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Structural and spectroscopic characterization of photoconverting fluorescent protein DENDRA2
Analyse Structural and spectroscopic characterization of photoconverting fluorescent… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2VZX
- Type
- protein
- Length
- 1,775 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Green fluorescent protein
- UniProt
- Q8T6U0
- Ligands
- 5SQ
- Pockets
- 20 · best druggability 0.77
Structure
x-ray diffraction · 5 distinct chains · 3% helix, 56% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, F, G | Green fluorescent protein | protein | 220 | 4% helix, 56% strand | Q8T6U0 |
| B, E | Green fluorescent protein | protein | 222 | 2% helix, 56% strand | Q8T6U0 |
| C | Green fluorescent protein | protein | 224 | 4% helix, 55% strand | Q8T6U0 |
| D | Green fluorescent protein | protein | 221 | 4% helix, 56% strand | Q8T6U0 |
| H | Green fluorescent protein | protein | 226 | 4% helix, 55% strand | Q8T6U0 |
Ligands and binding sites
- 5SQ · 2-[2-[(1S)-1-azanyl-2-(1H-imidazol-4-yl)ethyl]-4-[(4-hydroxyphenyl)methylidene]-5-oxidanylidene-imidazol-1-yl]ethanoic acid · ligand · 8 copies · chains A, B, C, D, E, F, G, H
- PG4 · Tetraethylene glycol · additive · 2 copies · chains A, B, C, D, G
- GOL · Glycerol · additive · 2 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 16 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 788 | 0.77 | 0.81 | 87 | empty |
| 2 | 87 | 0.76 | 0.98 | 30 | 5SQ |
| 3 | 79 | 0.76 | 0.98 | 30 | 5SQ |
| 4 | 83 | 0.75 | 0.98 | 29 | 5SQ |
| 5 | 83 | 0.75 | 0.97 | 29 | 5SQ |
Interfaces
20 interfaces between chains.
- G–H · 1592 Ų buried · 27 hydrogen bonds · protein-protein
- A–B · 1575 Ų buried · 26 hydrogen bonds · protein-protein
- C–D · 1574 Ų buried · 24 hydrogen bonds · protein-protein
- E–F · 1567 Ų buried · 27 hydrogen bonds · protein-protein
- B–E · 292 Ų buried · 1 hydrogen bond · protein-protein
Modifications
Observed in the structure: 16 covalent (covalent ligand).
Compared structures
- 2VZX · Structural and spectroscopic characterization of photoconverting fluorescent protein… · 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 Q8T6U0
- Elsewhere: RCSB PDB 2VZX · PDBe 2VZX · UniProt Q8T6U0
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