Research workbench
The dyw domain of a. thaliana OTP86 in its inactive state
Analyse The dyw domain of a. thaliana OTP86 in its inactive state in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7O4E
- Type
- protein
- Length
- 257 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Pentatricopeptide repeat-containing protein AT3G63370, chloroplastic
- UniProt
- Q9M1V3
- Ligands
- ZN
- Pockets
- 2 · best druggability 0.52
Structure
x-ray diffraction · 2 distinct chains · 33% helix, 23% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Pentatricopeptide repeat-containing protein AT3G63370, chloroplastic | protein | 132 | 33% helix, 24% strand | Q9M1V3 |
| B | Pentatricopeptide repeat-containing protein AT3G63370, chloroplastic | protein | 125 | 34% helix, 22% strand | Q9M1V3 |
Ligands and binding sites
- ZN · Zinc ion · metal · 4 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
2 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 271 | 0.52 | 0.75 | 26 | empty |
| 2 | 205 | 0.46 | 0.74 | 32 | ZN |
Interfaces
1 interface between chains.
- A–B · 179 Ų buried · 5 hydrogen bonds · protein-protein
Compared structures
- 7O4E · The DYW domain of A. thaliana OTP86 in its inactive state · the same entry in another collection · chain A against A, TM-score 1.00
- Q9M1V3 · AlphaFold monomer V2.0 prediction for pentatricopeptide repeat- containing protein… · a predicted model of the same protein · chain B against A, TM-score 0.89
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 Q9M1V3
- Elsewhere: RCSB PDB 7O4E · PDBe 7O4E · UniProt Q9M1V3
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