MolNFT v1 · #81300 · protein
Crystal structure of D311E lipase
3UMJ · Thermostable lipase: “Crystal structure of D311E lipase”. X-ray diffraction, 4 ligands (ZN, NA, CA), 4 pockets (best druggability 0.70). MolNFT v1 #81300 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 3UMJ
- Type
- protein
- Length
- 773 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Thermostable lipase
- EC
- 3.1.1.3
- UniProt
- Q842J9
- Ligands
- ZN, NA, CA, CL
- Pockets
- 4 · best druggability 0.70
Structure
x-ray diffraction · 2 distinct chains · 39% helix, 15% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Thermostable lipase (EC 3.1.1.3) | protein | 386 | 38% helix, 15% strand | Q842J9 |
| B | Thermostable lipase (EC 3.1.1.3) | protein | 387 | 39% helix, 15% strand | Q842J9 |
Ligands and binding sites
- ZN · Zinc ion · metal · 2 copies · chains A, B
- NA · Sodium ion · metal · 2 copies · chains A, B
- CA · Calcium ion · metal · 2 copies · chains A, B
- CL · Chloride ion · ion · 2 copies · chains A, B
- GOL · Glycerol · additive · 3 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 750 | 0.70 | 0.77 | 62 | GOL |
| 2 | 199 | 0.55 | 0.79 | 22 | empty |
| 3 | 104 | 0.36 | 0.74 | 16 | empty |
| 4 | 78 | 0.32 | 0.74 | 16 | empty |
Interfaces
1 interface between chains.
- A–B · 443 Ų buried · 3 hydrogen bonds · protein-protein
Compared structures
- 3UMJ · Crystal Structure of D311E Lipase · 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 Q842J9
- Elsewhere: RCSB PDB 3UMJ · PDBe 3UMJ · UniProt Q842J9
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