Research workbench
Padron on (fluorescent) icis intermediate state
Analyse Padron on (fluorescent) icis intermediate state in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3ZUL
- Type
- protein
- Length
- 1,280 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Fluorescent protein dronpa
- UniProt
- Q5TLG6
- Ligands
- GYC
- Pockets
- 20 · best druggability 0.75
Structure
x-ray diffraction · 2 distinct chains · 4% helix, 58% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, D, E, F | Fluorescent protein dronpa | protein | 213 | 4% helix, 58% strand | Q5TLG6 |
| C | Fluorescent protein dronpa | protein | 215 | 5% helix, 58% strand | Q5TLG6 |
Ligands and binding sites
- GYC · [(4Z)-2-[(1R)-1-amino-2-mercaptoethyl]-4-(4-hydroxybenzylidene)-5-oxo-4,5-dihydro-1H-imidazol-1-yl]acetic acid · ligand · 6 copies · chains A, B, C, D, E, F
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 10 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 779 | 0.75 | 0.80 | 70 | empty |
| 2 | 70 | 0.74 | 0.98 | 24 | GYC |
| 3 | 71 | 0.73 | 0.98 | 24 | GYC |
| 4 | 73 | 0.73 | 0.97 | 24 | GYC |
| 5 | 69 | 0.72 | 0.97 | 21 | GYC |
Interfaces
9 interfaces between chains.
- C–E · 902 Ų buried · 24 hydrogen bonds · protein-protein
- D–F · 893 Ų buried · 17 hydrogen bonds · protein-protein
- A–B · 881 Ų buried · 19 hydrogen bonds · protein-protein
- C–F · 390 Ų buried · 3 hydrogen bonds · protein-protein
- B–C · 388 Ų buried · 8 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 12 covalent (covalent ligand).
Compared structures
- 3ZUL · Padron on (fluorescent) Icis intermediate state · 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 3ZUL · PDBe 3ZUL · UniProt Q5TLG6
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.