Research workbench
Pseudomonas lipase complexed with rc-(rp, sp)- dibutylcarbamoylglycero-3-O-butylphosphonate
Analyse Pseudomonas lipase complexed with rc-(rp, sp)… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4LIP
- Type
- protein
- Length
- 638 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Triacyl-glycerol-hydrolase
- EC
- 3.1.1.3
- UniProt
- P22088
- Ligands
- CCP, CA
- Pockets
- 4 · best druggability 0.66
Structure
x-ray diffraction · 1 distinct chain · 38% helix, 19% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| D, E | Triacyl-glycerol-hydrolase (EC 3.1.1.3) | protein | 319 | 38% helix, 19% strand | P22088 |
Ligands and binding sites
- CCP · Butylphosphonate · ligand · 2 copies · chains D, E
- CA · Calcium ion · metal · 2 copies · chains D, E
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 | 448 | 0.66 | 0.78 | 39 | CCP |
| 2 | 393 | 0.65 | 0.78 | 38 | CCP |
| 3 | 180 | 0.46 | 0.75 | 34 | empty |
| 4 | 159 | 0.42 | 0.74 | 29 | empty |
Interfaces
1 interface between chains.
- D–E · 283 Ų buried · 6 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 covalent, 2 disulfide (covalent ligand, disulfide).
Compared structures
- 4LIP · Pseudomonas lipase complexed with rc-(rp, sp)-dibutylcarbamoylglycero-3-O-butylphosphonate · the same entry in another collection · chain D against D, TM-score 1.00
- P22088 · AlphaFold monomer V2.0 prediction for triacylglycerol lipase (P22088) · a predicted model of the same protein · chain D against A, TM-score 0.99
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 P22088
- Elsewhere: RCSB PDB 4LIP · PDBe 4LIP · UniProt P22088
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