Research workbench
Structure of the C-terminal dimerization domain of ATG38
Analyse Structure of the C-terminal dimerization domain of ATG38 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5KC1
- Type
- protein
- Length
- 518 residues
- Chains
- 12
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Autophagy-related protein 38
- UniProt
- Q05789
- Ligands
- NA, NO3, CL, NH4, SO4, IOD
- Pockets
- 7 · best druggability 0.64
Structure
x-ray diffraction · 12 distinct chains · 84% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| C | Autophagy-related protein 38 | protein | 33 | 76% helix, 0% strand | Q05789 |
| D | Autophagy-related protein 38 | protein | 51 | 88% helix, 0% strand | Q05789 |
| A | Autophagy-related protein 38 | protein | 29 | 62% helix, 0% strand | Q05789 |
| B | Autophagy-related protein 38 | protein | 57 | 95% helix, 0% strand | Q05789 |
| G | Autophagy-related protein 38 | protein | 33 | 79% helix, 0% strand | Q05789 |
| H | Autophagy-related protein 38 | protein | 53 | 92% helix, 0% strand | Q05789 |
| K | Autophagy-related protein 38 | protein | 24 | 71% helix, 0% strand | Q05789 |
| L | Autophagy-related protein 38 | protein | 60 | 88% helix, 0% strand | Q05789 |
| E | Autophagy-related protein 38 | protein | 30 | 73% helix, 0% strand | Q05789 |
| F | Autophagy-related protein 38 | protein | 61 | 84% helix, 0% strand | Q05789 |
| I | Autophagy-related protein 38 | protein | 29 | 76% helix, 0% strand | Q05789 |
| J | Autophagy-related protein 38 | protein | 58 | 91% helix, 0% strand | Q05789 |
Ligands and binding sites
- NA · Sodium ion · metal · 14 copies · chains C, D, F, B, K, J, E, A, I, L
- NO3 · Nitrate ion · ion · 18 copies · chains C, D, A, F, B, G, J, I, H, K, L, E
- CL · Chloride ion · ion · 6 copies · chains D, E, F
- NH4 · Ammonium ion · ion · 2 copies · chains K, H, J
- SO4 · Sulfate ion · ion · chains K
- IOD · Iodide ion · ion · chains E
- EDO · 1,2-ethanediol · additive · 9 copies · chains C, B, A, G, F, D, K, L, J, I
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 407 | 0.64 | 0.78 | 39 | NO3, EDO |
| 2 | 141 | 0.52 | 0.80 | 20 | NA, NO3 |
| 3 | 198 | 0.47 | 0.75 | 20 | empty |
| 4 | 107 | 0.47 | 0.79 | 16 | NO3 |
| 5 | 90 | 0.34 | 0.74 | 16 | EDO |
Interfaces
25 interfaces between chains.
- H–F · 1151 Ų buried · 9 hydrogen bonds · protein-protein
- D–B · 1092 Ų buried · 5 hydrogen bonds · protein-protein
- L–J · 1078 Ų buried · 9 hydrogen bonds · protein-protein
- C–B · 762 Ų buried · 10 hydrogen bonds · protein-protein
- C–D · 717 Ų buried · 10 hydrogen bonds · protein-protein
Compared structures
- 5KC1 · Structure of the C-terminal dimerization domain of Atg38 · the same entry in another collection · chain J against J, 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 Q05789
- Elsewhere: RCSB PDB 5KC1 · PDBe 5KC1 · UniProt Q05789
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