Research workbench
Crystal structure of the ATPase domain from bacterial mismatch repair endonuclease aquifex aeolicus mutl.
Analyse Crystal structure of the ATPase domain from bacterial mismatch repair… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5X9Y
- Type
- protein
- Length
- 741 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- DNA mismatch repair protein mutl
- UniProt
- O67518
- Pockets
- 10 · best druggability 0.64
Structure
x-ray diffraction · 1 distinct chain · 26% helix, 30% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| C, A, B | DNA mismatch repair protein mutl | protein | 247 | 26% helix, 30% strand | O67518 |
Ligands and binding sites
- PEG · Di(hydroxyethyl)ether · additive · 2 copies · chains C, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
10 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 375 | 0.64 | 0.78 | 51 | empty |
| 2 | 184 | 0.61 | 0.82 | 29 | empty |
| 3 | 142 | 0.61 | 0.84 | 20 | empty |
| 4 | 248 | 0.60 | 0.79 | 32 | PEG |
| 5 | 238 | 0.56 | 0.78 | 28 | empty |
Interfaces
3 interfaces between chains.
- C–B · 444 Ų buried · 2 hydrogen bonds · protein-protein
- C–A · 404 Ų buried · 2 hydrogen bonds · protein-protein
- A–B · 102 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 5X9Y · Crystal structure of the ATPase domain from bacterial mismatch repair endonuclease… · the same entry in another collection · chain C against C, TM-score 1.00
- O67518 · AlphaFold monomer V2.0 prediction for DNA mismatch repair protein mutl (O67518) · a predicted model of the same protein · chain C against A, TM-score 0.98
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 O67518
- Elsewhere: RCSB PDB 5X9Y · PDBe 5X9Y · UniProt O67518
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