
x-ray diffraction · 2 distinct chains · 14% helix, 46% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Violaxanthin de-epoxidase, chloroplast (EC 1.10.99.3) | protein | 162 | 14% helix, 45% strand | Q39249 |
| B | Violaxanthin de-epoxidase, chloroplast (EC 1.10.99.3) | protein | 161 | 14% helix, 47% strand | Q39249 |
Pockets
4 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 157 | 0.56 | 0.80 | 18 | empty |
| 2 | 156 | 0.55 | 0.80 | 19 | empty |
| 3 | 139 | 0.36 | 0.72 | 23 | empty |
| 4 | 72 | 0.29 | 0.73 | 12 | empty |
Interfaces
1 interface between chains.
- A–B · 77 Ų buried · 3 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 disulfide (disulfide).
Compared structures
- 3CQN · Crystal Structure of the Lipocalin domain of Violaxanthin de-epoxidase (VDE) at pH7 · the same entry in another collection · chain A against A, TM-score 1.00
- Q39249 · AlphaFold monomer V2.0 prediction for violaxanthin de-epoxidase, chloroplastic (Q39249) · a predicted model of the same protein · chain B against A, TM-score 0.97
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 Q39249
- Elsewhere: RCSB PDB 3CQN · PDBe 3CQN · UniProt Q39249
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