Research workbench
Crystal structure of arabidopsis thaliana ATG7NTD-ATG3 complex
Analyse Crystal structure of arabidopsis thaliana ATG7NTD-ATG3 complex in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3VX8
- Type
- protein
- Length
- 952 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Ubiquitin-like modifier-activating enzyme ATG7; Autophagy-related protein 3
- UniProt
- Q94CD5, Q0WWQ1
- Pockets
- 14 · best druggability 0.78
Structure
x-ray diffraction · 4 distinct chains · 30% helix, 30% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| D | Ubiquitin-like modifier-activating enzyme ATG7 | protein | 300 | 29% helix, 34% strand | Q94CD5 |
| A | Ubiquitin-like modifier-activating enzyme ATG7 | protein | 305 | 29% helix, 32% strand | Q94CD5 |
| B | Autophagy-related protein 3 | protein | 175 | 34% helix, 24% strand | Q0WWQ1 |
| C | Autophagy-related protein 3 | protein | 172 | 33% helix, 23% strand | Q0WWQ1 |
Pockets
14 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 171 | 0.78 | 0.94 | 41 | empty |
| 2 | 118 | 0.77 | 0.97 | 30 | empty |
| 3 | 780 | 0.77 | 0.81 | 69 | empty |
| 4 | 66 | 0.62 | 0.91 | 22 | empty |
| 5 | 293 | 0.59 | 0.78 | 55 | empty |
Interfaces
5 interfaces between chains.
- A–B · 1189 Ų buried · 10 hydrogen bonds · protein-protein
- D–C · 1128 Ų buried · 8 hydrogen bonds · protein-protein
- B–C · 632 Ų buried · 15 hydrogen bonds · protein-protein
- D–B · 187 Ų buried · 1 hydrogen bond · protein-protein
- A–C · 170 Ų buried · 1 hydrogen bond · protein-protein
Compared structures
- 3VX8 · Crystal structure of Arabidopsis thaliana Atg7NTD-Atg3 complex · the same entry in another collection · chain C against C, TM-score 1.00
- Q94CD5 · AlphaFold monomer V2.0 prediction for ubiquitin-like modifier- activating enzyme ATG7… · a predicted model of the same protein · chain D against A, TM-score 1.00
- Q0WWQ1 · AlphaFold monomer V2.0 prediction for autophagy-related protein 3 (Q0WWQ1) · a predicted model of the same protein · chain C against A, TM-score 0.99
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 Q94CD5
- Every structure of UniProt Q0WWQ1
- Elsewhere: RCSB PDB 3VX8 · PDBe 3VX8 · UniProt Q94CD5 · UniProt Q0WWQ1
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