MolNFT v1 · #116329 · protein
ATP-gamma-S bound RAD50 from chaetomium thermophilum in complex with the RAD50-binding domain of MRE11
5DA9 · Putative uncharacterized PROTEIN,PUTATIVE uncharacterized…: “ATP-gamma-S bound RAD50 from chaetomium thermophilum in complex with the RAD50-binding domain of MRE11”. X-ray diffraction, 2 ligands (AGS, MG), 15 pockets (best…
- PDB
- 5DA9
- Type
- protein
- Length
- 978 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Putative uncharacterized PROTEIN,PUTATIVE uncharacterized protein; Putative double-strand…
- UniProt
- G0SHW7, G0RYR3
- Ligands
- AGS, MG
- Pockets
- 15 · best druggability 0.82
Structure
x-ray diffraction · 4 distinct chains · 48% helix, 24% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Putative uncharacterized PROTEIN,PUTATIVE uncharacterized protein | protein | 433 | 47% helix, 26% strand | G0SHW7 |
| B | Putative uncharacterized PROTEIN,PUTATIVE uncharacterized protein | protein | 400 | 41% helix, 30% strand | G0SHW7 |
| C | Putative double-strand break protein | protein | 85 | 76% helix, 0% strand | G0RYR3 |
| D | Putative double-strand break protein | protein | 60 | 70% helix, 0% strand | G0RYR3 |
Ligands and binding sites
- AGS · Phosphothiophosphoric acid-adenylate ester · 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
15 pockets found on a 1 Å grid, 11 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 351 | 0.82 | 0.92 | 54 | MG, AGS |
| 2 | 307 | 0.81 | 0.92 | 54 | MG, AGS |
| 3 | 537 | 0.73 | 0.81 | 51 | empty |
| 4 | 276 | 0.70 | 0.84 | 39 | empty |
| 5 | 111 | 0.65 | 0.90 | 24 | empty |
Interfaces
3 interfaces between chains.
- A–B · 1835 Ų buried · 33 hydrogen bonds · protein-protein
- A–C · 1579 Ų buried · 9 hydrogen bonds · protein-protein
- B–D · 1145 Ų buried · 5 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 24 modified (engineered).
Compared structures
- 5DA9 · ATP-gamma-S bound Rad50 from Chaetomium thermophilum in complex with the Rad50-binding… · the same entry in another collection · chain A against A, TM-score 1.00
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 G0SHW7
- Every structure of UniProt G0RYR3
- Elsewhere: RCSB PDB 5DA9 · PDBe 5DA9 · UniProt G0SHW7 · UniProt G0RYR3
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