MolNFT v1 · #46569 · protein + DNA
Human mutsalpha (MSH2/MSH6) bound to ADP and an O6-methyl-guanine T mispair
2O8C · 5'-D(*GP*AP*AP*CP*CP*GP*CP*(6OG)P*CP*GP*CP*TP*AP*GP*G)-3': “Human mutsalpha (MSH2/MSH6) bound to ADP and an O6-methyl-guanine T mispair”. X-ray diffraction, 2 ligands (ADP, MG), 20 pockets (best druggability 0.81). MolNFT v1 #46569…
- PDB
- 2O8C
- Type
- protein + DNA
- Length
- 1,792 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 5'-D(*GP*AP*AP*CP*CP*GP*CP*(6OG)P*CP*GP*CP*TP*AP*GP*G)-3'…
- UniProt
- P43246, P52701
- Ligands
- ADP, MG
- Pockets
- 20 · best druggability 0.81
Structure
x-ray diffraction · 4 distinct chains · 41% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| E | 5'-D(*GP*AP*AP*CP*CP*GP*CP*(6OG)P*CP*GP*CP*TP*AP*GP*G)-3' | dna | 15 | — | — |
| F | 5'-D(*CP*CP*TP*AP*GP*CP*GP*TP*GP*CP*GP*GP*TP*TP*C)-3' | dna | 15 | — | — |
| A | DNA mismatch repair protein MSH2 | protein | 830 | 40% helix, 19% strand | P43246 |
| B | DNA mismatch repair protein MSH6 | protein | 932 | 42% helix, 16% strand | P52701 |
Ligands and binding sites
- ADP · Adenosine-5'-diphosphate · ligand · 2 copies · chains A, B
- MG · Magnesium ion · metal · 2 copies · chains A, B
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 | 1121 | 0.81 | 0.83 | 103 | empty |
| 2 | 1148 | 0.81 | 0.82 | 107 | empty |
| 3 | 765 | 0.78 | 0.81 | 93 | MG, ADP |
| 4 | 603 | 0.76 | 0.82 | 79 | empty |
| 5 | 920 | 0.68 | 0.74 | 52 | empty |
Interfaces
6 interfaces between chains.
- A–B · 3557 Ų buried · 23 hydrogen bonds · protein-protein
- F–B · 694 Ų buried · 11 hydrogen bonds · protein-nucleic
- E–F · 688 Ų buried · 60 hydrogen bonds · nucleic-nucleic
- E–B · 587 Ų buried · 16 hydrogen bonds · protein-nucleic
- F–A · 198 Ų buried · 4 hydrogen bonds · protein-nucleic
Modifications
Observed in the structure: 1 modified (nucleotide modification).
Compared structures
- 2O8C · human MutSalpha (MSH2/MSH6) bound to ADP and an O6-methyl-guanine T mispair · the same entry in another collection · chain E against E, TM-score 1.00
- P52701 · AlphaFold monomer V2.0 prediction for DNA mismatch repair protein MSH6 (P52701) · a predicted model of the same protein · chain B against A, TM-score 0.97
- 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 0.95
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
- Every structure of UniProt P52701
- Elsewhere: RCSB PDB 2O8C · PDBe 2O8C · UniProt P43246 · UniProt P52701
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