MolNFT v1 · #79936 · protein + DNA
Human mutsbeta complexed with an idl of 3 bases (LOOP3) and ADP
3THX · DNA mismatch repair protein MSH2: “Human mutsbeta complexed with an idl of 3 bases (LOOP3) and ADP”. X-ray diffraction, 2 ligands (ADP, NA), 20 pockets (best druggability 0.83). MolNFT v1 #79936 on GenesisL1: 3D structure, binding…
- PDB
- 3THX
- Type
- protein + DNA
- Length
- 1,766 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 LOOP3 minus…
- UniProt
- P43246
- Ligands
- ADP, NA
- Pockets
- 20 · best druggability 0.83
Structure
x-ray diffraction · 4 distinct chains · 49% helix, 19% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | DNA mismatch repair protein MSH2 | protein | 868 | 49% helix, 19% strand | P43246 |
| B | DNA mismatch repair protein MSH3 | protein | 852 | 48% helix, 19% strand | — |
| D | DNA LOOP3 minus strand | dna | 21 | — | — |
| E | DNA LOOP3 plus strand | dna | 25 | — | — |
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, 12 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 825 | 0.83 | 0.86 | 91 | empty |
| 2 | 1002 | 0.76 | 0.78 | 94 | empty |
| 3 | 1032 | 0.74 | 0.77 | 55 | empty |
| 4 | 72 | 0.73 | 0.98 | 23 | empty |
| 5 | 61 | 0.67 | 0.94 | 20 | empty |
Interfaces
6 interfaces between chains.
- A–B · 4567 Ų buried · 42 hydrogen bonds · protein-protein
- D–E · 992 Ų buried · 86 hydrogen bonds · nucleic-nucleic
- B–E · 746 Ų buried · 16 hydrogen bonds · protein-nucleic
- B–D · 523 Ų buried · 11 hydrogen bonds · protein-nucleic
- A–E · 345 Ų buried · 2 hydrogen bonds · protein-nucleic
Compared structures
- 3THX · Human MutSbeta complexed with an IDL of 3 bases (Loop3) 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 3THX · PDBe 3THX · UniProt P43246
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