Research workbench
Irisfp fluorescent protein in its green form, trans conformation
Analyse Irisfp fluorescent protein in its green form, trans conformation in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2VVI
- Type
- protein
- Length
- 877 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Green to red photoconvertible GFP-like protein eosfp
- UniProt
- Q5S6Z9
- Ligands
- 7R0, SO4, SO3
- Pockets
- 10 · best druggability 0.81
Structure
x-ray diffraction · 4 distinct chains · 4% helix, 57% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Green to red photoconvertible GFP-like protein eosfp | protein | 217 | 3% helix, 57% strand | Q5S6Z9 |
| B | Green to red photoconvertible GFP-like protein eosfp | protein | 219 | 3% helix, 57% strand | Q5S6Z9 |
| C | Green to red photoconvertible GFP-like protein eosfp | protein | 222 | 4% helix, 56% strand | Q5S6Z9 |
| D | Green to red photoconvertible GFP-like protein eosfp | protein | 219 | 5% helix, 57% strand | Q5S6Z9 |
Ligands and binding sites
- 7R0 · 2-[(4E)-2-[(1S)-1-azanyl-2-(1H-imidazol-4-yl)ethyl]-4-[(4-hydroxyphenyl)methylidene]-5-oxidanylidene-imidazol-1-yl]ethanoic acid · ligand · 4 copies · chains A, B, C, D
- SO4 · Sulfate ion · ion · 16 copies · chains A, C, B, D
- SO3 · Sulfite ion · ion · 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, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1171 | 0.81 | 0.83 | 72 | empty |
| 2 | 83 | 0.76 | 0.98 | 24 | 7R0 |
| 3 | 77 | 0.75 | 0.98 | 20 | 7R0 |
| 4 | 73 | 0.74 | 0.98 | 23 | 7R0 |
| 5 | 73 | 0.73 | 0.98 | 23 | 7R0 |
Interfaces
4 interfaces between chains.
- A–B · 1199 Ų buried · 14 hydrogen bonds · protein-protein
- C–D · 1165 Ų buried · 10 hydrogen bonds · protein-protein
- B–D · 1008 Ų buried · 19 hydrogen bonds · protein-protein
- A–C · 994 Ų buried · 15 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 8 covalent (covalent ligand).
Compared structures
- 2VVI · IrisFP fluorescent protein in its green form, trans conformation · 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 Q5S6Z9
- Elsewhere: RCSB PDB 2VVI · PDBe 2VVI · UniProt Q5S6Z9
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