Research workbench
Crystal structure of stony coral fluorescent protein kaede, red form
Analyse Crystal structure of stony coral fluorescent protein kaede, red form in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2GW4
- Type
- protein
- Length
- 436 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Kaede
- Ligands
- RC7, NI
- Pockets
- 4 · best druggability 0.76
Structure
x-ray diffraction · 2 distinct chains · 3% helix, 57% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C | Kaede | protein | 62 | 10% helix, 53% strand | — |
| B, D | Kaede | protein | 156 | 0% helix, 59% strand | — |
Ligands and binding sites
- RC7 · 2-[(4Z)-4-[(4-hydroxyphenyl)methylidene]-2-[(E)-2-(1H-imidazol-4-yl)ethenyl]-5-oxidanylidene-imidazol-1-yl]ethanoic acid · ligand · 2 copies · chains A, B, C, D
- NI · Nickel (II) ion · metal · 4 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 79 | 0.76 | 0.99 | 24 | RC7 |
| 2 | 80 | 0.73 | 0.96 | 27 | RC7 |
| 3 | 133 | 0.43 | 0.77 | 26 | empty |
| 4 | 53 | 0.25 | 0.73 | 14 | empty |
Interfaces
3 interfaces between chains.
- A–B · 2238 Ų buried · 40 hydrogen bonds · protein-protein
- C–D · 2226 Ų buried · 38 hydrogen bonds · protein-protein
- B–D · 1073 Ų buried · 11 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 covalent, 2 modified (covalent ligand, nonstandard).
Compared structures
- 2GW4 · Crystal structure of stony coral fluorescent protein Kaede, red form · 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 2GW4 · PDBe 2GW4
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