MolNFT v1 · #116819 · protein
Sfgfp double mutant - 133/149 P-ethynyl-L-phenylalanine
5DPJ · Green fluorescent protein: “Sfgfp double mutant - 133/149 P-ethynyl-L-phenylalanine”. X-ray diffraction, 1 ligand (CRO), 12 pockets (best druggability 0.77). MolNFT v1 #116819 on GenesisL1: 3D structure, binding sites and pockets in…
- PDB
- 5DPJ
- Type
- protein
- Length
- 898 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Green fluorescent protein
- UniProt
- A0A059PIQ0
- Ligands
- CRO
- Pockets
- 12 · best druggability 0.77
Structure
x-ray diffraction · 3 distinct chains · 10% helix, 52% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Green fluorescent protein | protein | 226 | 11% helix, 52% strand | A0A059PIQ0 |
| B, C | Green fluorescent protein | protein | 224 | 9% helix, 52% strand | A0A059PIQ0 |
| D | Green fluorescent protein | protein | 224 | 10% 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 · 4 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
12 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 95 | 0.77 | 0.98 | 25 | CRO |
| 2 | 87 | 0.76 | 0.98 | 29 | CRO |
| 3 | 85 | 0.76 | 0.98 | 21 | CRO |
| 4 | 88 | 0.76 | 0.98 | 27 | CRO |
| 5 | 925 | 0.74 | 0.78 | 89 | empty |
Interfaces
4 interfaces between chains.
- C–D · 972 Ų buried · 18 hydrogen bonds · protein-protein
- A–B · 929 Ų buried · 13 hydrogen bonds · protein-protein
- B–C · 293 Ų buried · 4 hydrogen bonds · protein-protein
- A–C · 170 Ų buried · 1 hydrogen bond · protein-protein
Modifications
Observed in the structure: 8 cofactor, 8 modified (chromophore, nonstandard).
Compared structures
- 5DPJ · sfGFP double mutant - 133/149 p-ethynyl-L-phenylalanine · the same entry in another collection · chain C against C, 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 5DPJ · PDBe 5DPJ · UniProt A0A059PIQ0
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