MolNFT v1 · #92611 · protein
Crystal structure of human ATG12~ATG5 conjugate in complex with an N- terminal fragment of ATG16L1
4GDL · Ubiquitin-like protein ATG12: “Crystal structure of human ATG12~ATG5 conjugate in complex with an N- terminal fragment of ATG16L1”. X-ray diffraction, 1 ligand (NA), 7 pockets (best druggability 0.63). MolNFT v1 #92611 on GenesisL1…
- PDB
- 4GDL
- Type
- protein
- Length
- 387 residues
- Chains
- 3
- 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
- UniProt
- O94817, Q9H1Y0, Q676U5
- Ligands
- NA
- Pockets
- 7 · best druggability 0.63
Structure
x-ray diffraction · 3 distinct chains · 35% helix, 20% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Ubiquitin-like protein ATG12 | protein | 88 | 22% helix, 32% strand | O94817 |
| B | Autophagy protein 5 | protein | 265 | 32% helix, 18% strand | Q9H1Y0 |
| C | Autophagy-related protein 16-1 | protein | 34 | 85% helix, 0% strand | Q676U5 |
Ligands and binding sites
- NA · Sodium ion · metal · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 416 | 0.63 | 0.77 | 38 | empty |
| 2 | 80 | 0.48 | 0.82 | 22 | empty |
| 3 | 150 | 0.48 | 0.77 | 21 | empty |
| 4 | 116 | 0.41 | 0.76 | 19 | empty |
| 5 | 110 | 0.39 | 0.75 | 24 | empty |
Interfaces
2 interfaces between chains.
- B–C · 1188 Ų buried · 8 hydrogen bonds · protein-protein
- A–B · 737 Ų buried · 9 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 isopeptide (isopeptide).
Compared structures
- 4GDL · Crystal Structure of Human Atg12~Atg5 Conjugate in Complex with an N-terminal Fragment of… · the same entry in another collection · chain A against A, TM-score 1.00
- Q9H1Y0 · AlphaFold monomer V2.0 prediction for autophagy protein 5 (Q9H1Y0) · a predicted model of the same protein · chain B against A, TM-score 0.98
- O94817 · AlphaFold monomer V2.0 prediction for ubiquitin-like protein ATG12 (O94817) · a predicted model of the same protein · chain A against A, TM-score 0.97
- Q676U5 · AlphaFold monomer V2.0 prediction for autophagy-related protein 16-1 (Q676U5) · a predicted model of the same protein · chain C against A, TM-score 0.68
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
- Elsewhere: RCSB PDB 4GDL · PDBe 4GDL · UniProt O94817 · UniProt Q9H1Y0 · UniProt Q676U5
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