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Crystal structure of a novel green fluorescent protein from marine copepod pontellina plumata
Analyse Crystal structure of a 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
- 2G6X
- 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
- 12 · best druggability 0.84
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 | 10% helix, 57% strand | — |
| B | Green fluorescent protein 2 | protein | 215 | 11% helix, 55% strand | — |
| C | Green fluorescent protein 2 | protein | 215 | 11% helix, 55% strand | — |
| D | Green fluorescent protein 2 | protein | 214 | 11% 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
12 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 890 | 0.84 | 0.87 | 109 | empty |
| 2 | 53 | 0.71 | 0.99 | 22 | CR2 |
| 3 | 50 | 0.71 | 0.99 | 19 | CR2 |
| 4 | 64 | 0.70 | 0.97 | 23 | CR2 |
| 5 | 52 | 0.70 | 0.98 | 23 | CR2 |
Interfaces
6 interfaces between chains.
- C–D · 1051 Ų buried · 7 hydrogen bonds · protein-protein
- A–B · 991 Ų buried · 8 hydrogen bonds · protein-protein
- B–C · 735 Ų buried · 0 hydrogen bonds · protein-protein
- A–D · 578 Ų buried · 1 hydrogen bond · protein-protein
- B–D · 42 Ų buried · 1 hydrogen bond · protein-protein
Modifications
Observed in the structure: 8 cofactor (chromophore).
Compared structures
- 2G6X · Crystal structure of a 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 2G6X · PDBe 2G6X
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