MolNFT v1 · #79432 · protein
Arabidopsis thaliana dynamin-related protein 1A (ATDRP1A) in prefission state
3T34 · Dynamin-related protein 1A, linker, dynamin-related protein…: “Arabidopsis thaliana dynamin-related protein 1A (ATDRP1A) in prefission state”. X-ray diffraction, 4 ligands (GDP, ALF, MG), 6 pockets (best druggability 0.86). MolNFT…
- PDB
- 3T34
- Type
- protein
- Length
- 676 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Dynamin-related protein 1A, linker, dynamin-related protein 1A
- UniProt
- P42697
- Ligands
- GDP, ALF, MG, NA
- Pockets
- 6 · best druggability 0.86
Structure
x-ray diffraction · 2 distinct chains · 38% helix, 13% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Dynamin-related protein 1A, linker, dynamin-related protein 1A | protein | 335 | 38% helix, 14% strand | P42697 |
| B | Dynamin-related protein 1A, linker, dynamin-related protein 1A | protein | 341 | 38% helix, 12% strand | P42697 |
Ligands and binding sites
- GDP · Guanosine-5'-diphosphate · ligand · 2 copies · chains A, B
- ALF · Tetrafluoroaluminate ion · ligand · 2 copies · chains A, B
- MG · Magnesium ion · metal · 2 copies · chains A, B
- NA · Sodium ion · metal · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 951 | 0.86 | 0.87 | 125 | GDP, ALF, MG, NA |
| 2 | 265 | 0.64 | 0.82 | 39 | empty |
| 3 | 205 | 0.63 | 0.83 | 36 | empty |
| 4 | 252 | 0.55 | 0.77 | 26 | empty |
| 5 | 162 | 0.55 | 0.80 | 18 | empty |
Interfaces
1 interface between chains.
- A–B · 1290 Ų buried · 17 hydrogen bonds · protein-protein
Compared structures
- 3T34 · Arabidopsis thaliana dynamin-related protein 1A (AtDRP1A) in prefission state · the same entry in another collection · chain A against A, TM-score 1.00
- P42697 · AlphaFold monomer V2.0 prediction for dynamin-related protein 1A (P42697) · a predicted model of the same protein · chain A against A, TM-score 0.73
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 P42697
- Elsewhere: RCSB PDB 3T34 · PDBe 3T34 · UniProt P42697
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