Research workbench
Crystal structure of E. COLI DNA mismatch repair enzyme muts, E38Q mutant, in complex with a G.T mismatch
Analyse Crystal structure of E. COLI DNA mismatch repair enzyme muts, E38Q mutant, in… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1WBD
- Type
- protein + DNA
- Length
- 1,577 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- DNA mismatch repair protein muts; 5'-D(*AP*GP*CP*TP*GP*CP*CP*AP*GP*GP…
- UniProt
- P23909
- Ligands
- ADP, MG
- Pockets
- 20 · best druggability 0.74
Structure
x-ray diffraction · 4 distinct chains · 46% helix, 19% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | DNA mismatch repair protein muts | protein | 788 | 46% helix, 19% strand | P23909 |
| B | DNA mismatch repair protein muts | protein | 754 | 47% helix, 18% strand | P23909 |
| E | 5'-D(*AP*GP*CP*TP*GP*CP*CP*AP*GP*GP *CP*AP*CP*CP*AP*GP*TP*G)-3' | dna | 18 | — | — |
| F | 5'-D(*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 | 781 | 0.74 | 0.79 | 77 | empty |
| 2 | 337 | 0.71 | 0.84 | 42 | empty |
| 3 | 545 | 0.69 | 0.79 | 60 | empty |
| 4 | 283 | 0.68 | 0.84 | 30 | empty |
| 5 | 486 | 0.67 | 0.78 | 73 | ADP, MG |
Interfaces
6 interfaces between chains.
- A–B · 2755 Ų buried · 34 hydrogen bonds · protein-protein
- E–F · 803 Ų buried · 69 hydrogen bonds · nucleic-nucleic
- A–E · 670 Ų buried · 15 hydrogen bonds · protein-nucleic
- A–F · 642 Ų buried · 12 hydrogen bonds · protein-nucleic
- B–E · 341 Ų buried · 5 hydrogen bonds · protein-nucleic
Compared structures
- 1WBD · Crystal structure of E. coli DNA mismatch repair enzyme MutS, E38Q mutant, in complex… · 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 1WBD · PDBe 1WBD · UniProt P23909
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