MolNFT v1 · #89722 · protein
Crystal structure of a reconstructed kaede-type red fluorescent protein, lea X(6)
4DXO · Lea X(6) GFP-like proteins: “Crystal structure of a reconstructed kaede-type red fluorescent protein, lea X(6)”. X-ray diffraction, 2 ligands (CR8, NA), 2 pockets (best druggability 0.76). MolNFT v1 #89722 on GenesisL1: 3D…
- PDB
- 4DXO
- Type
- protein
- Length
- 212 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Lea X(6) GFP-like proteins
- Ligands
- CR8, NA
- Pockets
- 2 · best druggability 0.76
Structure
x-ray diffraction · 1 distinct chain · 3% helix, 58% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Lea X(6) GFP-like proteins | protein | 212 | 3% helix, 58% strand | — |
Ligands and binding sites
- CR8 · 2-[1-amino-2-(1H-imidazol-5-yl)ethyl]-1-(carboxymethyl)-4-[(4-oxocyclohexa-2,5-dien-1-ylidene)methyl]-1H-imidazol-5-olate · ligand · chains A
- NA · Sodium ion · metal
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
2 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 95 | 0.76 | 0.97 | 27 | CR8 |
| 2 | 50 | 0.42 | 0.83 | 20 | empty |
Modifications
Observed in the structure: 2 covalent (covalent ligand).
Compared structures
- 4DXO · Crystal Structure of a reconstructed Kaede-type Red Fluorescent Protein, LEA X(6) · 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 4DXO · PDBe 4DXO
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