Research workbench
Crystal structure of GFP-like protein ACEGFP_G222E (a. coerulescens). colorless form.
Analyse Crystal structure of GFP-like protein ACEGFP_G222E (a. coerulescens). colorless… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3LVC
- Type
- protein
- Length
- 452 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Green fluorescent protein
- UniProt
- Q6YGZ0
- Ligands
- GYS
- Pockets
- 9 · best druggability 0.77
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 | 226 | 11% helix, 52% strand | Q6YGZ0 |
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 · 2 copies · chains A, B
- GOL · Glycerol · additive · 5 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 84 | 0.77 | 0.98 | 25 | GYS |
| 2 | 85 | 0.75 | 0.97 | 25 | GYS |
| 3 | 207 | 0.51 | 0.77 | 33 | empty |
| 4 | 72 | 0.48 | 0.84 | 19 | empty |
| 5 | 189 | 0.47 | 0.76 | 29 | empty |
Interfaces
1 interface between chains.
- A–B · 1085 Ų buried · 14 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 cofactor (chromophore).
Compared structures
- 3LVC · Crystal structure of GFP-like protein aceGFP_G222E (A. coerulescens). Colorless form. · 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
- Every structure of UniProt Q6YGZ0
- Elsewhere: RCSB PDB 3LVC · PDBe 3LVC · UniProt Q6YGZ0
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