MolNFT v1 · #146723 · protein
Sfgfp D133 mutated to 4-nitro-L-phenylalanine
6DQ0 · Superfolder green fluorescent protein: “Sfgfp D133 mutated to 4-nitro-L-phenylalanine”. X-ray diffraction, 2 ligands (CRO, NA), 7 pockets (best druggability 0.79). MolNFT v1 #146723 on GenesisL1: 3D structure, binding sites and…
- PDB
- 6DQ0
- Type
- protein
- Length
- 454 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Superfolder green fluorescent protein
- Ligands
- CRO, NA
- Pockets
- 7 · best druggability 0.79
Structure
x-ray diffraction · 1 distinct chain · 12% helix, 52% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Superfolder green fluorescent protein | protein | 227 | 12% helix, 52% strand | — |
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 · 2 copies · chains A, B
- NA · Sodium ion · metal · chains A
- EDO · 1,2-ethanediol · additive · 4 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 100 | 0.79 | 0.98 | 26 | CRO |
| 2 | 81 | 0.74 | 0.97 | 25 | CRO |
| 3 | 309 | 0.54 | 0.75 | 43 | empty |
| 4 | 153 | 0.53 | 0.80 | 21 | empty |
| 5 | 220 | 0.48 | 0.74 | 26 | empty |
Interfaces
1 interface between chains.
- A–B · 660 Ų buried · 10 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 cofactor, 2 modified (chromophore, nonstandard).
Compared structures
- 6DQ0 · sfGFP D133 mutated to 4-nitro-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
- Elsewhere: RCSB PDB 6DQ0 · PDBe 6DQ0
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