MolNFT v1 · #169139 · protein
MRE11 dimer in complex with small molecule modulator pfmj
6X1Z · Nuclease sbccd subunit D: “MRE11 dimer in complex with small molecule modulator pfmj”. X-ray diffraction, 2 ligands (UL1, MG), 6 pockets (best druggability 0.77). MolNFT v1 #169139 on GenesisL1: 3D structure, binding sites and…
- PDB
- 6X1Z
- Type
- protein
- Length
- 655 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Nuclease sbccd subunit D
- UniProt
- Q9X1X0
- Ligands
- UL1, MG
- Pockets
- 6 · best druggability 0.77
Structure
x-ray diffraction · 2 distinct chains · 27% helix, 27% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Nuclease sbccd subunit D | protein | 329 | 26% helix, 27% strand | Q9X1X0 |
| B | Nuclease sbccd subunit D | protein | 326 | 28% helix, 27% strand | Q9X1X0 |
Ligands and binding sites
- UL1 · (5Z)-5-[(3,4-dimethoxyphenyl)methylidene]-2-sulfanylidene-1,3-thiazolidin-4-one · ligand · 2 copies · chains A, B
- MG · Magnesium ion · metal · 2 copies · chains A, B
- MES · 2-(N-morpholino)-ethanesulfonic acid · additive · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 732 | 0.77 | 0.82 | 100 | UL1, MG, MES |
| 2 | 137 | 0.52 | 0.81 | 18 | empty |
| 3 | 136 | 0.52 | 0.81 | 17 | empty |
| 4 | 72 | 0.35 | 0.76 | 17 | empty |
| 5 | 61 | 0.32 | 0.76 | 14 | empty |
Interfaces
1 interface between chains.
- A–B · 868 Ų buried · 2 hydrogen bonds · protein-protein
Compared structures
- 6X1Z · Mre11 dimer in complex with small molecule modulator PFMJ · 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 Q9X1X0
- Elsewhere: RCSB PDB 6X1Z · PDBe 6X1Z · UniProt Q9X1X0
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