MolNFT v1 · #118284 · protein
Photoconverted red fluorescent protein dendrfp
5EXC · Green fluorescent protein: “Photoconverted red fluorescent protein dendrfp”. X-ray diffraction, 2 ligands (RC7, MG), 20 pockets (best druggability 0.85). MolNFT v1 #118284 on GenesisL1: 3D structure, binding sites and pockets in…
- PDB
- 5EXC
- Type
- protein
- Length
- 1,782 residues
- Chains
- 16
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Green fluorescent protein
- UniProt
- Q8T6U0
- Ligands
- RC7, MG
- Pockets
- 20 · best druggability 0.85
Structure
x-ray diffraction · 6 distinct chains · 3% helix, 55% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Green fluorescent protein | protein | 60 | 7% helix, 55% strand | Q8T6U0 |
| I | Green fluorescent protein | protein | 164 | 2% helix, 55% strand | Q8T6U0 |
| J | Green fluorescent protein | protein | 166 | 2% helix, 55% strand | Q8T6U0 |
| C, D, E, F, G, H | Green fluorescent protein | protein | 59 | 7% helix, 51% strand | Q8T6U0 |
| K, L, O | Green fluorescent protein | protein | 165 | 3% helix, 55% strand | Q8T6U0 |
| M, N, P | Green fluorescent protein | protein | 161 | 0% helix, 57% strand | Q8T6U0 |
Ligands and binding sites
- RC7 · 2-[(4Z)-4-[(4-hydroxyphenyl)methylidene]-2-[(E)-2-(1H-imidazol-4-yl)ethenyl]-5-oxidanylidene-imidazol-1-yl]ethanoic acid · ligand · 8 copies · chains A, I, B, J, C, K, D, L, E, M, F, N, G, O, H, P
- MG · Magnesium ion · metal · 11 copies · chains E, M, F, N, G, O, H, P
- GOL · Glycerol · additive · 3 copies · chains L, E, M, P, N, G, O
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 10 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 955 | 0.85 | 0.87 | 114 | empty |
| 2 | 1143 | 0.76 | 0.79 | 127 | GOL |
| 3 | 87 | 0.75 | 0.97 | 28 | RC7 |
| 4 | 71 | 0.72 | 0.97 | 30 | RC7 |
| 5 | 59 | 0.72 | 0.99 | 25 | RC7 |
Interfaces
30 interfaces between chains.
- B–J · 2189 Ų buried · 39 hydrogen bonds · protein-protein
- E–M · 2187 Ų buried · 40 hydrogen bonds · protein-protein
- F–N · 2186 Ų buried · 45 hydrogen bonds · protein-protein
- A–I · 2169 Ų buried · 37 hydrogen bonds · protein-protein
- H–P · 2156 Ų buried · 39 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 9 covalent, 8 modified (covalent ligand, nonstandard).
Compared structures
- 5EXC · Photoconverted red fluorescent protein DendRFP · 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 5EXC · PDBe 5EXC · UniProt Q8T6U0
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