Research workbench
Human mutsbeta complexed with an idl of 2 bases (LOOP2) and ADP
Analyse Human mutsbeta complexed with an idl of 2 bases (LOOP2) and ADP in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3THY
- Type
- protein + DNA
- Length
- 1,785 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 LOOP2 minus…
- UniProt
- P43246
- Ligands
- ADP
- Pockets
- 20 · best druggability 0.84
Structure
x-ray diffraction · 4 distinct chains · 47% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | DNA mismatch repair protein MSH2 | protein | 883 | 48% helix, 18% strand | P43246 |
| B | DNA mismatch repair protein MSH3 | protein | 857 | 47% helix, 18% strand | — |
| D | DNA LOOP2 minus strand | dna | 21 | — | — |
| E | DNA LOOP2 plus strand | dna | 24 | — | — |
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, 14 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1039 | 0.84 | 0.85 | 129 | empty |
| 2 | 832 | 0.77 | 0.81 | 62 | empty |
| 3 | 462 | 0.72 | 0.82 | 68 | ADP |
| 4 | 468 | 0.69 | 0.80 | 61 | empty |
| 5 | 77 | 0.68 | 0.94 | 26 | empty |
Interfaces
6 interfaces between chains.
- A–B · 4550 Ų buried · 38 hydrogen bonds · protein-protein
- D–E · 1000 Ų buried · 92 hydrogen bonds · nucleic-nucleic
- B–E · 751 Ų buried · 17 hydrogen bonds · protein-nucleic
- B–D · 459 Ų buried · 10 hydrogen bonds · protein-nucleic
- A–E · 244 Ų buried · 0 hydrogen bonds · protein-nucleic
Compared structures
- 3THY · Human MutSbeta complexed with an IDL of 2 bases (Loop2) 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 0.89
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 3THY · PDBe 3THY · UniProt P43246
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