MolNFT v1 · #113280 · protein
Crystal structure of fluorogen-activating designed ankyrin repeat protein (darpin) dimer in complex with malachite green
5AAO · FAD3210: “Crystal structure of fluorogen-activating designed ankyrin repeat protein (darpin) dimer in complex with…”. X-ray diffraction, 1 ligand (6FE), 20 pockets (best druggability 0.84). MolNFT v1 #113280 on GenesisL1: 3D…
- PDB
- 5AAO
- Type
- protein
- Length
- 1,864 residues
- Chains
- 12
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- FAD3210
- Ligands
- 6FE
- Pockets
- 20 · best druggability 0.84
Structure
x-ray diffraction · 5 distinct chains · 55% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | FAD3210 | protein | 156 | 54% helix, 0% strand | — |
| B, D, F, H, K | FAD3210 | protein | 154 | 55% helix, 0% strand | — |
| C, G | FAD3210 | protein | 156 | 55% helix, 0% strand | — |
| E, I, J | FAD3210 | protein | 157 | 55% helix, 0% strand | — |
| L | FAD3210 | protein | 155 | 55% helix, 0% strand | — |
Ligands and binding sites
- 6FE · 4-[[4-(dimethylamino)cyclohexa-2,5-dien-1-ylidene]-(4-methoxyphenyl)methyl]-N,N-dimethyl-aniline · ligand · 6 copies · chains A, I, B, C, D, E, F, G, H, J, K, L
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 11 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 668 | 0.84 | 0.88 | 57 | 6FE |
| 2 | 662 | 0.84 | 0.88 | 53 | 6FE |
| 3 | 695 | 0.84 | 0.87 | 57 | 6FE |
| 4 | 728 | 0.84 | 0.87 | 60 | 6FE |
| 5 | 669 | 0.84 | 0.88 | 54 | 6FE |
Interfaces
13 interfaces between chains.
- B–C · 1023 Ų buried · 11 hydrogen bonds · protein-protein
- F–G · 967 Ų buried · 8 hydrogen bonds · protein-protein
- D–E · 921 Ų buried · 11 hydrogen bonds · protein-protein
- H–J · 921 Ų buried · 8 hydrogen bonds · protein-protein
- K–L · 912 Ų buried · 12 hydrogen bonds · protein-protein
Compared structures
- 5AAO · Crystal structure of fluorogen-activating designed ankyrin repeat protein (DARPin) dimer… · 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 5AAO · PDBe 5AAO
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