MolNFT v1 · #108423 · protein
Crystal structure of full-length split GFP mutant K26C disulfide dimer, P 32 2 1 space group, form 2
4W6F · Fluorescent protein D21H/K26C: “Crystal structure of full-length split GFP mutant K26C disulfide dimer, P 32 2 1 space group, form 2”. X-ray diffraction, 2 ligands (CRO, NI), 5 pockets (best druggability 0.80). MolNFT v1 #108423 on…
- PDB
- 4W6F
- Type
- protein
- Length
- 442 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Fluorescent protein D21H/K26C
- Ligands
- CRO, NI
- Pockets
- 5 · best druggability 0.80
Structure
x-ray diffraction · 2 distinct chains · 11% helix, 53% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Fluorescent protein D21H/K26C | protein | 224 | 11% helix, 52% strand | — |
| B | Fluorescent protein D21H/K26C | protein | 218 | 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
- NI · Nickel (II) ion · metal · chains B
- IMD · Imidazole · additive · 4 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 | 114 | 0.80 | 0.98 | 29 | CRO |
| 2 | 97 | 0.77 | 0.97 | 26 | CRO |
| 3 | 162 | 0.45 | 0.76 | 30 | IMD |
| 4 | 70 | 0.39 | 0.79 | 15 | empty |
| 5 | 62 | 0.33 | 0.77 | 14 | IMD, NI |
Interfaces
1 interface between chains.
- A–B · 279 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 cofactor, 1 disulfide (chromophore, disulfide).
Compared structures
- 4W6F · Crystal Structure of Full-Length Split GFP Mutant K26C Disulfide Dimer, P 32 2 1 Space… · the same entry in another collection · chain B against B, 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 4W6F · PDBe 4W6F
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