MolNFT v1 · #170110 · protein
Highly pH-resistant long stokes-shift, red fluorescent protein mcrispred
6XWY · Red fluorescent protein EQFP611: “Highly pH-resistant long stokes-shift, red fluorescent protein mcrispred”. X-ray diffraction, 1 ligand (NRQ), 9 pockets (best druggability 0.76). MolNFT v1 #170110 on GenesisL1: 3D structure…
- PDB
- 6XWY
- Type
- protein
- Length
- 865 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Red fluorescent protein EQFP611
- UniProt
- Q8ISF8
- Ligands
- NRQ
- Pockets
- 9 · best druggability 0.76
Structure
x-ray diffraction · 3 distinct chains · 7% helix, 58% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C | Red fluorescent protein EQFP611 | protein | 217 | 6% helix, 58% strand | Q8ISF8 |
| B | Red fluorescent protein EQFP611 | protein | 215 | 9% helix, 58% strand | Q8ISF8 |
| D | Red fluorescent protein EQFP611 | protein | 216 | 6% helix, 58% strand | Q8ISF8 |
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
- EDO · 1,2-ethanediol · additive · 3 copies · chains A, B, D
- MLA · Malonic acid · additive · 3 copies · chains A, D, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 100 | 0.76 | 0.97 | 28 | NRQ |
| 2 | 83 | 0.76 | 0.98 | 28 | NRQ |
| 3 | 85 | 0.75 | 0.98 | 27 | NRQ |
| 4 | 71 | 0.72 | 0.97 | 26 | NRQ |
| 5 | 464 | 0.58 | 0.74 | 46 | empty |
Interfaces
5 interfaces between chains.
- A–C · 853 Ų buried · 9 hydrogen bonds · protein-protein
- B–D · 835 Ų buried · 6 hydrogen bonds · protein-protein
- B–C · 511 Ų buried · 2 hydrogen bonds · protein-protein
- A–D · 63 Ų buried · 0 hydrogen bonds · protein-protein
- A–B · 24 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 8 cofactor (chromophore).
Compared structures
- 6XWY · Highly pH-resistant long stokes-shift, red fluorescent protein mCRISPRed · the same entry in another collection · chain A against A, TM-score 1.00
- Q8ISF8 · AlphaFold monomer V2.0 prediction for red fluorescent protein EQFP611 (Q8ISF8) · a predicted model of the same protein · chain B 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 Q8ISF8
- Elsewhere: RCSB PDB 6XWY · PDBe 6XWY · UniProt Q8ISF8
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