MolNFT v1 · #79938 · protein + DNA
Human mutsbeta complexed with an idl of 6 bases (LOOP6) and ADP
3THZ · DNA mismatch repair protein MSH2: “Human mutsbeta complexed with an idl of 6 bases (LOOP6) and ADP”. X-ray diffraction, 1 ligand (ADP), 20 pockets (best druggability 0.78). MolNFT v1 #79938 on GenesisL1: 3D structure, binding sites…
- PDB
- 3THZ
- Type
- protein + DNA
- Length
- 1,781 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- DNA mismatch repair protein MSH2; DNA mismatch repair protein MSH3; DNA LOOP6 minus…
- UniProt
- P43246
- Ligands
- ADP
- Pockets
- 20 · best druggability 0.78
Structure
x-ray diffraction · 4 distinct chains · 46% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | DNA mismatch repair protein MSH2 | protein | 888 | 46% helix, 17% strand | P43246 |
| B | DNA mismatch repair protein MSH3 | protein | 846 | 47% helix, 19% strand | — |
| D | DNA LOOP6 minus strand | dna | 20 | — | — |
| E | DNA LOOP6 plus strand | dna | 27 | — | — |
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, 16 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 515 | 0.78 | 0.85 | 59 | empty |
| 2 | 655 | 0.77 | 0.83 | 78 | empty |
| 3 | 671 | 0.75 | 0.80 | 66 | empty |
| 4 | 496 | 0.72 | 0.81 | 65 | empty |
| 5 | 460 | 0.70 | 0.81 | 63 | empty |
Interfaces
6 interfaces between chains.
- A–B · 4034 Ų buried · 31 hydrogen bonds · protein-protein
- D–E · 945 Ų buried · 82 hydrogen bonds · nucleic-nucleic
- B–E · 753 Ų buried · 15 hydrogen bonds · protein-nucleic
- B–D · 550 Ų buried · 6 hydrogen bonds · protein-nucleic
- A–E · 330 Ų buried · 0 hydrogen bonds · protein-nucleic
Compared structures
- 3THZ · Human MutSbeta complexed with an IDL of 6 bases (Loop6) and ADP · the same entry in another collection · chain A against A, TM-score 1.00
- P43246 · AlphaFold monomer V2.0 prediction for DNA mismatch repair protein MSH2 (P43246) · a predicted model of the same protein · chain A against A, TM-score 0.88
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 P43246
- Elsewhere: RCSB PDB 3THZ · PDBe 3THZ · UniProt P43246
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