MolNFT v1 · #102304 · protein
The structure of a far-red fluorescent protein, AQ143
4OHS · Far-red fluorescent protein AQ143: “The structure of a far-red fluorescent protein, AQ143”. X-ray diffraction, 2 ligands (CH6, CL), 20 pockets (best druggability 0.85). MolNFT v1 #102304 on GenesisL1: 3D structure, binding sites and…
- PDB
- 4OHS
- Type
- protein
- Length
- 1,754 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Far-red fluorescent protein AQ143
- Ligands
- CH6, CL
- Pockets
- 20 · best druggability 0.85
Structure
x-ray diffraction · 6 distinct chains · 5% helix, 57% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Far-red fluorescent protein AQ143 | protein | 219 | 5% helix, 58% strand | — |
| B, F | Far-red fluorescent protein AQ143 | protein | 225 | 3% helix, 56% strand | — |
| C | Far-red fluorescent protein AQ143 | protein | 221 | 5% helix, 57% strand | — |
| D, E | Far-red fluorescent protein AQ143 | protein | 217 | 6% helix, 58% strand | — |
| G | Far-red fluorescent protein AQ143 | protein | 214 | 5% helix, 58% strand | — |
| H | Far-red fluorescent protein AQ143 | protein | 216 | 5% helix, 57% strand | — |
Ligands and binding sites
- CH6 · {(4Z)-2-[(1S)-1-amino-3-(methylsulfanyl)propyl]-4-[(4-hydroxyphenyl)methylidene]-5-oxo-4,5-dihydro-1H-imidazol-1-yl}acetic acid · ligand · 8 copies · chains A, B, C, D, E, F, G, H
- CL · Chloride ion · ion · 4 copies · chains A, B, C, D
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 | 745 | 0.85 | 0.89 | 66 | empty |
| 2 | 637 | 0.85 | 0.90 | 62 | empty |
| 3 | 1034 | 0.79 | 0.81 | 117 | empty |
| 4 | 110 | 0.77 | 0.97 | 30 | CH6 |
| 5 | 96 | 0.77 | 0.98 | 28 | CH6 |
Interfaces
16 interfaces between chains.
- C–F · 1479 Ų buried · 21 hydrogen bonds · protein-protein
- B–E · 1364 Ų buried · 20 hydrogen bonds · protein-protein
- A–D · 1173 Ų buried · 10 hydrogen bonds · protein-protein
- G–H · 1052 Ų buried · 11 hydrogen bonds · protein-protein
- D–E · 1043 Ų buried · 19 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 16 cofactor (chromophore).
Compared structures
- 4OHS · The structure of a far-red fluorescent protein, AQ143 · 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
- Elsewhere: RCSB PDB 4OHS · PDBe 4OHS
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