Research workbench
Crystal structure of red fluorescent protein mcherry complexed with the nanobody LAM4 at 1.9 angstron resolution
Analyse Crystal structure of red fluorescent protein mcherry complexed with the… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6IR1
- Type
- protein
- Length
- 340 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Mcherry fluorescent protein; MCHERRY'S nanobody LAM4
- UniProt
- X5DSL3
- Ligands
- CH6
- Pockets
- 3 · best druggability 0.70
Structure
x-ray diffraction · 2 distinct chains · 6% helix, 54% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Mcherry fluorescent protein | protein | 216 | 5% helix, 58% strand | X5DSL3 |
| B | MCHERRY'S nanobody LAM4 | 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, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 51 | 0.70 | 0.98 | 20 | CH6 |
| 2 | 88 | 0.52 | 0.84 | 19 | empty |
| 3 | 61 | 0.40 | 0.80 | 15 | empty |
Interfaces
1 interface between chains.
- A–B · 796 Ų buried · 11 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 cofactor (chromophore).
Compared structures
- 6IR1 · Crystal structure of red fluorescent protein mCherry complexed with the nanobody LaM4 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 6IR1 · PDBe 6IR1 · UniProt X5DSL3
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