MolNFT v1 · #57479 · protein
Crystal structure analysis of the fluorescent protein killerred
3A8S: “Crystal structure analysis of the fluorescent protein killerred”. X-ray diffraction, 1 ligand (CRQ), 5 pockets (best druggability 0.82). MolNFT v1 #57479 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 3A8S
- Type
- protein
- Length
- 440 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Killerred
- UniProt
- Q2TCH5
- Ligands
- CRQ
- Pockets
- 5 · best druggability 0.82
Structure
x-ray diffraction · 2 distinct chains · 5% helix, 53% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Killerred | protein | 220 | 5% helix, 52% strand | Q2TCH5 |
| B | Killerred | protein | 220 | 5% helix, 54% strand | Q2TCH5 |
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 · 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, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 165 | 0.82 | 0.98 | 39 | CRQ |
| 2 | 125 | 0.80 | 0.98 | 33 | CRQ |
| 3 | 71 | 0.35 | 0.77 | 20 | empty |
| 4 | 67 | 0.34 | 0.77 | 13 | empty |
| 5 | 68 | 0.33 | 0.75 | 16 | empty |
Interfaces
1 interface between chains.
- A–B · 1371 Ų buried · 13 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 cofactor (chromophore).
Compared structures
- 3A8S · Crystal structure analysis of the fluorescent protein KillerRed · 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
- Every structure of UniProt Q2TCH5
- Elsewhere: RCSB PDB 3A8S · PDBe 3A8S · UniProt Q2TCH5
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