MolNFT v1 · #160515 · protein
Crystal structure of a fragment of rat phospholipase cepsilon EF3-RA1
6PMP · 1-phosphatidylinositol 4,5-bisphosphate phosphodiesterase…: “Crystal structure of a fragment of rat phospholipase cepsilon EF3-RA1”. X-ray diffraction, 1 ligand (CA), 20 pockets (best druggability 0.82). MolNFT v1 #160515 on…
- PDB
- 6PMP
- Type
- protein
- Length
- 2,442 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 1-phosphatidylinositol 4,5-bisphosphate phosphodiesterase epsilon-1
- EC
- 3.1.4.11
- UniProt
- Q99P84
- Ligands
- CA
- Pockets
- 20 · best druggability 0.82
Structure
x-ray diffraction · 4 distinct chains · 29% helix, 28% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | 1-phosphatidylinositol 4,5-bisphosphate phosphodiesterase epsilon-1 (EC 3.1.4.11) | protein | 609 | 29% helix, 28% strand | Q99P84 |
| B | 1-phosphatidylinositol 4,5-bisphosphate phosphodiesterase epsilon-1 (EC 3.1.4.11) | protein | 611 | 29% helix, 28% strand | Q99P84 |
| C | 1-phosphatidylinositol 4,5-bisphosphate phosphodiesterase epsilon-1 (EC 3.1.4.11) | protein | 617 | 29% helix, 28% strand | Q99P84 |
| D | 1-phosphatidylinositol 4,5-bisphosphate phosphodiesterase epsilon-1 (EC 3.1.4.11) | protein | 605 | 30% helix, 27% strand | Q99P84 |
Ligands and binding sites
- CA · Calcium ion · metal · 4 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, 13 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 814 | 0.82 | 0.85 | 70 | empty |
| 2 | 805 | 0.82 | 0.85 | 85 | empty |
| 3 | 895 | 0.82 | 0.84 | 83 | empty |
| 4 | 762 | 0.81 | 0.85 | 72 | empty |
| 5 | 1013 | 0.80 | 0.82 | 75 | empty |
Interfaces
5 interfaces between chains.
- C–D · 1280 Ų buried · 13 hydrogen bonds · protein-protein
- A–B · 1226 Ų buried · 14 hydrogen bonds · protein-protein
- A–C · 641 Ų buried · 6 hydrogen bonds · protein-protein
- B–D · 515 Ų buried · 3 hydrogen bonds · protein-protein
- B–C · 497 Ų buried · 5 hydrogen bonds · protein-protein
Compared structures
- 6PMP · Crystal structure of a fragment of rat phospholipase Cepsilon EF3-RA1 · the same entry in another collection · chain D against D, TM-score 1.00
- Q99P84 · AlphaFold monomer V2.0 prediction for 1-phosphatidylinositol 4,5-bisphosphate… · a predicted model of the same protein · chain B against A, TM-score 0.99
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 Q99P84
- Elsewhere: RCSB PDB 6PMP · PDBe 6PMP · UniProt Q99P84
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