Research workbench
Green fluorescent protein from dendronephthya sp. ssal-2002
Analyse Green fluorescent protein from dendronephthya sp. ssal-2002 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7DIG
- Type
- protein
- Length
- 1,744 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Green fluorescent protein
- UniProt
- Q8T6U0
- Ligands
- CR8
- Pockets
- 17 · best druggability 0.86
Structure
x-ray diffraction · 1 distinct chain · 4% helix, 57% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D, E, F, G, H | Green fluorescent protein | protein | 218 | 4% helix, 57% strand | Q8T6U0 |
Ligands and binding sites
- CR8 · 2-[1-amino-2-(1H-imidazol-5-yl)ethyl]-1-(carboxymethyl)-4-[(4-oxocyclohexa-2,5-dien-1-ylidene)methyl]-1H-imidazol-5-olate · ligand · 8 copies · chains A, B, C, D, E, F, G, H
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
17 pockets found on a 1 Å grid, 11 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1050 | 0.86 | 0.88 | 123 | empty |
| 2 | 914 | 0.85 | 0.87 | 125 | empty |
| 3 | 95 | 0.77 | 0.98 | 28 | CR8 |
| 4 | 93 | 0.77 | 0.98 | 26 | CR8 |
| 5 | 97 | 0.77 | 0.98 | 27 | CR8 |
Interfaces
14 interfaces between chains.
- C–D · 1542 Ų buried · 27 hydrogen bonds · protein-protein
- A–B · 1539 Ų buried · 24 hydrogen bonds · protein-protein
- G–H · 1524 Ų buried · 25 hydrogen bonds · protein-protein
- E–F · 1518 Ų buried · 26 hydrogen bonds · protein-protein
- E–H · 906 Ų buried · 14 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 16 covalent (covalent ligand).
Compared structures
- 7DIG · Green fluorescent protein from Dendronephthya sp. SSAL-2002 · 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 7DIG · PDBe 7DIG · UniProt Q8T6U0
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