MolNFT v1 · #149066 · protein
MTFP1/DARPIN 1238_E11 complex in space group C2
6FP8 · GFP-like fluorescent chromoprotein CFP484: “MTFP1/DARPIN 1238_E11 complex in space group C2”. X-ray diffraction, 2 ligands (PIA, SO4), 5 pockets (best druggability 0.72). MolNFT v1 #149066 on GenesisL1: 3D structure, binding sites…
- PDB
- 6FP8
- Type
- protein
- Length
- 383 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- GFP-like fluorescent chromoprotein CFP484; DARPIN1238_E11
- UniProt
- Q9U6Y3
- Ligands
- PIA, SO4
- Pockets
- 5 · best druggability 0.72
Structure
x-ray diffraction · 2 distinct chains · 28% helix, 33% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | GFP-like fluorescent chromoprotein CFP484 | protein | 216 | 5% helix, 58% strand | Q9U6Y3 |
| B | DARPIN1238_E11 | protein | 167 | 57% helix, 0% strand | — |
Ligands and binding sites
- PIA · [(4Z)-2-[(1S)-1-aminoethyl]-4-(4-hydroxybenzylidene)-5-oxo-4,5-dihydro-1H-imidazol-1-yl]acetic acid · ligand · chains A
- SO4 · Sulfate ion · ion · 4 copies · chains A, B
- MPD · (4S)-2-methyl-2,4-pentanediol · additive · 3 copies · chains A
- EDO · 1,2-ethanediol · additive · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 64 | 0.72 | 0.98 | 27 | PIA |
| 2 | 236 | 0.70 | 0.86 | 33 | SO4 |
| 3 | 68 | 0.45 | 0.82 | 14 | empty |
| 4 | 73 | 0.31 | 0.74 | 14 | empty |
| 5 | 68 | 0.28 | 0.73 | 16 | empty |
Interfaces
1 interface between chains.
- A–B · 965 Ų buried · 7 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 covalent (covalent ligand).
Compared structures
- 6FP8 · mTFP1/DARPin 1238_E11 complex in space group C2 · the same entry in another collection · chain A against A, TM-score 1.00
- Q9U6Y3 · AlphaFold monomer V2.0 prediction for GFP-like fluorescent chromoprotein CFP484 (Q9U6Y3) · a predicted model of the same protein · chain A against A, TM-score 0.99
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 Q9U6Y3
- Elsewhere: RCSB PDB 6FP8 · PDBe 6FP8 · UniProt Q9U6Y3
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