MolNFT v1 · #126682 · protein
GFP-binding darpin 3G124NC
5MA6 · Green fluorescent protein: “GFP-binding darpin 3G124NC”. X-ray diffraction, 2 ligands (CRO, PO4), 4 pockets (best druggability 0.79). MolNFT v1 #126682 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 5MA6
- Type
- protein
- Length
- 385 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Green fluorescent protein; 3G124NC
- UniProt
- P42212
- Ligands
- CRO, PO4
- Pockets
- 4 · best druggability 0.79
Structure
x-ray diffraction · 2 distinct chains · 28% helix, 31% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Green fluorescent protein | protein | 226 | 11% helix, 52% strand | P42212 |
| B | 3G124NC | protein | 159 | 53% helix, 0% 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 · chains A
- PO4 · Phosphate ion · ion · 5 copies · chains A, B
- EDO · 1,2-ethanediol · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 126 | 0.79 | 0.97 | 25 | CRO |
| 2 | 230 | 0.58 | 0.79 | 39 | empty |
| 3 | 122 | 0.54 | 0.82 | 21 | PO4 |
| 4 | 72 | 0.36 | 0.77 | 14 | empty |
Interfaces
1 interface between chains.
- A–B · 910 Ų buried · 10 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 cofactor (chromophore).
Compared structures
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 5MA6 · PDBe 5MA6 · UniProt P42212
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