MolNFT v1 · #100635 · protein
Crystal structure of the dimeric variant egfp-K162Q in P61 space group
4N3D · Green fluorescent protein: “Crystal structure of the dimeric variant egfp-K162Q in P61 space group”. X-ray diffraction, 3 ligands (CRO, K, PO4), 8 pockets (best druggability 0.78). MolNFT v1 #100635 on GenesisL1: 3D structure…
- PDB
- 4N3D
- Type
- protein
- Length
- 450 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Green fluorescent protein
- UniProt
- P42212
- Ligands
- CRO, K, PO4
- Pockets
- 8 · best druggability 0.78
Structure
x-ray diffraction · 1 distinct chain · 11% helix, 52% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Green fluorescent protein | protein | 225 | 11% helix, 52% strand | P42212 |
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
- K · Potassium ion · metal · 3 copies · chains A, B
- PO4 · Phosphate ion · ion · 2 copies · chains A
- GOL · Glycerol · additive · 3 copies · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 97 | 0.78 | 0.98 | 25 | CRO |
| 2 | 90 | 0.76 | 0.98 | 25 | CRO |
| 3 | 139 | 0.42 | 0.75 | 20 | empty |
| 4 | 97 | 0.38 | 0.75 | 15 | empty |
| 5 | 51 | 0.36 | 0.80 | 14 | empty |
Interfaces
1 interface between chains.
- A–B · 872 Ų buried · 8 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 cofactor (chromophore).
Compared structures
- 4N3D · Crystal structure of the dimeric variant EGFP-K162Q in P61 space group · the same entry in another collection · chain A against A, TM-score 1.00
- P42212 · AlphaFold monomer V2.0 prediction for green fluorescent protein (P42212) · a predicted model of the same protein · chain A against A, TM-score 0.99
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 P42212
- Elsewhere: RCSB PDB 4N3D · PDBe 4N3D · UniProt P42212
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