MolNFT v1 · #59414 · protein
Monomeric far-red fluorescent protein mkate crystallized at pH 7.0
3BXB: “Monomeric far-red fluorescent protein mkate crystallized at pH 7.0”. X-ray diffraction, 1 ligand (NRQ), 20 pockets (best druggability 0.84). MolNFT v1 #59414 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 3BXB
- Type
- protein
- Length
- 1,776 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Far-red fluorescent protein mkate
- Ligands
- NRQ
- Pockets
- 20 · best druggability 0.84
Structure
x-ray diffraction · 1 distinct chain · 7% helix, 56% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D, E, F, G, H | Far-red fluorescent protein mkate | protein | 222 | 7% 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 · 8 copies · chains A, B, C, D, E, F, G, H
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 15 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 628 | 0.84 | 0.89 | 56 | empty |
| 2 | 572 | 0.83 | 0.89 | 50 | empty |
| 3 | 107 | 0.79 | 0.98 | 34 | NRQ |
| 4 | 104 | 0.78 | 0.98 | 27 | NRQ |
| 5 | 109 | 0.77 | 0.97 | 31 | NRQ |
Interfaces
17 interfaces between chains.
- E–F · 1552 Ų buried · 27 hydrogen bonds · protein-protein
- G–H · 1548 Ų buried · 32 hydrogen bonds · protein-protein
- A–B · 1526 Ų buried · 33 hydrogen bonds · protein-protein
- C–D · 1507 Ų buried · 26 hydrogen bonds · protein-protein
- F–G · 1022 Ų buried · 13 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 16 cofactor (chromophore).
Compared structures
- 3BXB · Monomeric Far-red Fluorescent Protein mKate Crystallized at pH 7.0 · 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 3BXB · PDBe 3BXB
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