Research workbench
Crystal structural and functional analysis of GFP-like fluorescent protein dronpa
Analyse Crystal structural and functional analysis of GFP-like fluorescent protein… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2GX2
- Type
- protein
- Length
- 2,580 residues
- Chains
- 12
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Fluorescent protein dronpa
- UniProt
- Q5TLG6
- Ligands
- GYS, MG
- Pockets
- 20 · best druggability 0.85
Structure
x-ray diffraction · 5 distinct chains · 4% helix, 58% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, D, G | Fluorescent protein dronpa | protein | 214 | 4% helix, 58% strand | Q5TLG6 |
| B, K | Fluorescent protein dronpa | protein | 212 | 4% helix, 58% strand | Q5TLG6 |
| C, E, F, H, I | Fluorescent protein dronpa | protein | 217 | 4% helix, 57% strand | Q5TLG6 |
| J | Fluorescent protein dronpa | protein | 216 | 4% helix, 57% strand | Q5TLG6 |
| L | Fluorescent protein dronpa | protein | 213 | 4% helix, 58% strand | Q5TLG6 |
Ligands and binding sites
- GYS · [(4Z)-2-(1-amino-2-hydroxyethyl)-4-(4-hydroxybenzylidene)-5-oxo-4,5-dihydro-1H-imidazol-1-yl]acetic acid · ligand · 12 copies · chains A, B, C, D, E, F, G, H, I, J, K, L
- MG · Magnesium ion · metal · 62 copies · chains A, L, E, H, B, G, C, F, D, I, J, K
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 18 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 999 | 0.85 | 0.86 | 96 | MG |
| 2 | 1147 | 0.83 | 0.84 | 97 | MG |
| 3 | 1178 | 0.83 | 0.84 | 96 | MG |
| 4 | 75 | 0.76 | 0.99 | 26 | GYS |
| 5 | 75 | 0.75 | 0.99 | 26 | GYS |
Interfaces
18 interfaces between chains.
- I–J · 1266 Ų buried · 24 hydrogen bonds · protein-protein
- F–G · 1207 Ų buried · 25 hydrogen bonds · protein-protein
- A–H · 1192 Ų buried · 25 hydrogen bonds · protein-protein
- D–E · 1183 Ų buried · 24 hydrogen bonds · protein-protein
- B–C · 1107 Ų buried · 23 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 24 cofactor (chromophore).
Compared structures
- 2GX2 · Crystal structural and functional analysis of GFP-like fluorescent protein Dronpa · 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 Q5TLG6
- Elsewhere: RCSB PDB 2GX2 · PDBe 2GX2 · UniProt Q5TLG6
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