Research workbench
Crystal structure of kluyveromyces marxianus ATG5
Analyse Crystal structure of kluyveromyces marxianus ATG5 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3VQI
- Type
- protein
- Length
- 1,262 residues
- Chains
- 5
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- ATG5
- Ligands
- SO4
- Pockets
- 10 · best druggability 0.87
Structure
x-ray diffraction · 4 distinct chains · 37% helix, 23% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | ATG5 | protein | 252 | 37% helix, 22% strand | — |
| B | ATG5 | protein | 257 | 39% helix, 21% strand | — |
| C | ATG5 | protein | 241 | 33% helix, 24% strand | — |
| D, E | ATG5 | protein | 256 | 39% helix, 23% strand | — |
Ligands and binding sites
- SO4 · Sulfate ion · ion · 15 copies · chains A, D, B, C, E
- EPE · 4-(2-hydroxyethyl)-1-piperazine ethanesulfonic acid · additive · 3 copies · chains A, D, B, E
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
10 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 975 | 0.87 | 0.88 | 86 | EPE |
| 2 | 949 | 0.87 | 0.88 | 98 | EPE |
| 3 | 78 | 0.74 | 0.97 | 19 | empty |
| 4 | 59 | 0.70 | 0.97 | 17 | empty |
| 5 | 62 | 0.70 | 0.96 | 16 | empty |
Interfaces
5 interfaces between chains.
- A–D · 959 Ų buried · 10 hydrogen bonds · protein-protein
- B–E · 947 Ų buried · 10 hydrogen bonds · protein-protein
- A–B · 900 Ų buried · 7 hydrogen bonds · protein-protein
- B–C · 689 Ų buried · 10 hydrogen bonds · protein-protein
- A–C · 14 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 3VQI · Crystal structure of Kluyveromyces marxianus Atg5 · the same entry in another collection · chain A against A, 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
- Elsewhere: RCSB PDB 3VQI · PDBe 3VQI
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