MolNFT v1 · #40842 · protein
The native structure of a beta-diketone hydrolase from the cyanobacterium anabaena sp. pcc 7120
2J5G · ALR4455 protein: “The native structure of a beta-diketone hydrolase from the cyanobacterium anabaena sp. pcc 7120”. X-ray diffraction, 1 ligand (SO4), 20 pockets (best druggability 0.90). MolNFT v1 #40842 on GenesisL1: 3D structure…
- PDB
- 2J5G
- Type
- protein
- Length
- 2,979 residues
- Chains
- 12
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- ALR4455 protein
- EC
- 3.7.1.7
- UniProt
- Q8YNV6
- Ligands
- SO4
- Pockets
- 20 · best druggability 0.90
Structure
x-ray diffraction · 4 distinct chains · 53% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C, F, G, H, I, J, K, L | ALR4455 protein (EC 3.7.1.7) | protein | 248 | 52% helix, 18% strand | Q8YNV6 |
| B | ALR4455 protein (EC 3.7.1.7) | protein | 249 | 51% helix, 18% strand | Q8YNV6 |
| D | ALR4455 protein (EC 3.7.1.7) | protein | 249 | 54% helix, 18% strand | Q8YNV6 |
| E | ALR4455 protein (EC 3.7.1.7) | protein | 249 | 53% helix, 18% strand | Q8YNV6 |
Ligands and binding sites
- SO4 · Sulfate ion · ion · 4 copies · chains A, B, C, D, E, F, G, H, I, 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, 19 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1200 | 0.90 | 0.92 | 125 | empty |
| 2 | 915 | 0.89 | 0.92 | 93 | empty |
| 3 | 232 | 0.82 | 0.95 | 43 | empty |
| 4 | 524 | 0.79 | 0.86 | 60 | empty |
| 5 | 515 | 0.78 | 0.85 | 54 | empty |
Interfaces
27 interfaces between chains.
- D–F · 1434 Ų buried · 16 hydrogen bonds · protein-protein
- A–B · 1426 Ų buried · 17 hydrogen bonds · protein-protein
- G–H · 1423 Ų buried · 19 hydrogen bonds · protein-protein
- J–K · 1421 Ų buried · 20 hydrogen bonds · protein-protein
- H–I · 1421 Ų buried · 19 hydrogen bonds · protein-protein
Compared structures
- 2J5G · The Native structure of a beta-Diketone Hydrolase from the Cyanobacterium Anabaena sp.… · the same entry in another collection · chain H against H, 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 Q8YNV6
- Elsewhere: RCSB PDB 2J5G · PDBe 2J5G · UniProt Q8YNV6
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