MolNFT v1 · #38767 · protein
Crystal structure of a redshifted mutant (K83M) of the red fluorescent protein DRFP583/DSRED
2H8Q: “Crystal structure of a redshifted mutant (K83M) of the red fluorescent protein DRFP583/DSRED”. X-ray diffraction, 1 ligand (CRQ), 8 pockets (best druggability 0.77). MolNFT v1 #38767 on GenesisL1: 3D structure, binding sites and…
- PDB
- 2H8Q
- Type
- protein
- Length
- 864 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Red fluorescent protein DRFP583
- UniProt
- Q9U6Y8
- Ligands
- CRQ
- Pockets
- 8 · best druggability 0.77
Structure
x-ray diffraction · 1 distinct chain · 6% helix, 57% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | Red fluorescent protein DRFP583 | protein | 216 | 6% helix, 57% strand | Q9U6Y8 |
Ligands and binding sites
- CRQ · [2-(3-carbamoyl-1-imino-propyl)-4-(4-hydroxy-benzylidene)-5-oxo-4,5-dihydro-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
8 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 94 | 0.77 | 0.98 | 28 | CRQ |
| 2 | 1085 | 0.77 | 0.79 | 92 | empty |
| 3 | 93 | 0.76 | 0.97 | 30 | CRQ |
| 4 | 97 | 0.75 | 0.97 | 28 | CRQ |
| 5 | 88 | 0.75 | 0.97 | 29 | CRQ |
Interfaces
4 interfaces between chains.
- C–D · 1125 Ų buried · 17 hydrogen bonds · protein-protein
- A–B · 1109 Ų buried · 17 hydrogen bonds · protein-protein
- A–D · 238 Ų buried · 3 hydrogen bonds · protein-protein
- A–C · 204 Ų buried · 3 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 8 cofactor (chromophore).
Compared structures
- 2H8Q · Crystal Structure of a Redshifted Mutant (K83M) of the Red Fluorescent Protein… · the same entry in another collection · chain A against A, TM-score 1.00
- Q9U6Y8 · AlphaFold monomer V2.0 prediction for red fluorescent protein DRFP583 (Q9U6Y8) · 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 Q9U6Y8
- Elsewhere: RCSB PDB 2H8Q · PDBe 2H8Q · UniProt Q9U6Y8
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