MolNFT v1 · #186831 · protein
Crystal structure of fast switching S142A/M159T mutant of fluorescent protein dronpa (DRONPA2)
7RRI: “Crystal structure of fast switching S142A/M159T mutant of fluorescent protein dronpa (DRONPA2)”. X-ray diffraction, 1 ligand (GYC), 20 pockets (best druggability 0.82). MolNFT v1 #186831 on GenesisL1: 3D structure, binding sites and…
- PDB
- 7RRI
- Type
- protein
- Length
- 1,735 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Fluorescent protein dronpa
- UniProt
- Q5TLG6
- Ligands
- GYC
- Pockets
- 20 · best druggability 0.82
Structure
x-ray diffraction · 4 distinct chains · 5% helix, 57% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, G, H | Fluorescent protein dronpa | protein | 215 | 5% helix, 58% strand | Q5TLG6 |
| C | Fluorescent protein dronpa | protein | 220 | 5% helix, 56% strand | Q5TLG6 |
| D | Fluorescent protein dronpa | protein | 219 | 5% helix, 57% strand | Q5TLG6 |
| E, F | Fluorescent protein dronpa | protein | 218 | 5% helix, 57% 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 · 8 copies · chains A, B, C, D, E, F, G, H
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 13 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 151 | 0.82 | 0.98 | 33 | GYC |
| 2 | 887 | 0.82 | 0.84 | 106 | empty |
| 3 | 1191 | 0.81 | 0.83 | 125 | empty |
| 4 | 139 | 0.79 | 0.97 | 30 | GYC |
| 5 | 112 | 0.79 | 0.98 | 26 | GYC |
Interfaces
10 interfaces between chains.
- C–G · 1267 Ų buried · 16 hydrogen bonds · protein-protein
- B–F · 1262 Ų buried · 18 hydrogen bonds · protein-protein
- A–E · 1234 Ų buried · 17 hydrogen bonds · protein-protein
- D–H · 1181 Ų buried · 10 hydrogen bonds · protein-protein
- B–H · 859 Ų buried · 17 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 16 covalent (covalent ligand).
Compared structures
- 7RRI · Crystal structure of fast switching S142A/M159T mutant of fluorescent protein Dronpa… · the same entry in another collection · chain H against H, 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 7RRI · PDBe 7RRI · UniProt Q5TLG6
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