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Crystal structure of D60N mutant of arabidopsis ACD11 (accelerated- cell-death 11) complexed with C12 ceramide-1-phosphate (D18:1/12:0) at 2.9 ångström resolution
Analyse Crystal structure of D60N mutant of arabidopsis ACD11 (accelerated- cell-death… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4NTI
- Type
- protein
- Length
- 404 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Accelerated-cell-death 11
- UniProt
- O64587
- Ligands
- 1PZ
- Pockets
- 4 · best druggability 0.79
Structure
x-ray diffraction · 1 distinct chain · 68% helix, 2% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Accelerated-cell-death 11 | protein | 202 | 68% helix, 2% strand | O64587 |
Ligands and binding sites
- 1PZ · (2S,3R,4E)-2-(dodecanoylamino)-3-hydroxyoctadec-4-en-1-yl dihydrogen phosphate · ligand · 4 copies · chains A, B
- PEG · Di(hydroxyethyl)ether · additive · 4 copies · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 341 | 0.79 | 0.88 | 35 | 1PZ |
| 2 | 248 | 0.69 | 0.85 | 36 | 1PZ |
| 3 | 215 | 0.52 | 0.77 | 30 | empty |
| 4 | 57 | 0.31 | 0.76 | 16 | empty |
Interfaces
1 interface between chains.
- A–B · 402 Ų buried · 2 hydrogen bonds · protein-protein
Compared structures
- 4NTI · Crystal structure of D60N mutant of Arabidopsis ACD11 (accelerated-cell-death 11)… · the same entry in another collection · chain A against A, TM-score 1.00
- O64587 · AlphaFold monomer V2.0 prediction for accelerated cell death 11 (O64587) · 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 O64587
- Elsewhere: RCSB PDB 4NTI · PDBe 4NTI · UniProt O64587
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