MolNFT v1 · #157273 · protein
Lysosomal phospholipase A2 in complex with zinc
6MTW · Group xv phospholipase A2: “Lysosomal phospholipase A2 in complex with zinc”. X-ray diffraction, 3 ligands (NAG, ZN, CL), 6 pockets (best druggability 0.78). MolNFT v1 #157273 on GenesisL1: 3D structure, binding sites and pockets in…
- PDB
- 6MTW
- Type
- protein
- Length
- 752 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Group xv phospholipase A2
- EC
- 2.3.1.-
- UniProt
- Q8NCC3
- Ligands
- NAG, ZN, CL
- Pockets
- 6 · best druggability 0.78
Structure
x-ray diffraction · 1 distinct chain · 36% helix, 20% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Group xv phospholipase A2 (EC 2.3.1.-) | protein | 376 | 36% helix, 20% strand | Q8NCC3 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 4 copies · chains A, B
- ZN · Zinc ion · metal · 8 copies · chains A, B
- CL · Chloride ion · ion · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 263 | 0.78 | 0.90 | 40 | empty |
| 2 | 333 | 0.78 | 0.88 | 50 | empty |
| 3 | 75 | 0.39 | 0.78 | 14 | empty |
| 4 | 141 | 0.38 | 0.73 | 22 | empty |
| 5 | 75 | 0.38 | 0.77 | 12 | empty |
Interfaces
1 interface between chains.
- A–B · 238 Ų buried · 6 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 disulfide, 4 glycan (disulfide, N-glycosylation).
Compared structures
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 Q8NCC3
- Elsewhere: RCSB PDB 6MTW · PDBe 6MTW · UniProt Q8NCC3
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