MolNFT v1 · #186542 · protein
A new fluorescent protein darkmruby at pH 5.0
7RHA: “A new fluorescent protein darkmruby at pH 5.0”. X-ray diffraction, 2 ligands (NRQ, SO4), 4 pockets (best druggability 0.76). MolNFT v1 #186542 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 7RHA
- Type
- protein
- Length
- 439 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Darkmruby
- Ligands
- NRQ, SO4
- Pockets
- 4 · best druggability 0.76
Structure
x-ray diffraction · 2 distinct chains · 6% helix, 57% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| B | Darkmruby | protein | 219 | 6% helix, 57% strand | — |
| A | Darkmruby | protein | 220 | 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 · 2 copies · chains B, A
- SO4 · Sulfate ion · ion · 2 copies · chains B, A
- EDO · 1,2-ethanediol · additive · 12 copies · chains B, A
- ACT · Acetate ion · additive · 2 copies · chains B, A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 103 | 0.76 | 0.97 | 29 | NRQ |
| 2 | 88 | 0.75 | 0.97 | 30 | NRQ |
| 3 | 464 | 0.67 | 0.79 | 65 | EDO |
| 4 | 161 | 0.42 | 0.74 | 25 | empty |
Interfaces
1 interface between chains.
- B–A · 498 Ų buried · 4 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 cofactor (chromophore).
Compared structures
- 7RHA · A new fluorescent protein darkmRuby at pH 5.0 · the same entry in another collection · chain B against B, 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 7RHA · PDBe 7RHA
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