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Crystal structure of D60A mutant of arabidopsis ACD11 (accelerated- cell-death 11) complexed with C2 ceramide-1-phosphate (D18:1/2:0) at 2.15 ångström resolution
Analyse Crystal structure of D60A 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
- 4NTO
- Type
- protein
- Length
- 601 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Accelerated-cell-death 11
- UniProt
- O64587
- Ligands
- 1PW
- Pockets
- 7 · best druggability 0.59
Structure
x-ray diffraction · 2 distinct chains · 73% helix, 1% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C | Accelerated-cell-death 11 | protein | 200 | 74% helix, 1% strand | O64587 |
| B | Accelerated-cell-death 11 | protein | 201 | 73% helix, 1% strand | O64587 |
Ligands and binding sites
- 1PW · (2S,3R,4E)-2-(acetylamino)-3-hydroxyoctadec-4-en-1-yl dihydrogen phosphate · ligand · 6 copies · chains A, B, C
- PEG · Di(hydroxyethyl)ether · additive · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 281 | 0.59 | 0.78 | 43 | empty |
| 2 | 209 | 0.48 | 0.75 | 34 | 1PW |
| 3 | 160 | 0.42 | 0.74 | 32 | empty |
| 4 | 148 | 0.37 | 0.72 | 14 | empty |
| 5 | 76 | 0.37 | 0.77 | 17 | empty |
Interfaces
2 interfaces between chains.
- A–B · 424 Ų buried · 0 hydrogen bonds · protein-protein
- B–C · 362 Ų buried · 7 hydrogen bonds · protein-protein
Compared structures
- 4NTO · Crystal structure of D60A 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 0.97
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 4NTO · PDBe 4NTO · UniProt O64587
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