Research workbench
A GFP-like protein from marine copepod, chiridius poppei
Analyse A GFP-like protein from marine copepod, chiridius poppei in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2DD7
- Type
- protein
- Length
- 427 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Green fluorescent protein
- UniProt
- Q2MHN7
- Ligands
- CR2, CL
- Pockets
- 2 · best druggability 0.70
Structure
x-ray diffraction · 2 distinct chains · 9% helix, 57% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Green fluorescent protein | protein | 214 | 9% helix, 57% strand | Q2MHN7 |
| B | Green fluorescent protein | protein | 213 | 9% 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 · 2 copies · chains A, B
- CL · Chloride ion · ion · chains A
- CXS · 3-cyclohexyl-1-propylsulfonic acid · additive · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
2 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 50 | 0.70 | 0.98 | 22 | CR2 |
| 2 | 52 | 0.69 | 0.98 | 25 | CR2 |
Modifications
Observed in the structure: 4 cofactor (chromophore).
Compared structures
- 2DD7 · A GFP-like protein from marine copepod, 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 2DD7 · PDBe 2DD7 · UniProt Q2MHN7
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