MolNFT v1 · #103738 · protein
Crystal structure of phanta, a weakly fluorescent photochromic GFP- like protein. on state
4PPJ · Monomeric azami green: “Crystal structure of phanta, a weakly fluorescent photochromic GFP- like protein. on state”. X-ray diffraction, 1 ligand (NRQ), 14 pockets (best druggability 0.85). MolNFT v1 #103738 on GenesisL1: 3D…
- PDB
- 4PPJ
- Type
- protein
- Length
- 861 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Monomeric azami green
- Ligands
- NRQ
- Pockets
- 14 · best druggability 0.85
Structure
x-ray diffraction · 3 distinct chains · 5% helix, 57% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Monomeric azami green | protein | 215 | 5% helix, 58% strand | — |
| B, C | Monomeric azami green | protein | 215 | 5% helix, 58% strand | — |
| D | Monomeric azami green | protein | 216 | 6% helix, 57% strand | — |
Ligands and binding sites
- NRQ · {(4Z)-4-(4-hydroxybenzylidene)-2-[3-(methylthio) propanimidoyl]-5-oxo-4,5-dihydro-1H-imidazol-1-yl}acetic acid · ligand · 4 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
14 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 617 | 0.85 | 0.90 | 53 | empty |
| 2 | 90 | 0.77 | 0.99 | 26 | NRQ |
| 3 | 86 | 0.75 | 0.98 | 27 | NRQ |
| 4 | 77 | 0.75 | 0.98 | 26 | NRQ |
| 5 | 78 | 0.75 | 0.98 | 25 | NRQ |
Interfaces
6 interfaces between chains.
- A–B · 1063 Ų buried · 7 hydrogen bonds · protein-protein
- A–D · 1008 Ų buried · 16 hydrogen bonds · protein-protein
- C–D · 982 Ų buried · 13 hydrogen bonds · protein-protein
- B–C · 856 Ų buried · 24 hydrogen bonds · protein-protein
- B–D · 307 Ų buried · 3 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 8 cofactor (chromophore).
Compared structures
- 4PPJ · Crystal structure of Phanta, a weakly fluorescent photochromic GFP-like protein. ON state · 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 4PPJ · PDBe 4PPJ
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