Research workbench
Human givd cytosolic phospholipase A2 in complex with methyl gamma- linolenyl fluorophosphonate
Analyse Human givd cytosolic phospholipase A2 in complex with methyl gamma- linolenyl… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5IXC
- Type
- protein
- Length
- 1,364 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
- 7FA, BA
- Pockets
- 18 · best druggability 0.85
Structure
x-ray diffraction · 2 distinct chains · 28% helix, 27% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Cytosolic phospholipase A2 delta (EC 3.1.1.4) | protein | 684 | 28% helix, 27% strand | Q86XP0 |
| B | Cytosolic phospholipase A2 delta (EC 3.1.1.4) | protein | 680 | 27% helix, 27% strand | Q86XP0 |
Ligands and binding sites
- 7FA · methyl (R)-(6Z,9Z,12Z)-octadeca-6,9,12-trien-1-ylphosphonofluoridate · ligand · 2 copies · chains A, B
- BA · Barium ion · metal · 6 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
18 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1042 | 0.85 | 0.86 | 120 | 7FA |
| 2 | 558 | 0.76 | 0.83 | 67 | empty |
| 3 | 314 | 0.68 | 0.81 | 31 | 7FA |
| 4 | 101 | 0.55 | 0.84 | 23 | empty |
| 5 | 89 | 0.55 | 0.85 | 18 | empty |
Interfaces
1 interface between chains.
- A–B · 463 Ų buried · 3 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 covalent, 2 disulfide (covalent ligand, disulfide).
Compared structures
- 5IXC · Human GIVD cytosolic phospholipase A2 in complex with Methyl gamma-Linolenyl… · the same entry in another collection · chain A against A, TM-score 1.00
- Q86XP0 · AlphaFold monomer V2.0 prediction for cytosolic phospholipase A2 delta (Q86XP0) · a predicted model of the same protein · chain B against A, TM-score 0.93
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 5IXC · PDBe 5IXC · UniProt Q86XP0
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