Research workbench
The 2.1A crystal structure of copgfp
Analyse The 2.1A crystal structure of copgfp in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2G3O
- Type
- protein
- Length
- 1,283 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Green fluorescent protein 2
- UniProt
- Q6WV12
- Ligands
- CR2
- Pockets
- 15 · best druggability 0.72
Structure
x-ray diffraction · 3 distinct chains · 5% helix, 55% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Green fluorescent protein 2 | protein | 211 | 7% helix, 55% strand | Q6WV12 |
| B | Green fluorescent protein 2 | protein | 212 | 5% helix, 54% strand | Q6WV12 |
| C, D, E, F | Green fluorescent protein 2 | protein | 215 | 5% helix, 54% strand | Q6WV12 |
Ligands and binding sites
- CR2 · {(4Z)-2-(aminomethyl)-4-[(4-hydroxyphenyl)methylidene]-5-oxo-4,5-dihydro-1H-imidazol-1-yl}acetic acid · ligand · 6 copies · chains A, B, C, D, E, F
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
15 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 785 | 0.72 | 0.78 | 86 | empty |
| 2 | 52 | 0.71 | 0.99 | 19 | CR2 |
| 3 | 234 | 0.57 | 0.79 | 34 | empty |
| 4 | 62 | 0.57 | 0.89 | 20 | empty |
| 5 | 111 | 0.55 | 0.84 | 28 | empty |
Interfaces
6 interfaces between chains.
- A–B · 1106 Ų buried · 7 hydrogen bonds · protein-protein
- D–F · 1052 Ų buried · 4 hydrogen bonds · protein-protein
- C–E · 668 Ų buried · 14 hydrogen bonds · protein-protein
- A–D · 243 Ų buried · 0 hydrogen bonds · protein-protein
- A–C · 102 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 12 cofactor (chromophore).
Compared structures
- 2G3O · The 2.1A crystal structure of copGFP · 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 Q6WV12
- Elsewhere: RCSB PDB 2G3O · PDBe 2G3O · UniProt Q6WV12
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