Research workbench
Crystal structure of human atlastin-1 (residues 1-447) bound to GDP, crystal form 1
Analyse Crystal structure of human atlastin-1 (residues 1-447) bound to GDP, crystal… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3Q5D
- Type
- protein
- Length
- 410 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Atlastin-1
- EC
- 3.6.5.-
- UniProt
- Q8WXF7
- Ligands
- GDP, MG
- Pockets
- 5 · best druggability 0.65
Structure
x-ray diffraction · 1 distinct chain · 46% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Atlastin-1 (EC 3.6.5.-) | protein | 410 | 46% helix, 18% strand | Q8WXF7 |
Ligands and binding sites
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 314 | 0.65 | 0.81 | 37 | GDP, MG |
| 2 | 91 | 0.49 | 0.82 | 21 | empty |
| 3 | 68 | 0.41 | 0.80 | 20 | empty |
| 4 | 103 | 0.37 | 0.74 | 18 | empty |
| 5 | 59 | 0.36 | 0.78 | 16 | empty |
Modifications
Observed in the structure: 9 modified (engineered).
Compared structures
- 3Q5D · crystal structure of human Atlastin-1 (residues 1-447) bound to GDP, crystal form 1 · the same entry in another collection · chain A against A, TM-score 1.00
- Q8WXF7 · AlphaFold monomer V2.0 prediction for atlastin-1 (Q8WXF7) · a predicted model of the same protein · chain A against A, TM-score 0.82
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 Q8WXF7
- Elsewhere: RCSB PDB 3Q5D · PDBe 3Q5D · UniProt Q8WXF7
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