Research workbench
The crystal structure of E. coli MutS binding to DNA with a G:T mismatch
Analyse The crystal structure of E. coli MutS binding to DNA with a G:T mismatch in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1E3M
- Type
- protein + DNA
- Length
- 1,577 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 2.2
- Source
- ESCHERICHIA COLI; SYNTHETIC CONSTRUCT
- Molecule
- DNA mismatch repair protein muts; 5'-D(*AP*GP*CP*TP*GP*CP*CP*AP*GP*GP*CP*AP*CP*CP*AP*…
- UniProt
- P23909
- Ligands
- ADP, MG
- Pockets
- 20 · best druggability 0.75
Structure
x-ray diffraction · resolution 2.2 · 4 distinct chains · 47% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | DNA mismatch repair protein muts | protein | 788 | 45% helix, 19% strand | P23909 |
| B | DNA mismatch repair protein muts | protein | 754 | 48% helix, 18% strand | P23909 |
| E | 5'-D(*AP*GP*CP*TP*GP*CP*CP*AP*GP*GP*CP*AP*CP*CP*AP* GP*TP*GP*TP*CP*AP*GP*CP*GP*TP*CP*CP*TP*AP*T)-3' | dna | 18 | — | — |
| F | 5'-D(*AP*TP*AP*GP*GP*AP*CP*GP*CP*TP*GP*AP*CP*AP*CP* TP*GP*GP*TP*GP*CP*TP*TP*GP*GP*CP*AP*GP*CP*T)-3' | dna | 17 | — | — |
Ligands and binding sites
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 10 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 859 | 0.75 | 0.79 | 100 | empty |
| 2 | 334 | 0.69 | 0.83 | 48 | empty |
| 3 | 480 | 0.68 | 0.79 | 75 | ADP, MG |
| 4 | 271 | 0.68 | 0.84 | 28 | empty |
| 5 | 71 | 0.68 | 0.94 | 17 | empty |
Interfaces
6 interfaces between chains.
- A–B · 2707 Ų buried · 33 hydrogen bonds · protein-protein
- E–F · 804 Ų buried · 69 hydrogen bonds · nucleic-nucleic
- A–E · 659 Ų buried · 16 hydrogen bonds · protein-nucleic
- A–F · 644 Ų buried · 12 hydrogen bonds · protein-nucleic
- B–E · 327 Ų buried · 5 hydrogen bonds · protein-nucleic
Modifications
Observed in the structure: 45 modified (engineered).
Compared structures
- 1E3M · The crystal structure of E. COLI muts binding to DNA with a G:T mismatch · the same entry in another collection · chain A against A, TM-score 1.00
- P23909 · AlphaFold monomer V2.0 prediction for DNA mismatch repair protein muts (P23909) · a predicted model of the same protein · chain A against A, TM-score 0.99
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 P23909
- Elsewhere: RCSB PDB 1E3M · PDBe 1E3M · UniProt P23909
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