MolNFT v1 · #116774 · protein + DNA
Structure of the atprs-MRE11/RAD50-DNA complex
5DNY · DNA double-strand break repair protein MRE11: “Structure of the atprs-MRE11/RAD50-DNA complex”. X-ray diffraction, 2 ligands (AGS, MG), 20 pockets (best druggability 0.87). MolNFT v1 #116774 on GenesisL1: 3D structure, binding sites…
- PDB
- 5DNY
- Type
- protein + DNA
- Length
- 1,468 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- DNA double-strand break repair protein MRE11; DNA double-strand break repair RAD50…
- UniProt
- Q58719, Q58718
- Ligands
- AGS, MG
- Pockets
- 20 · best druggability 0.87
Structure
x-ray diffraction · 6 distinct chains · 38% helix, 24% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | DNA double-strand break repair protein MRE11 | protein | 352 | 33% helix, 22% strand | Q58719 |
| B | DNA double-strand break repair RAD50 ATPASE,DNA double- strand break repair RAD50 ATPase | protein | 359 | 42% helix, 26% strand | Q58718 |
| C | DNA double-strand break repair protein MRE11 | protein | 351 | 34% helix, 22% strand | Q58719 |
| D | DNA double-strand break repair RAD50 ATPASE,DNA double- strand break repair RAD50 ATPase | protein | 358 | 41% helix, 25% strand | Q58718 |
| E | DNA (27-mer) | dna | 25 | — | — |
| F | DNA (27-mer) | dna | 23 | — | — |
Ligands and binding sites
- AGS · Phosphothiophosphoric acid-adenylate ester · ligand · 2 copies · chains B, D
- MG · Magnesium ion · metal · 4 copies · chains A, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 9 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 963 | 0.87 | 0.89 | 136 | empty |
| 2 | 405 | 0.76 | 0.86 | 56 | AGS |
| 3 | 369 | 0.76 | 0.86 | 53 | AGS |
| 4 | 310 | 0.71 | 0.84 | 45 | empty |
| 5 | 223 | 0.59 | 0.81 | 22 | empty |
Interfaces
11 interfaces between chains.
- C–D · 2267 Ų buried · 23 hydrogen bonds · protein-protein
- A–B · 2262 Ų buried · 24 hydrogen bonds · protein-protein
- B–D · 1603 Ų buried · 30 hydrogen bonds · protein-protein
- E–F · 954 Ų buried · 60 hydrogen bonds · nucleic-nucleic
- A–C · 723 Ų buried · 8 hydrogen bonds · protein-protein
Compared structures
- 5DNY · Structure of the ATPrS-Mre11/Rad50-DNA complex · the same entry in another collection · chain F against F, TM-score 1.00
- Q58719 · AlphaFold monomer V2.0 prediction for DNA double-strand break repair protein MRE11… · a predicted model of the same protein · chain A against A, TM-score 0.86
- Q58718 · AlphaFold monomer V2.0 prediction for DNA double-strand break repair RAD50 ATPase (Q58718) · a predicted model of the same protein · chain B against A, TM-score 0.74
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 Q58719
- Every structure of UniProt Q58718
- Elsewhere: RCSB PDB 5DNY · PDBe 5DNY · UniProt Q58719 · UniProt Q58718
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