Research workbench
Crystal structure of E.COLI DNA mismatch repair protein muts, D693N mutant, in complex with gt mismatched DNA
Analyse Crystal structure of E.COLI DNA mismatch repair protein muts, D693N mutant, in… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3K0S
- Type
- protein + DNA
- Length
- 1,575 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*CP*AP*CP*CP*AP*GP*TP…
- UniProt
- P23909
- Ligands
- ADP
- Pockets
- 20 · best druggability 0.75
Structure
x-ray diffraction · 4 distinct chains · 47% helix, 19% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | DNA mismatch repair protein muts | protein | 787 | 47% helix, 19% strand | P23909 |
| B | DNA mismatch repair protein muts | protein | 753 | 47% helix, 19% 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*C*AP*CP*T*GP*GP*T P*GP*CP*TP*TP*GP*GP*CP*AP*GP*CP*T)-3' | dna | 17 | — | — |
Ligands and binding sites
- ADP · Adenosine-5'-diphosphate · ligand · chains A
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 | 820 | 0.75 | 0.79 | 80 | empty |
| 2 | 753 | 0.75 | 0.80 | 79 | empty |
| 3 | 316 | 0.69 | 0.84 | 34 | empty |
| 4 | 492 | 0.63 | 0.76 | 69 | ADP |
| 5 | 130 | 0.62 | 0.87 | 25 | empty |
Interfaces
6 interfaces between chains.
- A–B · 2795 Ų buried · 36 hydrogen bonds · protein-protein
- E–F · 821 Ų buried · 83 hydrogen bonds · nucleic-nucleic
- A–E · 668 Ų buried · 15 hydrogen bonds · protein-nucleic
- A–F · 645 Ų buried · 15 hydrogen bonds · protein-nucleic
- B–E · 382 Ų buried · 9 hydrogen bonds · protein-nucleic
Compared structures
- 3K0S · Crystal structure of E.coli DNA mismatch repair protein MutS, D693N 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 3K0S · PDBe 3K0S · UniProt P23909
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