MolNFT v1 · #102565 · protein
Crystal structure of a putative lipase (LIP1) from acinetobacter baumannii aye at 1.70 a resolution
4OPM: “Crystal structure of a putative lipase (LIP1) from acinetobacter baumannii aye at 1.70 a resolution”. X-ray diffraction, 1 ligand (SO4), 4 pockets (best druggability 0.91). MolNFT v1 #102565 on GenesisL1: 3D structure, binding sites…
- PDB
- 4OPM
- Type
- protein
- Length
- 598 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Lipase
- EC
- 3.1.1.3
- UniProt
- B0V9K7
- Ligands
- SO4
- Pockets
- 4 · best druggability 0.91
Structure
x-ray diffraction · 1 distinct chain · 46% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Lipase (EC 3.1.1.3) | protein | 299 | 46% helix, 18% strand | B0V9K7 |
Ligands and binding sites
- SO4 · Sulfate ion · ion · 2 copies · chains A, B
- PE4 · 2-{2-[2-(2-{2-[2-(2-ethoxy-ethoxy)-ethoxy]-ethoxy}-ethoxy)-ethoxy]-ethoxy}-ethanol · additive · 9 copies · chains A, B
- 15P · Polyethylene glycol (N=34) · additive · chains A, B
- GOL · Glycerol · additive · 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 | 1093 | 0.91 | 0.93 | 140 | 15P |
| 2 | 288 | 0.54 | 0.75 | 38 | PE4, GOL |
| 3 | 159 | 0.47 | 0.76 | 23 | empty |
| 4 | 90 | 0.33 | 0.74 | 16 | empty |
Interfaces
1 interface between chains.
- A–B · 1466 Ų buried · 40 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 6 modified (engineered).
Compared structures
- 4OPM · Crystal structure of a putative lipase (lip1) from Acinetobacter baumannii AYE at 1.70 A… · 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 B0V9K7
- Elsewhere: RCSB PDB 4OPM · PDBe 4OPM · UniProt B0V9K7
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