MolNFT v1 · #31708 · protein
Crystal structure of a well-folded variant of green fluorescent protein
2B3Q: “Crystal structure of a well-folded variant of green fluorescent protein”. X-ray diffraction, 2 ligands (CRO, MG), 15 pockets (best druggability 0.79). MolNFT v1 #31708 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 2B3Q
- Type
- protein
- Length
- 904 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Green fluorescent protein
- UniProt
- P42212
- Ligands
- CRO, MG
- Pockets
- 15 · best druggability 0.79
Structure
x-ray diffraction · 1 distinct chain · 10% helix, 52% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | Green fluorescent protein | protein | 226 | 10% 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 · 4 copies · chains A, B, C, D
- MG · Magnesium ion · metal · 3 copies · chains A, D, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
15 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 114 | 0.79 | 0.98 | 30 | CRO |
| 2 | 96 | 0.78 | 0.98 | 24 | CRO |
| 3 | 96 | 0.77 | 0.98 | 25 | CRO |
| 4 | 93 | 0.77 | 0.98 | 22 | CRO |
| 5 | 1200 | 0.73 | 0.77 | 103 | MG |
Interfaces
4 interfaces between chains.
- A–D · 983 Ų buried · 18 hydrogen bonds · protein-protein
- B–C · 965 Ų buried · 15 hydrogen bonds · protein-protein
- A–C · 289 Ų buried · 3 hydrogen bonds · protein-protein
- A–B · 201 Ų buried · 5 hydrogen bonds · protein-protein
Compared structures
- 2B3Q · Crystal structure of a well-folded variant of green fluorescent protein · the same entry in another collection · chain C against C, TM-score 1.00
- P42212 · AlphaFold monomer V2.0 prediction for green fluorescent protein (P42212) · a predicted model of the same protein · chain B 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
- Every structure of UniProt P42212
- Elsewhere: RCSB PDB 2B3Q · PDBe 2B3Q · UniProt P42212
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