Research workbench
Crystal structure of ATG13 lir-fused human LC3B_2-119
Analyse Crystal structure of ATG13 lir-fused human LC3B_2-119 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3WAO
- Type
- protein
- Length
- 498 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Autophagy-related protein 13, microtubule-associated proteins 1A/1B light chain 3B
- UniProt
- O75143, Q9GZQ8
- Pockets
- 6 · best druggability 0.78
Structure
x-ray diffraction · 3 distinct chains · 29% helix, 21% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Autophagy-related protein 13, microtubule-associated proteins 1A/1B light chain 3B | protein | 126 | 29% helix, 21% strand | O75143, Q9GZQ8 |
| B, C | Autophagy-related protein 13, microtubule-associated proteins 1A/1B light chain 3B | protein | 124 | 27% helix, 22% strand | O75143, Q9GZQ8 |
| D | Autophagy-related protein 13, microtubule-associated proteins 1A/1B light chain 3B | protein | 124 | 31% helix, 21% strand | O75143, Q9GZQ8 |
Pockets
6 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 770 | 0.78 | 0.82 | 66 | empty |
| 2 | 138 | 0.64 | 0.87 | 27 | empty |
| 3 | 126 | 0.56 | 0.83 | 27 | empty |
| 4 | 135 | 0.43 | 0.76 | 28 | empty |
| 5 | 115 | 0.41 | 0.76 | 23 | empty |
Interfaces
5 interfaces between chains.
- B–C · 873 Ų buried · 9 hydrogen bonds · protein-protein
- A–D · 749 Ų buried · 6 hydrogen bonds · protein-protein
- B–D · 444 Ų buried · 5 hydrogen bonds · protein-protein
- C–D · 193 Ų buried · 1 hydrogen bond · protein-protein
- A–C · 186 Ų buried · 1 hydrogen bond · protein-protein
Compared structures
- 3WAO · Crystal structure of Atg13 LIR-fused human LC3B_2-119 · the same entry in another collection · chain D against D, TM-score 1.00
- Q9GZQ8 · AlphaFold monomer V2.0 prediction for microtubule-associated proteins 1A/1B light chain… · a predicted model of the same protein · chain D against A, TM-score 0.88
- 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 0.35
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 Q9GZQ8
- Elsewhere: RCSB PDB 3WAO · PDBe 3WAO · UniProt O75143 · UniProt Q9GZQ8
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