Research workbench
The dyw domain of a. thaliana OTP86 in its active state
Analyse The dyw domain of a. thaliana OTP86 in its active state in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7O4F
- Type
- protein
- Length
- 543 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Pentatricopeptide repeat-containing protein AT3G63370, chloroplastic
- UniProt
- Q9M1V3
- Ligands
- ZN
- Pockets
- 6 · best druggability 0.75
Structure
x-ray diffraction · 2 distinct chains · 32% helix, 28% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, G | Pentatricopeptide repeat-containing protein AT3G63370, chloroplastic | protein | 136 | 32% helix, 27% strand | Q9M1V3 |
| D | Pentatricopeptide repeat-containing protein AT3G63370, chloroplastic | protein | 135 | 32% helix, 29% strand | Q9M1V3 |
Ligands and binding sites
- ZN · Zinc ion · metal · 8 copies · chains A, B, D, G
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 633 | 0.75 | 0.81 | 65 | empty |
| 2 | 471 | 0.70 | 0.80 | 48 | empty |
| 3 | 56 | 0.68 | 0.96 | 16 | empty |
| 4 | 234 | 0.59 | 0.80 | 34 | empty |
| 5 | 87 | 0.49 | 0.82 | 18 | empty |
Interfaces
4 interfaces between chains.
- A–G · 723 Ų buried · 11 hydrogen bonds · protein-protein
- B–D · 719 Ų buried · 12 hydrogen bonds · protein-protein
- A–B · 599 Ų buried · 9 hydrogen bonds · protein-protein
- D–G · 272 Ų buried · 7 hydrogen bonds · protein-protein
Compared structures
- 7O4F · The DYW domain of A. thaliana OTP86 in its active 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 D against A, TM-score 0.83
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 7O4F · PDBe 7O4F · UniProt Q9M1V3
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