Research workbench
Crystal structure of near-infrared fluorescent protein with an extended stokes shift, pH 4.5
Analyse Crystal structure of near-infrared fluorescent protein with an extended stokes… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4KGE
- Type
- protein
- Length
- 443 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- TAGRFP675, red fluorescent protein
- Ligands
- NRQ, CL
- Pockets
- 4 · best druggability 0.76
Structure
x-ray diffraction · 2 distinct chains · 6% helix, 57% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | TAGRFP675, red fluorescent protein | protein | 224 | 7% helix, 56% strand | — |
| B | TAGRFP675, red fluorescent protein | protein | 219 | 5% helix, 58% strand | — |
Ligands and binding sites
- NRQ · {(4Z)-4-(4-hydroxybenzylidene)-2-[3-(methylthio) propanimidoyl]-5-oxo-4,5-dihydro-1H-imidazol-1-yl}acetic acid · ligand · 2 copies · chains A, B
- CL · Chloride ion · ion · 3 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 | 91 | 0.76 | 0.98 | 27 | NRQ |
| 2 | 74 | 0.75 | 0.99 | 26 | NRQ |
| 3 | 50 | 0.71 | 0.99 | 17 | CL |
| 4 | 111 | 0.42 | 0.77 | 23 | empty |
Interfaces
1 interface between chains.
- A–B · 1366 Ų buried · 15 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 cofactor (chromophore).
Compared structures
- 4KGE · Crystal structure of near-infrared fluorescent protein with an extended stokes shift, pH… · 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 4KGE · PDBe 4KGE
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