MolNFT v1 · #152717 · protein
Crystal structure of red fluorescent protein mcherry complexed with the nanobody LAM2 at 1.4 angstron resolution
6IR2 · Mcherry fluorescent protein: “Crystal structure of red fluorescent protein mcherry complexed with the nanobody LAM2 at 1.4 angstron…”. X-ray diffraction, 1 ligand (CH6), 3 pockets (best druggability 0.75). MolNFT v1 #152717 on…
- PDB
- 6IR2
- Type
- protein
- Length
- 338 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Mcherry fluorescent protein; MCHERRY'S nanobody LAM2
- UniProt
- X5DSL3
- Ligands
- CH6
- Pockets
- 3 · best druggability 0.75
Structure
x-ray diffraction · 2 distinct chains · 6% helix, 54% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Mcherry fluorescent protein | protein | 214 | 5% helix, 58% strand | X5DSL3 |
| B | MCHERRY'S nanobody LAM2 | protein | 124 | 7% helix, 47% strand | — |
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 · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 76 | 0.75 | 0.98 | 26 | CH6 |
| 2 | 71 | 0.39 | 0.79 | 19 | empty |
| 3 | 69 | 0.37 | 0.78 | 21 | empty |
Interfaces
1 interface between chains.
- A–B · 750 Ų buried · 9 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 cofactor (chromophore).
Compared structures
- 6IR2 · Crystal structure of red fluorescent protein mCherry complexed with the nanobody LaM2 at… · 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 6IR2 · PDBe 6IR2 · UniProt X5DSL3
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