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Room temperature structure of irisfp determined by serial femtosecond crystallography.
Analyse Room temperature structure of irisfp determined by serial femtosecond… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5FVF
- Type
- protein
- Length
- 884 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
- 5SQ, SO4, NH4
- Pockets
- 12 · best druggability 0.81
Structure
x-ray diffraction · 2 distinct chains · 6% helix, 57% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Green to red photoconvertible GFP-like protein eosfp | protein | 222 | 6% helix, 56% strand | Q5S6Z9 |
| C, D | Green to red photoconvertible GFP-like protein eosfp | protein | 220 | 6% helix, 57% strand | Q5S6Z9 |
Ligands and binding sites
- 5SQ · 2-[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 · 19 copies · chains A, D, B, C
- NH4 · Ammonium ion · ion · 2 copies
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 | 1104 | 0.81 | 0.83 | 67 | empty |
| 2 | 120 | 0.78 | 0.97 | 29 | 5SQ |
| 3 | 121 | 0.77 | 0.96 | 29 | 5SQ |
| 4 | 119 | 0.76 | 0.95 | 28 | 5SQ |
| 5 | 123 | 0.72 | 0.92 | 27 | 5SQ |
Interfaces
4 interfaces between chains.
- B–C · 1209 Ų buried · 9 hydrogen bonds · protein-protein
- A–D · 1186 Ų buried · 10 hydrogen bonds · protein-protein
- C–D · 978 Ų buried · 13 hydrogen bonds · protein-protein
- A–B · 962 Ų buried · 13 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 8 covalent (covalent ligand).
Compared structures
- 5FVF · Room temperature structure of IrisFP determined by serial femtosecond crystallography. · 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 5FVF · PDBe 5FVF · UniProt Q5S6Z9
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