MolNFT v1 · #82345 · protein
Green-fluorescent variant of the non-fluorescent chromoprotein RTMS5
3VK1 · GFP-like non-fluorescent chromoprotein: “Green-fluorescent variant of the non-fluorescent chromoprotein RTMS5”. X-ray diffraction, 3 ligands (QFG, CL, IOD), 2 pockets (best druggability 0.75). MolNFT v1 #82345 on GenesisL1: 3D…
- PDB
- 3VK1
- Type
- protein
- Length
- 216 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- GFP-like non-fluorescent chromoprotein
- UniProt
- P83690
- Ligands
- QFG, CL, IOD
- Pockets
- 2 · best druggability 0.75
Structure
x-ray diffraction · 1 distinct chain · 5% helix, 57% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | GFP-like non-fluorescent chromoprotein | protein | 216 | 5% helix, 57% strand | P83690 |
Ligands and binding sites
- QFG · {(4E)-2-[(1E)-4-amino-4-oxobutanimidoyl]-4-benzylidene-5-oxo-4,5-dihydro-1H-imidazol-1-yl}acetic acid · ligand · chains A
- CL · Chloride ion · ion · 3 copies · chains A
- IOD · Iodide ion · ion · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
2 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 90 | 0.75 | 0.97 | 28 | QFG, CL |
| 2 | 95 | 0.40 | 0.77 | 21 | empty |
Modifications
Observed in the structure: 2 covalent (covalent ligand).
Compared structures
- 3VK1 · Green-fluorescent variant of the non-fluorescent chromoprotein Rtms5 · the same entry in another collection · chain A against A, TM-score 1.00
- P83690 · AlphaFold monomer V2.0 prediction for GFP-like non-fluorescent chromoprotein (P83690) · a predicted model of the same protein · 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 P83690
- Elsewhere: RCSB PDB 3VK1 · PDBe 3VK1 · UniProt P83690
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