Research workbench
Crystal structure of pea TOC34 - a novel GTPase of the chloroplast protein translocon
Analyse Crystal structure of pea TOC34 - a novel GTPase of the chloroplast protein… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1H65
- Type
- protein
- Length
- 769 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Chloroplast outer envelope protein OEP34
- UniProt
- Q41009
- Ligands
- GDP, MG
- Pockets
- 7 · best druggability 0.83
Structure
x-ray diffraction · 3 distinct chains · 41% helix, 21% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Chloroplast outer envelope protein OEP34 | protein | 257 | 42% helix, 20% strand | Q41009 |
| B | Chloroplast outer envelope protein OEP34 | protein | 256 | 41% helix, 21% strand | Q41009 |
| C | Chloroplast outer envelope protein OEP34 | protein | 256 | 40% helix, 21% strand | Q41009 |
Ligands and binding sites
- GDP · Guanosine-5'-diphosphate · ligand · 3 copies · chains A, B, C
- MG · Magnesium ion · metal · 3 copies · chains A, B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 744 | 0.83 | 0.86 | 76 | empty |
| 2 | 961 | 0.79 | 0.81 | 102 | GDP |
| 3 | 417 | 0.61 | 0.76 | 46 | empty |
| 4 | 121 | 0.45 | 0.78 | 29 | GDP |
| 5 | 102 | 0.43 | 0.78 | 18 | empty |
Interfaces
3 interfaces between chains.
- B–C · 1315 Ų buried · 27 hydrogen bonds · protein-protein
- A–B · 623 Ų buried · 1 hydrogen bond · protein-protein
- A–C · 45 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 9 modified (engineered).
Compared structures
- 1H65 · Crystal structure of pea Toc34 - a novel GTPase of the chloroplast protein translocon · the same entry in another collection · chain C against C, TM-score 1.00
- Q41009 · AlphaFold monomer V2.0 prediction for translocase of chloroplast 34 (Q41009) · a predicted model of the same protein · chain B against A, TM-score 0.99
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 Q41009
- Elsewhere: RCSB PDB 1H65 · PDBe 1H65 · UniProt Q41009
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