Research workbench
Crystal structure of the novel green fluorescent protein from marine copepod pontellina plumata
Analyse Crystal structure of the novel green fluorescent protein from marine copepod… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2G6Y
- Type
- protein
- Length
- 857 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Green fluorescent protein 2
- Ligands
- CR2
- Pockets
- 10 · best druggability 0.83
Structure
x-ray diffraction · 4 distinct chains · 11% helix, 56% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Green fluorescent protein 2 | protein | 213 | 11% helix, 55% strand | — |
| B | Green fluorescent protein 2 | protein | 215 | 11% helix, 55% strand | — |
| C | Green fluorescent protein 2 | protein | 215 | 12% helix, 56% strand | — |
| D | Green fluorescent protein 2 | protein | 214 | 10% helix, 56% strand | — |
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
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
10 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 786 | 0.83 | 0.87 | 102 | empty |
| 2 | 62 | 0.72 | 0.98 | 20 | CR2 |
| 3 | 55 | 0.71 | 0.98 | 21 | CR2 |
| 4 | 58 | 0.71 | 0.98 | 21 | CR2 |
| 5 | 64 | 0.71 | 0.97 | 23 | CR2 |
Interfaces
6 interfaces between chains.
- A–B · 1098 Ų buried · 9 hydrogen bonds · protein-protein
- C–D · 1051 Ų buried · 13 hydrogen bonds · protein-protein
- B–C · 704 Ų buried · 0 hydrogen bonds · protein-protein
- A–D · 646 Ų buried · 2 hydrogen bonds · protein-protein
- A–C · 22 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 8 cofactor (chromophore).
Compared structures
- 2G6Y · Crystal structure of the novel green fluorescent protein from marine copepod Pontellina… · 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 2G6Y · PDBe 2G6Y
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