MolNFT v1 · #121585 · protein
Crystal structure of dronpa-NI2+
5HZU · Fluorescent protein dronpa: “Crystal structure of dronpa-NI2+”. X-ray diffraction, 2 ligands (GYS, NI), 20 pockets (best druggability 0.84). MolNFT v1 #121585 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 5HZU
- Type
- protein
- Length
- 2,551 residues
- Chains
- 12
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Fluorescent protein dronpa
- UniProt
- Q5TLG6
- Ligands
- GYS, NI
- Pockets
- 20 · best druggability 0.84
Structure
x-ray diffraction · 4 distinct chains · 4% helix, 58% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C, D, G, I, K | Fluorescent protein dronpa | protein | 212 | 5% helix, 58% strand | Q5TLG6 |
| B | Fluorescent protein dronpa | protein | 214 | 4% helix, 58% strand | Q5TLG6 |
| E, H, L | Fluorescent protein dronpa | protein | 213 | 4% helix, 58% strand | Q5TLG6 |
| F, J | Fluorescent protein dronpa | protein | 213 | 4% helix, 58% strand | Q5TLG6 |
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 · 12 copies · chains A, B, C, D, E, F, G, H, I, J, K, L
- NI · Nickel (II) ion · metal · 25 copies · chains A, B, C, D, E, J, F, G, H, I, 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 | 1101 | 0.84 | 0.86 | 124 | empty |
| 2 | 1188 | 0.82 | 0.84 | 105 | empty |
| 3 | 1189 | 0.82 | 0.83 | 104 | empty |
| 4 | 825 | 0.76 | 0.80 | 67 | NI |
| 5 | 72 | 0.75 | 0.99 | 25 | GYS |
Interfaces
20 interfaces between chains.
- E–F · 998 Ų buried · 18 hydrogen bonds · protein-protein
- A–B · 988 Ų buried · 19 hydrogen bonds · protein-protein
- G–H · 967 Ų buried · 18 hydrogen bonds · protein-protein
- K–L · 953 Ų buried · 18 hydrogen bonds · protein-protein
- I–J · 926 Ų buried · 20 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 24 cofactor (chromophore).
Compared structures
- 5HZU · Crystal structure of Dronpa-Ni2+ · 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 5HZU · PDBe 5HZU · UniProt Q5TLG6
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