MolNFT v1 · #64635 · protein
Green fluorescent protein bound to minimizer nanobody
3G9A: “Green fluorescent protein bound to minimizer nanobody”. X-ray diffraction, 1 ligand (GYS), 1 pocket (best druggability 0.75). MolNFT v1 #64635 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 3G9A
- Type
- protein
- Length
- 355 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Green fluorescent protein; Minimizer
- UniProt
- P42212
- Ligands
- GYS
- Pockets
- 1 · best druggability 0.75
Structure
x-ray diffraction · 2 distinct chains · 10% helix, 50% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Green fluorescent protein | protein | 226 | 12% helix, 52% strand | P42212 |
| B | Minimizer | protein | 129 | 7% helix, 48% strand | — |
Ligands and binding sites
- GYS · [(4Z)-2-(1-amino-2-hydroxyethyl)-4-(4-hydroxybenzylidene)-5-oxo-4,5-dihydro-1H-imidazol-1-yl]acetic acid · ligand · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
1 pocket found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 83 | 0.75 | 0.98 | 23 | GYS |
Interfaces
1 interface between chains.
- A–B · 690 Ų buried · 16 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 cofactor, 2 disulfide (chromophore, disulfide).
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 3G9A · PDBe 3G9A · UniProt P42212
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