MolNFT v1 · #68592 · protein + DNA
Crystal structure of E.COLI DNA mismatch repair protein muts, D693N mutant, in complex with gt mismatched DNA
3K0S: “Crystal structure of E.COLI DNA mismatch repair protein muts, D693N mutant, in complex with gt mismatched DNA”. X-ray diffraction, 1 ligand (ADP), 20 pockets (best druggability 0.75). MolNFT v1 #68592 on GenesisL1: 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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