MolNFT v1 · #108419 · protein
Crystal structure of a superfolder GFP mutant K26C disulfide dimer, P 21 21 21 space group
4W6B · Fluorescent protein K26C: “Crystal structure of a superfolder GFP mutant K26C disulfide dimer, P 21 21 21 space group”. X-ray diffraction, 3 ligands (CRO, MG, CL), 6 pockets (best druggability 0.78). MolNFT v1 #108419 on GenesisL1…
- PDB
- 4W6B
- Type
- protein
- Length
- 452 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Fluorescent protein K26C
- Ligands
- CRO, MG, CL
- Pockets
- 6 · best druggability 0.78
Structure
x-ray diffraction · 2 distinct chains · 11% helix, 52% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Fluorescent protein K26C | protein | 228 | 11% helix, 52% strand | — |
| B | Fluorescent protein K26C | protein | 224 | 11% helix, 53% strand | — |
Ligands and binding sites
- CRO · {2-[(1R,2R)-1-amino-2-hydroxypropyl]-4-(4-hydroxybenzylidene)-5-oxo-4,5-dihydro-1H-imidazol-1-yl}acetic acid · ligand · 2 copies · chains A, B
- MG · Magnesium ion · metal · chains A, B
- CL · Chloride ion · ion · 2 copies · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 103 | 0.78 | 0.97 | 23 | CRO |
| 2 | 78 | 0.73 | 0.97 | 26 | CRO |
| 3 | 198 | 0.61 | 0.82 | 32 | MG |
| 4 | 86 | 0.36 | 0.75 | 14 | empty |
| 5 | 60 | 0.29 | 0.74 | 14 | empty |
Interfaces
1 interface between chains.
- A–B · 484 Ų buried · 4 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 cofactor, 1 disulfide (chromophore, disulfide).
Compared structures
- 4W6B · Crystal Structure of a Superfolder GFP Mutant K26C Disulfide Dimer, P 21 21 21 Space Group · 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 4W6B · PDBe 4W6B
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