Research workbench
Structure of pcdronpa-A69T mutant
Analyse Structure of pcdronpa-A69T mutant in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4IZN
- Type
- protein
- Length
- 2,601 residues
- Chains
- 12
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Fluorescent protein dronpa
- UniProt
- Q5TLG6
- Ligands
- CR8, K
- Pockets
- 20 · best druggability 0.82
Structure
x-ray diffraction · 2 distinct chains · 4% helix, 57% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, D, E, F, G, J, K, L | Fluorescent protein dronpa | protein | 217 | 4% helix, 57% strand | Q5TLG6 |
| C, H, I | Fluorescent protein dronpa | protein | 216 | 5% helix, 57% strand | Q5TLG6 |
Ligands and binding sites
- CR8 · 2-[1-amino-2-(1H-imidazol-5-yl)ethyl]-1-(carboxymethyl)-4-[(4-oxocyclohexa-2,5-dien-1-ylidene)methyl]-1H-imidazol-5-olate · ligand · 12 copies · chains A, B, C, D, E, F, G, H, I, J, K, L
- K · Potassium ion · metal · 12 copies · chains A, B, C, D, E, F, G, H, I, J, K, L
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 18 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 979 | 0.82 | 0.84 | 86 | empty |
| 2 | 934 | 0.82 | 0.84 | 88 | empty |
| 3 | 929 | 0.82 | 0.84 | 87 | empty |
| 4 | 97 | 0.77 | 0.98 | 29 | CR8 |
| 5 | 92 | 0.77 | 0.98 | 27 | CR8 |
Interfaces
17 interfaces between chains.
- F–H · 1281 Ų buried · 18 hydrogen bonds · protein-protein
- I–K · 1279 Ų buried · 21 hydrogen bonds · protein-protein
- A–C · 1277 Ų buried · 22 hydrogen bonds · protein-protein
- E–G · 1268 Ų buried · 21 hydrogen bonds · protein-protein
- B–D · 1260 Ų buried · 18 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 24 covalent (covalent ligand).
Compared structures
- 4IZN · Structure of pcDronpa-A69T mutant · 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 Q5TLG6
- Elsewhere: RCSB PDB 4IZN · PDBe 4IZN · UniProt Q5TLG6
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