Research workbench
Human atlastin-3 (residues 1-334) bound to GDP-MG2+ exhibits an ordered amino terminus
Analyse Human atlastin-3 (residues 1-334) bound to GDP-MG2+ exhibits an ordered amino… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6XJO
- Type
- protein
- Length
- 621 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Atlastin-3
- EC
- 3.6.5.-
- UniProt
- Q6DD88
- Ligands
- GDP, MG
- Pockets
- 3 · best druggability 0.84
Structure
x-ray diffraction · 2 distinct chains · 42% helix, 23% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Atlastin-3 (EC 3.6.5.-) | protein | 326 | 43% helix, 23% strand | Q6DD88 |
| B | Atlastin-3 (EC 3.6.5.-) | protein | 295 | 41% helix, 23% strand | Q6DD88 |
Ligands and binding sites
- GDP · Guanosine-5'-diphosphate · ligand · 2 copies · chains A, B
- MG · Magnesium ion · metal · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1089 | 0.84 | 0.85 | 109 | GDP |
| 2 | 64 | 0.50 | 0.85 | 13 | empty |
| 3 | 52 | 0.29 | 0.75 | 17 | empty |
Interfaces
1 interface between chains.
- A–B · 828 Ų buried · 9 hydrogen bonds · protein-protein
Compared structures
- 6XJO · Human atlastin-3 (residues 1-334) bound to GDP-Mg2+ exhibits an ordered amino terminus · the same entry in another collection · chain B against B, TM-score 1.00
- Q6DD88 · AlphaFold monomer V2.0 prediction for atlastin-3 (Q6DD88) · a predicted model of the same protein · chain B against A, TM-score 0.94
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 Q6DD88
- Elsewhere: RCSB PDB 6XJO · PDBe 6XJO · UniProt Q6DD88
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