Research workbench
Structure of human nape-pld
Analyse Structure of human nape-pld in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4QN9
- Type
- protein
- Length
- 643 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- N-acyl-phosphatidylethanolamine-hydrolyzing phospholipase D
- EC
- 3.1.4.54
- UniProt
- Q6IQ20
- Ligands
- DXC, 3PE, ZN, SO4
- Pockets
- 5 · best druggability 0.80
Structure
x-ray diffraction · 2 distinct chains · 19% helix, 22% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | N-acyl-phosphatidylethanolamine-hydrolyzing phospholipase D (EC 3.1.4.54) | protein | 321 | 19% helix, 22% strand | Q6IQ20 |
| B | N-acyl-phosphatidylethanolamine-hydrolyzing phospholipase D (EC 3.1.4.54) | protein | 322 | 19% helix, 22% strand | Q6IQ20 |
Ligands and binding sites
- DXC · (3alpha,5beta,12alpha)-3,12-dihydroxycholan-24-oic acid · ligand · 11 copies · chains A, B
- 3PE · 1,2-diacyl-sn-glycero-3-phosphoethanolamine · ligand · 2 copies · chains A, B
- ZN · Zinc ion · metal · 4 copies · chains A, B
- SO4 · Sulfate ion · ion · 3 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1034 | 0.80 | 0.82 | 65 | SO4 |
| 2 | 135 | 0.45 | 0.76 | 19 | 3PE |
| 3 | 126 | 0.45 | 0.77 | 18 | empty |
| 4 | 125 | 0.43 | 0.76 | 20 | ZN, 3PE |
| 5 | 112 | 0.42 | 0.76 | 19 | empty |
Interfaces
1 interface between chains.
- A–B · 859 Ų buried · 12 hydrogen bonds · protein-protein
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 Q6IQ20
- Elsewhere: RCSB PDB 4QN9 · PDBe 4QN9 · UniProt Q6IQ20
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