Research workbench
Red fluorescent protein mkeima at pH 7.0
Analyse Red fluorescent protein mkeima at pH 7.0 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3IR8
- Type
- protein
- Length
- 427 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Large stokes shift fluorescent protein
- UniProt
- Q1JV70
- Ligands
- CRQ
- Pockets
- 4 · best druggability 0.76
Structure
x-ray diffraction · 2 distinct chains · 5% helix, 58% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Large stokes shift fluorescent protein | protein | 213 | 5% helix, 58% strand | Q1JV70 |
| B | Large stokes shift fluorescent protein | protein | 214 | 5% helix, 58% strand | Q1JV70 |
Ligands and binding sites
- CRQ · [2-(3-carbamoyl-1-imino-propyl)-4-(4-hydroxy-benzylidene)-5-oxo-4,5-dihydro-imidazol-1-yl]-acetic acid · ligand · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 95 | 0.76 | 0.98 | 28 | CRQ |
| 2 | 83 | 0.74 | 0.97 | 29 | CRQ |
| 3 | 135 | 0.54 | 0.82 | 28 | empty |
| 4 | 62 | 0.36 | 0.78 | 19 | empty |
Interfaces
1 interface between chains.
- A–B · 888 Ų buried · 18 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 cofactor (chromophore).
Compared structures
- 3IR8 · Red fluorescent protein mKeima at pH 7.0 · 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 Q1JV70
- Elsewhere: RCSB PDB 3IR8 · PDBe 3IR8 · UniProt Q1JV70
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