MolNFT v1 · #138850 · protein
Highly stable green fluorescent protein
5WWK: “Highly stable green fluorescent protein”. X-ray diffraction, 1 ligand (CR2), 19 pockets (best druggability 0.79). MolNFT v1 #138850 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 5WWK
- Type
- protein
- Length
- 1,368 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Green fluorescent protein
- Ligands
- CR2
- Pockets
- 19 · best druggability 0.79
Structure
x-ray diffraction · 1 distinct chain · 7% helix, 51% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D, E, F | Green fluorescent protein | protein | 228 | 7% helix, 51% strand | — |
Ligands and binding sites
- CR2 · {(4Z)-2-(aminomethyl)-4-[(4-hydroxyphenyl)methylidene]-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
19 pockets found on a 1 Å grid, 11 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1086 | 0.79 | 0.81 | 102 | empty |
| 2 | 77 | 0.75 | 0.98 | 19 | CR2 |
| 3 | 68 | 0.75 | 0.99 | 21 | CR2 |
| 4 | 69 | 0.74 | 0.98 | 18 | CR2 |
| 5 | 63 | 0.74 | 0.99 | 18 | CR2 |
Interfaces
7 interfaces between chains.
- D–F · 961 Ų buried · 15 hydrogen bonds · protein-protein
- A–B · 725 Ų buried · 9 hydrogen bonds · protein-protein
- C–E · 506 Ų buried · 4 hydrogen bonds · protein-protein
- B–C · 414 Ų buried · 5 hydrogen bonds · protein-protein
- A–F · 370 Ų buried · 1 hydrogen bond · protein-protein
Modifications
Observed in the structure: 12 cofactor (chromophore).
Compared structures
- 5WWK · Highly stable green fluorescent protein · 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 5WWK · PDBe 5WWK
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