Research workbench
Monomeric far-red fluorescent protein mkate crystallized at pH 2.0
Analyse Monomeric far-red fluorescent protein mkate crystallized at pH 2.0 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3BX9
- Type
- protein
- Length
- 448 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Far-red fluorescent protein mkate
- Ligands
- NRQ
- Pockets
- 5 · best druggability 0.76
Structure
x-ray diffraction · 1 distinct chain · 6% helix, 56% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Far-red fluorescent protein mkate | protein | 224 | 6% helix, 56% 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 A, B
- CIT · Citric acid · additive · 6 copies · chains A, B
- GOL · Glycerol · additive · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 83 | 0.76 | 0.98 | 29 | NRQ |
| 2 | 77 | 0.74 | 0.98 | 25 | NRQ |
| 3 | 271 | 0.57 | 0.78 | 30 | empty |
| 4 | 112 | 0.43 | 0.78 | 21 | CIT |
| 5 | 102 | 0.42 | 0.78 | 17 | CIT |
Interfaces
1 interface between chains.
- A–B · 738 Ų buried · 6 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 cofactor (chromophore).
Compared structures
- 3BX9 · Monomeric Far-red Fluorescent Protein mKate Crystallized at pH 2.0 · 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 3BX9 · PDBe 3BX9
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