Research workbench
1.60A resolution crystal structure of a superfolder green fluorescent protein (W57G) mutant
Analyse 1.60A resolution crystal structure of a superfolder green fluorescent protein… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4LQU
- Type
- protein
- Length
- 906 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Green fluorescent protein
- UniProt
- P42212
- Ligands
- CRO
- Pockets
- 10 · best druggability 0.80
Structure
x-ray diffraction · 4 distinct chains · 11% helix, 51% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Green fluorescent protein | protein | 225 | 11% helix, 52% strand | P42212 |
| B | Green fluorescent protein | protein | 228 | 12% helix, 51% strand | P42212 |
| C | Green fluorescent protein | protein | 227 | 10% helix, 51% strand | P42212 |
| D | Green fluorescent protein | protein | 226 | 10% helix, 51% 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
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
10 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1060 | 0.80 | 0.82 | 108 | empty |
| 2 | 96 | 0.78 | 0.98 | 24 | CRO |
| 3 | 93 | 0.77 | 0.98 | 24 | CRO |
| 4 | 961 | 0.77 | 0.80 | 95 | empty |
| 5 | 97 | 0.77 | 0.97 | 26 | CRO |
Interfaces
5 interfaces between chains.
- A–D · 585 Ų buried · 10 hydrogen bonds · protein-protein
- A–C · 543 Ų buried · 7 hydrogen bonds · protein-protein
- A–B · 419 Ų buried · 4 hydrogen bonds · protein-protein
- C–D · 291 Ų buried · 2 hydrogen bonds · protein-protein
- B–C · 63 Ų buried · 1 hydrogen bond · protein-protein
Modifications
Observed in the structure: 8 cofactor (chromophore).
Compared structures
- 4LQU · 1.60A resolution crystal structure of a superfolder green fluorescent protein (W57G)… · the same entry in another collection · chain D against D, 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 4LQU · PDBe 4LQU · UniProt P42212
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