MolNFT v1 · #67395 · protein
Crystal structure of an uncharacterized metal-dependent hydrolase from lactobacillus acidophilus
3IJ6: “Crystal structure of an uncharacterized metal-dependent hydrolase from lactobacillus acidophilus”. X-ray diffraction, 2 ligands (ZN, NA), 7 pockets (best druggability 0.63). MolNFT v1 #67395 on GenesisL1: 3D structure, binding sites…
- PDB
- 3IJ6
- Type
- protein
- Length
- 1,210 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Uncharacterized metal-dependent hydrolase
- UniProt
- Q5FK79
- Ligands
- ZN, NA
- Pockets
- 7 · best druggability 0.63
Structure
x-ray diffraction · 2 distinct chains · 48% helix, 15% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Uncharacterized metal-dependent hydrolase | protein | 303 | 50% helix, 15% strand | Q5FK79 |
| C, D | Uncharacterized metal-dependent hydrolase | protein | 302 | 47% helix, 15% strand | Q5FK79 |
Ligands and binding sites
- ZN · Zinc ion · metal · 4 copies · chains A, B, C, D
- NA · Sodium ion · metal · 4 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 310 | 0.63 | 0.79 | 41 | empty |
| 2 | 300 | 0.62 | 0.79 | 41 | empty |
| 3 | 287 | 0.61 | 0.79 | 40 | empty |
| 4 | 261 | 0.60 | 0.79 | 37 | empty |
| 5 | 336 | 0.59 | 0.77 | 54 | empty |
Interfaces
3 interfaces between chains.
- C–D · 2020 Ų buried · 24 hydrogen bonds · protein-protein
- A–B · 1994 Ų buried · 26 hydrogen bonds · protein-protein
- A–C · 348 Ų buried · 10 hydrogen bonds · protein-protein
Compared structures
- 3IJ6 · CRYSTAL STRUCTURE OF AN UNCHARACTERIZED METAL-DEPENDENT HYDROLASE FROM Lactobacillus… · 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 Q5FK79
- Elsewhere: RCSB PDB 3IJ6 · PDBe 3IJ6 · UniProt Q5FK79
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