Research workbench
Crystal structure of the pentatricopeptide repeat protein PPR10 (C256S/C430S/C449S) in complex with an 18-nt psaj RNA element
Analyse Crystal structure of the pentatricopeptide repeat protein PPR10… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4OE1
- Type
- protein + RNA
- Length
- 1,402 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Chloroplast pentatricopeptide repeat protein 10; Psaj RNA
- UniProt
- B8Y6I0
- Ligands
- PO4
- Pockets
- 20 · best druggability 0.80
Structure
x-ray diffraction · 4 distinct chains · 69% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Chloroplast pentatricopeptide repeat protein 10 | protein | 687 | 69% helix, 0% strand | B8Y6I0 |
| B | Chloroplast pentatricopeptide repeat protein 10 | protein | 683 | 70% helix, 0% strand | B8Y6I0 |
| D | Psaj RNA | rna | 18 | — | — |
| C | Psaj RNA | rna | 14 | — | — |
Ligands and binding sites
- PO4 · Phosphate ion · ion · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 10 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 573 | 0.80 | 0.86 | 60 | empty |
| 2 | 557 | 0.73 | 0.82 | 68 | empty |
| 3 | 418 | 0.71 | 0.82 | 35 | empty |
| 4 | 331 | 0.70 | 0.84 | 37 | empty |
| 5 | 369 | 0.66 | 0.80 | 41 | empty |
Interfaces
5 interfaces between chains.
- A–B · 3019 Ų buried · 35 hydrogen bonds · protein-protein
- A–D · 1145 Ų buried · 20 hydrogen bonds · protein-nucleic
- B–C · 1046 Ų buried · 21 hydrogen bonds · protein-nucleic
- B–D · 961 Ų buried · 16 hydrogen bonds · protein-nucleic
- A–C · 903 Ų buried · 11 hydrogen bonds · protein-nucleic
Compared structures
- 4OE1 · Crystal structure of the pentatricopeptide repeat protein PPR10 (C256S/C430S/C449S) in… · the same entry in another collection · chain A against A, TM-score 1.00
- B8Y6I0 · AlphaFold monomer V2.0 prediction for pentatricopeptide repeat- containing protein 10… · a predicted model of the same protein · chain A against A, TM-score 0.72
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 B8Y6I0
- Elsewhere: RCSB PDB 4OE1 · PDBe 4OE1 · UniProt B8Y6I0
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