Research workbench
Genetically encoded phenyl azide photochemistry drive positive and negative functional modulation of a red fluorescent protein
Analyse Genetically encoded phenyl azide photochemistry drive positive and negative… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4ZIN
- Type
- protein
- Length
- 648 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Mcherry fluorescent protein
- UniProt
- X5DSL3
- Ligands
- CH6, SO4
- Pockets
- 6 · best druggability 0.78
Structure
x-ray diffraction · 1 distinct chain · 5% helix, 58% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C | Mcherry fluorescent protein | protein | 216 | 5% helix, 58% strand | X5DSL3 |
Ligands and binding sites
- CH6 · {(4Z)-2-[(1S)-1-amino-3-(methylsulfanyl)propyl]-4-[(4-hydroxyphenyl)methylidene]-5-oxo-4,5-dihydro-1H-imidazol-1-yl}acetic acid · ligand · 3 copies · chains A, B, C
- SO4 · Sulfate ion · ion · 6 copies · chains A, B, C
- EDO · 1,2-ethanediol · additive · chains C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 937 | 0.78 | 0.80 | 89 | empty |
| 2 | 93 | 0.76 | 0.98 | 27 | CH6 |
| 3 | 62 | 0.73 | 0.98 | 18 | CH6 |
| 4 | 58 | 0.70 | 0.97 | 20 | CH6 |
| 5 | 183 | 0.52 | 0.78 | 33 | SO4 |
Interfaces
3 interfaces between chains.
- A–B · 542 Ų buried · 5 hydrogen bonds · protein-protein
- B–C · 494 Ų buried · 8 hydrogen bonds · protein-protein
- A–C · 136 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 6 cofactor, 3 modified (chromophore, nonstandard).
Compared structures
- 4ZIN · Genetically encoded Phenyl Azide Photochemistry Drive Positive and Negative Functional… · 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 X5DSL3
- Elsewhere: RCSB PDB 4ZIN · PDBe 4ZIN · UniProt X5DSL3
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