MolNFT v1 · #116818 · protein
Sfgfp double mutant - 133/149 P-cyano-L-phenylalanine
5DPI · Green fluorescent protein: “Sfgfp double mutant - 133/149 P-cyano-L-phenylalanine”. X-ray diffraction, 1 ligand (CRO), 20 pockets (best druggability 0.77). MolNFT v1 #116818 on GenesisL1: 3D structure, binding sites and pockets in…
- PDB
- 5DPI
- Type
- protein
- Length
- 1,347 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Green fluorescent protein
- UniProt
- A0A059PIQ0
- Ligands
- CRO
- Pockets
- 20 · best druggability 0.77
Structure
x-ray diffraction · 3 distinct chains · 9% helix, 52% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, D, E | Green fluorescent protein | protein | 225 | 12% helix, 52% strand | A0A059PIQ0 |
| C | Green fluorescent protein | protein | 223 | 8% helix, 52% strand | A0A059PIQ0 |
| F | Green fluorescent protein | protein | 224 | 8% helix, 52% strand | A0A059PIQ0 |
Ligands and binding sites
- CRO · {2-[(1R,2R)-1-amino-2-hydroxypropyl]-4-(4-hydroxybenzylidene)-5-oxo-4,5-dihydro-1H-imidazol-1-yl}acetic acid · ligand · 6 copies · chains A, B, C, D, E, F
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 104 | 0.77 | 0.97 | 29 | CRO |
| 2 | 92 | 0.77 | 0.98 | 31 | CRO |
| 3 | 89 | 0.76 | 0.98 | 28 | CRO |
| 4 | 88 | 0.76 | 0.98 | 26 | CRO |
| 5 | 90 | 0.76 | 0.97 | 25 | CRO |
Interfaces
6 interfaces between chains.
- A–B · 881 Ų buried · 14 hydrogen bonds · protein-protein
- D–F · 874 Ų buried · 15 hydrogen bonds · protein-protein
- C–E · 868 Ų buried · 17 hydrogen bonds · protein-protein
- A–C · 383 Ų buried · 9 hydrogen bonds · protein-protein
- B–D · 294 Ų buried · 2 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 12 cofactor, 12 modified (chromophore, nonstandard).
Compared structures
- 5DPI · sfGFP double mutant - 133/149 p-cyano-L-phenylalanine · 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 A0A059PIQ0
- Elsewhere: RCSB PDB 5DPI · PDBe 5DPI · UniProt A0A059PIQ0
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