Research workbench
Arabidopsis thaliana dynamin-related protein 1A in postfission state
Analyse Arabidopsis thaliana dynamin-related protein 1A in postfission state in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3T35
- Type
- protein
- Length
- 1,356 residues
- Chains
- 4
- 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
- Pockets
- 20 · best druggability 0.78
Structure
x-ray diffraction · 1 distinct chain · 30% helix, 6% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | Dynamin-related protein 1A, linker, dynamin-related protein 1A | protein | 339 | 30% helix, 6% strand | P42697 |
Ligands and binding sites
- GDP · Guanosine-5'-diphosphate · ligand · 4 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 16 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 654 | 0.78 | 0.83 | 65 | GDP |
| 2 | 566 | 0.78 | 0.85 | 54 | GDP |
| 3 | 549 | 0.75 | 0.83 | 59 | GDP |
| 4 | 482 | 0.75 | 0.83 | 54 | GDP |
| 5 | 112 | 0.74 | 0.95 | 33 | empty |
Interfaces
3 interfaces between chains.
- C–D · 1283 Ų buried · 18 hydrogen bonds · protein-protein
- A–B · 1221 Ų buried · 12 hydrogen bonds · protein-protein
- A–C · 620 Ų buried · 12 hydrogen bonds · protein-protein
Compared structures
- 3T35 · Arabidopsis thaliana dynamin-related protein 1A in postfission state · the same entry in another collection · chain D against D, TM-score 1.00
- P42697 · AlphaFold monomer V2.0 prediction for dynamin-related protein 1A (P42697) · a predicted model of the same protein · chain B against A, TM-score 0.96
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 3T35 · PDBe 3T35 · UniProt P42697
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