MolNFT v1 · #60406 · protein
Crystal structure of the lipocalin domain of violaxanthin de-epoxidase (vde) at PH5
3CQR · Violaxanthin de-epoxidase, chloroplast: “Crystal structure of the lipocalin domain of violaxanthin de-epoxidase (vde) at PH5”. X-ray diffraction, 1 ligand (GD), 1 pocket (best druggability 0.81). MolNFT v1 #60406 on GenesisL1: 3D…
- PDB
- 3CQR
- Type
- protein
- Length
- 341 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
- Ligands
- GD
- Pockets
- 1 · best druggability 0.81
Structure
x-ray diffraction · 2 distinct chains · 15% helix, 44% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Violaxanthin de-epoxidase, chloroplast (EC 1.10.99.3) | protein | 171 | 15% helix, 44% strand | Q39249 |
| B | Violaxanthin de-epoxidase, chloroplast (EC 1.10.99.3) | protein | 170 | 15% helix, 43% strand | Q39249 |
Ligands and binding sites
- GD · Gadolinium atom · metal · 3 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
1 pocket found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1066 | 0.81 | 0.83 | 93 | empty |
Interfaces
1 interface between chains.
- A–B · 1231 Ų buried · 12 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 disulfide (disulfide).
Compared structures
- 3CQR · Crystal Structure of the Lipocalin domain of Violaxanthin de-epoxidase (VDE) at pH5 · 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 A against A, TM-score 0.85
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 3CQR · PDBe 3CQR · UniProt Q39249
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