MolNFT v1 · #121583 · protein
Crystal structure of dronpa-CO2+
5HZS · Fluorescent protein dronpa: “Crystal structure of dronpa-CO2+”. X-ray diffraction, 2 ligands (GYS, CO), 20 pockets (best druggability 0.84). MolNFT v1 #121583 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 5HZS
- Type
- protein
- Length
- 2,557 residues
- Chains
- 12
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Fluorescent protein dronpa
- UniProt
- Q5TLG6
- Ligands
- GYS, CO
- 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, E | Fluorescent protein dronpa | protein | 214 | 3% helix, 58% strand | Q5TLG6 |
| B, I, K | Fluorescent protein dronpa | protein | 212 | 5% helix, 58% strand | Q5TLG6 |
| F, L | Fluorescent protein dronpa | protein | 213 | 4% helix, 58% strand | Q5TLG6 |
| G, H, J | Fluorescent protein dronpa | protein | 213 | 5% 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
- CO · Cobalt (II) ion · metal · 24 copies · chains A, J, B, C, D, E, 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, 17 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 953 | 0.84 | 0.86 | 100 | empty |
| 2 | 895 | 0.84 | 0.86 | 93 | empty |
| 3 | 1181 | 0.82 | 0.84 | 113 | empty |
| 4 | 79 | 0.75 | 0.98 | 28 | GYS |
| 5 | 73 | 0.75 | 0.99 | 28 | GYS |
Interfaces
19 interfaces between chains.
- D–E · 991 Ų buried · 19 hydrogen bonds · protein-protein
- F–G · 974 Ų buried · 19 hydrogen bonds · protein-protein
- A–H · 968 Ų buried · 21 hydrogen bonds · protein-protein
- B–C · 955 Ų buried · 19 hydrogen bonds · protein-protein
- K–L · 953 Ų buried · 19 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 24 cofactor (chromophore).
Compared structures
- 5HZS · Crystal structure of Dronpa-Co2+ · 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 5HZS · PDBe 5HZS · UniProt Q5TLG6
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