MolNFT v1 · #104347 · protein
Crystal structure of large stokes shift fluorescent protein lssmorange
4Q7R: “Crystal structure of large stokes shift fluorescent protein lssmorange”. X-ray diffraction, 2 ligands (OFM, ZN), 4 pockets (best druggability 0.84). MolNFT v1 #104347 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 4Q7R
- Type
- protein
- Length
- 437 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Lssmorange
- UniProt
- D0VWW2
- Ligands
- OFM, ZN
- Pockets
- 4 · best druggability 0.84
Structure
x-ray diffraction · 2 distinct chains · 5% helix, 56% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Lssmorange | protein | 223 | 6% helix, 56% strand | D0VWW2 |
| B | Lssmorange | protein | 214 | 5% helix, 56% strand | D0VWW2 |
Ligands and binding sites
- OFM · [(4Z)-2-{(2R,5R)-2-[(1S)-1-amino-2-phenylethyl]-2-hydroxy-5-methyl-2,5-dihydro-1,3-oxazol-4-yl}-4-(4-hydroxybenzylidene)-5-oxo-4,5-dihydro-1H-imidazol-1-yl]acetic acid · ligand · 2 copies · chains A, B
- ZN · Zinc ion · metal · 17 copies · chains A, B
- ACT · Acetate ion · additive · 9 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 207 | 0.84 | 0.97 | 39 | OFM |
| 2 | 198 | 0.83 | 0.96 | 40 | OFM |
| 3 | 487 | 0.66 | 0.78 | 66 | ZN, ACT |
| 4 | 182 | 0.55 | 0.80 | 24 | ACT, ZN |
Interfaces
1 interface between chains.
- A–B · 767 Ų buried · 21 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 covalent (covalent ligand).
Compared structures
- 4Q7R · Crystal structure of large Stokes shift fluorescent protein LSSmOrange · 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 D0VWW2
- Elsewhere: RCSB PDB 4Q7R · PDBe 4Q7R · UniProt D0VWW2
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