Research workbench
Crystal structure of apo-form of arabidopsis ACD11 (accelerated-cell- death 11) at 1.8 ångström resolution
Analyse Crystal structure of apo-form of arabidopsis ACD11 (accelerated-cell- death 11)… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4NT1
- Type
- protein
- Length
- 795 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Accelerated-cell-death 11
- UniProt
- O64587
- Ligands
- NA
- Pockets
- 3 · best druggability 0.85
Structure
x-ray diffraction · 2 distinct chains · 75% helix, 1% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C | Accelerated-cell-death 11 | protein | 200 | 76% helix, 1% strand | O64587 |
| D | Accelerated-cell-death 11 | protein | 195 | 75% helix, 1% strand | O64587 |
Ligands and binding sites
- NA · Sodium ion · metal · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 920 | 0.85 | 0.87 | 92 | empty |
| 2 | 169 | 0.60 | 0.83 | 27 | empty |
| 3 | 92 | 0.45 | 0.79 | 19 | empty |
Interfaces
6 interfaces between chains.
- B–C · 498 Ų buried · 5 hydrogen bonds · protein-protein
- A–B · 461 Ų buried · 4 hydrogen bonds · protein-protein
- A–D · 338 Ų buried · 2 hydrogen bonds · protein-protein
- A–C · 297 Ų buried · 1 hydrogen bond · protein-protein
- B–D · 44 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 modified (carboxylation).
Compared structures
- 4NT1 · Crystal structure of apo-form of Arabidopsis ACD11 (accelerated-cell-death 11) at 1.8… · the same entry in another collection · chain D against D, TM-score 1.00
- O64587 · AlphaFold monomer V2.0 prediction for accelerated cell death 11 (O64587) · a predicted model of the same protein · chain C 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 4NT1 · PDBe 4NT1 · UniProt O64587
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