Research workbench
Human givd cytosolic phospholipase A2 in complex with methyl gamma- linolenyl fluorophosphonate inhibitor and terbium chloride
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
- 5IZR
- Type
- protein
- Length
- 2,672 residues
- Chains
- 4
- 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, TB
- Pockets
- 20 · best druggability 0.82
Structure
x-ray diffraction · 4 distinct chains · 28% helix, 28% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Cytosolic phospholipase A2 delta (EC 3.1.1.4) | protein | 674 | 28% helix, 28% strand | Q86XP0 |
| B | Cytosolic phospholipase A2 delta (EC 3.1.1.4) | protein | 675 | 28% helix, 28% strand | Q86XP0 |
| C | Cytosolic phospholipase A2 delta (EC 3.1.1.4) | protein | 659 | 29% helix, 29% strand | Q86XP0 |
| D | Cytosolic phospholipase A2 delta (EC 3.1.1.4) | protein | 664 | 28% helix, 28% strand | Q86XP0 |
Ligands and binding sites
- 7FA · methyl (R)-(6Z,9Z,12Z)-octadeca-6,9,12-trien-1-ylphosphonofluoridate · ligand · 4 copies · chains A, B, C, D
- TB · Terbium(iii) ion · metal · 15 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 12 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1051 | 0.82 | 0.83 | 102 | 7FA |
| 2 | 997 | 0.80 | 0.81 | 94 | 7FA |
| 3 | 1119 | 0.79 | 0.80 | 98 | 7FA |
| 4 | 917 | 0.79 | 0.81 | 86 | 7FA |
| 5 | 651 | 0.63 | 0.74 | 56 | empty |
Interfaces
4 interfaces between chains.
- A–B · 178 Ų buried · 1 hydrogen bond · protein-protein
- C–D · 110 Ų buried · 1 hydrogen bond · protein-protein
- B–D · 96 Ų buried · 0 hydrogen bonds · protein-protein
- A–C · 71 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 covalent (covalent ligand).
Compared structures
- 5IZR · Human GIVD cytosolic phospholipase A2 in complex with Methyl gamma-Linolenyl… · the same entry in another collection · chain D against D, 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 0.94
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 5IZR · PDBe 5IZR · UniProt Q86XP0
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