MolNFT v1 · #120313 · protein
Crystal structure of a putative dag-like lipase (MGMDL2) from malassezia globosa
5GW8 · Hypothetical secretory lipase (family 3): “Crystal structure of a putative dag-like lipase (MGMDL2) from malassezia globosa”. X-ray diffraction, 1 ligand (NAG), 3 pockets (best druggability 0.81). MolNFT v1 #120313 on GenesisL1: 3D…
- PDB
- 5GW8
- Type
- protein
- Length
- 570 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Hypothetical secretory lipase (family 3)
- UniProt
- A8PUY5
- Ligands
- NAG
- Pockets
- 3 · best druggability 0.81
Structure
x-ray diffraction · 2 distinct chains · 31% helix, 22% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Hypothetical secretory lipase (family 3) | protein | 284 | 30% helix, 22% strand | A8PUY5 |
| B | Hypothetical secretory lipase (family 3) | protein | 286 | 31% helix, 22% strand | A8PUY5 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 6 copies · chains A, B
- ACY · Acetic acid · additive · 4 copies · chains A, B
- MLA · Malonic acid · additive · 2 copies · chains A, B
- FMT · Formic acid · additive · 2 copies · chains A, B
- GOL · Glycerol · additive · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 423 | 0.81 | 0.89 | 56 | MLA |
| 2 | 113 | 0.45 | 0.78 | 19 | empty |
| 3 | 112 | 0.43 | 0.77 | 20 | ACY |
Interfaces
1 interface between chains.
- A–B · 1226 Ų buried · 21 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 glycan, 2 disulfide (N-glycosylation, disulfide).
Compared structures
- 5GW8 · Crystal structure of a putative DAG-like lipase (MgMDL2) from Malassezia globosa · 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 A8PUY5
- Elsewhere: RCSB PDB 5GW8 · PDBe 5GW8 · UniProt A8PUY5
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