MolNFT v1 · #47938 · protein
1.7 ångström crystal structure of the photo-excited blue- light photoreceptor vivid
2PDR · Vivid pas protein vvd: “1.7 ångström crystal structure of the photo-excited blue- light photoreceptor vivid”. X-ray diffraction, 1 ligand (FAD), 8 pockets (best druggability 0.69). MolNFT v1 #47938 on GenesisL1: 3D structure…
- PDB
- 2PDR
- Type
- protein
- Length
- 588 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Vivid pas protein vvd
- UniProt
- Q9C3Y6
- Ligands
- FAD
- Pockets
- 8 · best druggability 0.69
Structure
x-ray diffraction · 1 distinct chain · 26% helix, 26% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | Vivid pas protein vvd | protein | 147 | 26% helix, 26% strand | Q9C3Y6 |
Ligands and binding sites
- FAD · Flavin-adenine dinucleotide · ligand · 4 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 210 | 0.69 | 0.86 | 33 | FAD |
| 2 | 215 | 0.68 | 0.86 | 30 | FAD |
| 3 | 220 | 0.68 | 0.85 | 31 | FAD |
| 4 | 227 | 0.67 | 0.84 | 31 | FAD |
| 5 | 191 | 0.45 | 0.74 | 28 | empty |
Interfaces
4 interfaces between chains.
- A–D · 432 Ų buried · 6 hydrogen bonds · protein-protein
- B–C · 419 Ų buried · 5 hydrogen bonds · protein-protein
- C–D · 152 Ų buried · 0 hydrogen bonds · protein-protein
- A–B · 109 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 cofactor (flavinylation).
Compared structures
- 2PDR · 1.7 Angstrom Crystal Structure of the Photo-excited Blue-light Photoreceptor Vivid · 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 Q9C3Y6
- Elsewhere: RCSB PDB 2PDR · PDBe 2PDR · UniProt Q9C3Y6
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