MolNFT v1 · #97476 · protein
Crystal structure of sfcherry
4KF4 · Fluorescent protein sfcherry: “Crystal structure of sfcherry”. X-ray diffraction, 1 ligand (CH6), 20 pockets (best druggability 0.78). MolNFT v1 #97476 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 4KF4
- Type
- protein
- Length
- 1,718 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Fluorescent protein sfcherry
- Ligands
- CH6
- Pockets
- 20 · best druggability 0.78
Structure
x-ray diffraction · 2 distinct chains · 5% helix, 58% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C, E, F, G, H | Fluorescent protein sfcherry | protein | 215 | 5% helix, 58% strand | — |
| B, D | Fluorescent protein sfcherry | protein | 214 | 6% helix, 57% strand | — |
Ligands and binding sites
- CH6 · {(4Z)-2-[(1S)-1-amino-3-(methylsulfanyl)propyl]-4-[(4-hydroxyphenyl)methylidene]-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, 20 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 649 | 0.78 | 0.84 | 68 | empty |
| 2 | 91 | 0.76 | 0.98 | 29 | CH6 |
| 3 | 96 | 0.76 | 0.97 | 28 | CH6 |
| 4 | 563 | 0.75 | 0.83 | 49 | empty |
| 5 | 89 | 0.74 | 0.96 | 28 | CH6 |
Interfaces
14 interfaces between chains.
- C–D · 944 Ų buried · 12 hydrogen bonds · protein-protein
- A–B · 918 Ų buried · 11 hydrogen bonds · protein-protein
- A–E · 397 Ų buried · 7 hydrogen bonds · protein-protein
- C–F · 392 Ų buried · 5 hydrogen bonds · protein-protein
- D–E · 354 Ų buried · 3 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 16 cofactor (chromophore).
Compared structures
- 4KF4 · Crystal Structure of sfCherry · 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 4KF4 · PDBe 4KF4
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