Research workbench
A mutant of GFP-like protein from chiridius poppei
Analyse A mutant of GFP-like protein from chiridius poppei in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2DD9
- Type
- protein
- Length
- 855 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Green fluorescent protein
- UniProt
- Q2MHN7
- Ligands
- CR2, CL
- Pockets
- 10 · best druggability 0.75
Structure
x-ray diffraction · 2 distinct chains · 9% helix, 57% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, D | Green fluorescent protein | protein | 214 | 9% helix, 57% strand | Q2MHN7 |
| C | Green fluorescent protein | protein | 213 | 8% helix, 57% strand | Q2MHN7 |
Ligands and binding sites
- CR2 · {(4Z)-2-(aminomethyl)-4-[(4-hydroxyphenyl)methylidene]-5-oxo-4,5-dihydro-1H-imidazol-1-yl}acetic acid · ligand · 4 copies · chains A, B, C, D
- CL · Chloride ion · ion · chains B
- CXS · 3-cyclohexyl-1-propylsulfonic acid · additive · 5 copies · chains A, C, B, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
10 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 830 | 0.75 | 0.79 | 69 | CXS |
| 2 | 67 | 0.73 | 0.98 | 24 | CR2 |
| 3 | 74 | 0.73 | 0.97 | 24 | CR2 |
| 4 | 66 | 0.72 | 0.97 | 23 | CR2 |
| 5 | 69 | 0.70 | 0.96 | 27 | CR2 |
Interfaces
4 interfaces between chains.
- C–D · 1383 Ų buried · 18 hydrogen bonds · protein-protein
- A–B · 1353 Ų buried · 22 hydrogen bonds · protein-protein
- A–C · 316 Ų buried · 2 hydrogen bonds · protein-protein
- B–C · 271 Ų buried · 3 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 8 cofactor (chromophore).
Compared structures
- 2DD9 · A mutant of GFP-like protein from Chiridius poppei · 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 Q2MHN7
- Elsewhere: RCSB PDB 2DD9 · PDBe 2DD9 · UniProt Q2MHN7
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