MolNFT v1 · #122761 · protein
Human givd cytosolic phospholipase A2
5IZ5 · Cytosolic phospholipase A2 delta: “Human givd cytosolic phospholipase A2”. X-ray diffraction, 1 ligand (SO4), 16 pockets (best druggability 0.79). MolNFT v1 #122761 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 5IZ5
- Type
- protein
- Length
- 1,503 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Cytosolic phospholipase A2 delta
- EC
- 3.1.1.4
- UniProt
- Q86XP0
- Ligands
- SO4
- Pockets
- 16 · best druggability 0.79
Structure
x-ray diffraction · 2 distinct chains · 28% helix, 27% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| B | Cytosolic phospholipase A2 delta (EC 3.1.1.4) | protein | 746 | 27% helix, 27% strand | Q86XP0 |
| A | Cytosolic phospholipase A2 delta (EC 3.1.1.4) | protein | 757 | 30% helix, 27% strand | Q86XP0 |
Ligands and binding sites
- SO4 · Sulfate ion · ion · 14 copies · chains B, A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
16 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1073 | 0.79 | 0.80 | 95 | empty |
| 2 | 350 | 0.74 | 0.85 | 33 | empty |
| 3 | 242 | 0.57 | 0.79 | 26 | empty |
| 4 | 130 | 0.57 | 0.83 | 29 | empty |
| 5 | 212 | 0.55 | 0.79 | 35 | SO4 |
Interfaces
1 interface between chains.
- B–A · 1467 Ų buried · 13 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 disulfide (disulfide).
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 Q86XP0
- Elsewhere: RCSB PDB 5IZ5 · PDBe 5IZ5 · UniProt Q86XP0
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