MolNFT v1 · #90551 · protein
Crystal structure of a single mutant of dronpa, the green-on-state PDM1-4
4EMQ · Fluorescent protein dronpa: “Crystal structure of a single mutant of dronpa, the green-on-state PDM1-4”. X-ray diffraction, 1 ligand (GYC), 19 pockets (best druggability 0.77). MolNFT v1 #90551 on GenesisL1: 3D structure, binding…
- PDB
- 4EMQ
- 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
- 19 · best druggability 0.77
Structure
x-ray diffraction · 3 distinct chains · 4% helix, 58% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, D | Fluorescent protein dronpa | protein | 214 | 3% helix, 58% strand | Q5TLG6 |
| B | Fluorescent protein dronpa | protein | 213 | 3% helix, 58% strand | Q5TLG6 |
| C, E, F | Fluorescent protein dronpa | protein | 213 | 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
- PEG · Di(hydroxyethyl)ether · additive · 7 copies · chains B, C, A, D, E, F
- EPE · 4-(2-hydroxyethyl)-1-piperazine ethanesulfonic acid · additive · 6 copies · chains A, C, B, D, E, F
- 1PE · Pentaethylene glycol · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
19 pockets found on a 1 Å grid, 10 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1200 | 0.77 | 0.80 | 122 | empty |
| 2 | 73 | 0.75 | 0.99 | 27 | GYC |
| 3 | 79 | 0.75 | 0.98 | 25 | GYC |
| 4 | 72 | 0.75 | 0.99 | 26 | GYC |
| 5 | 78 | 0.74 | 0.98 | 26 | GYC |
Interfaces
10 interfaces between chains.
- D–F · 932 Ų buried · 24 hydrogen bonds · protein-protein
- A–B · 903 Ų buried · 19 hydrogen bonds · protein-protein
- C–E · 897 Ų buried · 16 hydrogen bonds · protein-protein
- C–F · 392 Ų buried · 4 hydrogen bonds · protein-protein
- B–C · 379 Ų buried · 9 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 12 covalent (covalent ligand).
Compared structures
- 4EMQ · Crystal structure of a single mutant of Dronpa, the green-on-state PDM1-4 · 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 4EMQ · PDBe 4EMQ · UniProt Q5TLG6
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