MolNFT v1 · #51536 · protein
Fast maturing red fluorescent protein, DSRED.T4
2VAE: “Fast maturing red fluorescent protein, DSRED.T4”. X-ray diffraction, 1 ligand (CRQ), 20 pockets (best druggability 0.85). MolNFT v1 #51536 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 2VAE
- Type
- protein
- Length
- 1,728 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Red fluorescent protein
- Ligands
- CRQ
- Pockets
- 20 · best druggability 0.85
Structure
x-ray diffraction · 1 distinct chain · 6% helix, 57% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D, E, F, G, H | Red fluorescent protein | protein | 216 | 6% helix, 57% strand | — |
Ligands and binding sites
- CRQ · [2-(3-carbamoyl-1-imino-propyl)-4-(4-hydroxy-benzylidene)-5-oxo-4,5-dihydro-imidazol-1-yl]-acetic acid · ligand · 8 copies · chains A, B, C, D, E, F, G, H
- EDO · 1,2-ethanediol · additive · 27 copies · chains A, C, B, D, F, E, G, H
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 13 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1065 | 0.85 | 0.86 | 115 | empty |
| 2 | 948 | 0.84 | 0.86 | 88 | empty |
| 3 | 847 | 0.77 | 0.80 | 84 | EDO |
| 4 | 92 | 0.76 | 0.97 | 29 | CRQ |
| 5 | 91 | 0.75 | 0.97 | 28 | CRQ |
Interfaces
15 interfaces between chains.
- C–D · 1387 Ų buried · 19 hydrogen bonds · protein-protein
- G–H · 1385 Ų buried · 19 hydrogen bonds · protein-protein
- E–F · 1383 Ų buried · 19 hydrogen bonds · protein-protein
- A–B · 1378 Ų buried · 19 hydrogen bonds · protein-protein
- F–H · 1081 Ų buried · 14 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 16 cofactor (chromophore).
Compared structures
- 2VAE · Fast maturing red fluorescent protein, DsRed.T4 · 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
- Elsewhere: RCSB PDB 2VAE · PDBe 2VAE
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