Research workbench
Crystal structure of ATG101-ATG13HORMA
Analyse Crystal structure of ATG101-ATG13HORMA in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5XV3
- Type
- protein
- Length
- 774 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Autophagy-related protein 13; Autophagy-related protein 101
- UniProt
- O75143, Q9BSB4
- Pockets
- 4 · best druggability 0.74
Structure
x-ray diffraction · 2 distinct chains · 34% helix, 31% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C | Autophagy-related protein 13 | protein | 183 | 36% helix, 30% strand | O75143 |
| B, D | Autophagy-related protein 101 | protein | 204 | 33% helix, 32% strand | Q9BSB4 |
Ligands and binding sites
- PEG · Di(hydroxyethyl)ether · additive · chains B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 693 | 0.74 | 0.80 | 85 | PEG |
| 2 | 304 | 0.68 | 0.83 | 34 | empty |
| 3 | 104 | 0.36 | 0.74 | 20 | empty |
| 4 | 68 | 0.33 | 0.76 | 18 | empty |
Interfaces
5 interfaces between chains.
- A–B · 1425 Ų buried · 30 hydrogen bonds · protein-protein
- C–D · 1316 Ų buried · 28 hydrogen bonds · protein-protein
- B–C · 322 Ų buried · 1 hydrogen bond · protein-protein
- A–D · 294 Ų buried · 2 hydrogen bonds · protein-protein
- B–D · 51 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 5XV3 · Crystal structure of ATG101-ATG13HORMA · the same entry in another collection · chain C against C, TM-score 1.00
- O75143 · AlphaFold monomer V2.0 prediction for autophagy-related protein 13 (O75143) · a predicted model of the same protein · chain A against A, TM-score 0.98
- Q9BSB4 · AlphaFold monomer V2.0 prediction for autophagy-related protein 101 (Q9BSB4) · a predicted model of the same protein · chain B against A, TM-score 0.95
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 O75143
- Every structure of UniProt Q9BSB4
- Elsewhere: RCSB PDB 5XV3 · PDBe 5XV3 · UniProt O75143 · UniProt Q9BSB4
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