Research workbench
Crystal structure of human ATG12~ATG5-ATG16N in complex with a fragment of ATG3
Analyse Crystal structure of human ATG12~ATG5-ATG16N in complex with a fragment of ATG3 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4NAW
- Type
- protein
- Length
- 1,596 residues
- Chains
- 16
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Ubiquitin-like protein ATG12; Autophagy protein 5; Autophagy-related protein 16-1…
- EC
- 6.3.2.-
- UniProt
- O94817, Q9H1Y0, Q676U5, Q9NT62
- Ligands
- NA, SO4
- Pockets
- 20 · best druggability 0.76
Structure
x-ray diffraction · 8 distinct chains · 37% helix, 19% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, E, I, M | Ubiquitin-like protein ATG12 | protein | 88 | 22% helix, 30% strand | O94817 |
| B | Autophagy protein 5 | protein | 266 | 36% helix, 18% strand | Q9H1Y0 |
| C, G, K, O | Autophagy-related protein 16-1 | protein | 34 | 91% helix, 0% strand | Q676U5 |
| D, P | Ubiquitin-like-conjugating enzyme ATG3 (EC 6.3.2.-) | protein | 13 | 54% helix, 15% strand | Q9NT62 |
| F | Autophagy protein 5 | protein | 265 | 35% helix, 18% strand | Q9H1Y0 |
| H, L | Ubiquitin-like-conjugating enzyme ATG3 (EC 6.3.2.-) | protein | 12 | 42% helix, 17% strand | Q9NT62 |
| J | Autophagy protein 5 | protein | 263 | 36% helix, 19% strand | Q9H1Y0 |
| N | Autophagy protein 5 | protein | 264 | 37% helix, 19% strand | Q9H1Y0 |
Ligands and binding sites
- NA · Sodium ion · metal · 4 copies · chains B, F, J, N
- SO4 · Sulfate ion · ion · 11 copies · chains B, C, F, G, J, O, N
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 14 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 418 | 0.76 | 0.85 | 60 | empty |
| 2 | 499 | 0.73 | 0.82 | 58 | SO4 |
| 3 | 760 | 0.73 | 0.79 | 77 | empty |
| 4 | 591 | 0.72 | 0.80 | 52 | empty |
| 5 | 348 | 0.72 | 0.84 | 40 | empty |
Interfaces
23 interfaces between chains.
- N–O · 1210 Ų buried · 12 hydrogen bonds · protein-protein
- B–C · 1182 Ų buried · 9 hydrogen bonds · protein-protein
- J–K · 1164 Ų buried · 8 hydrogen bonds · protein-protein
- F–G · 1125 Ų buried · 10 hydrogen bonds · protein-protein
- E–F · 742 Ų buried · 7 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 isopeptide (isopeptide).
Compared structures
- 4NAW · Crystal Structure of Human ATG12~ATG5-ATG16N in complex with a fragment of ATG3 · the same entry in another collection · chain I against I, TM-score 1.00
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 O94817
- Every structure of UniProt Q9H1Y0
- Every structure of UniProt Q676U5
- Every structure of UniProt Q9NT62
- Elsewhere: RCSB PDB 4NAW · PDBe 4NAW · UniProt O94817 · UniProt Q9H1Y0 · UniProt Q676U5 · UniProt Q9NT62
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