MolNFT v1 · #163830 · protein
Recognition and processing of branched DNA substrates by SLX1-SLX4 nuclease
6SEH · Structure-specific endonuclease subunit SLX1: “Recognition and processing of branched DNA substrates by SLX1-SLX4 nuclease”. X-ray diffraction, 1 ligand (ZN), 11 pockets (best druggability 0.65). MolNFT v1 #163830 on GenesisL1: 3D…
- PDB
- 6SEH
- Type
- protein
- Length
- 660 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Structure-specific endonuclease subunit SLX1; Structure-specific endonuclease subunit SLX4
- EC
- 3.1.-.-
- UniProt
- G2QV68, A0A3S4CYR8
- Ligands
- ZN
- Pockets
- 11 · best druggability 0.65
Structure
x-ray diffraction · 4 distinct chains · 41% helix, 14% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| C | Structure-specific endonuclease subunit SLX1 (EC 3.1.-.-) | protein | 252 | 38% helix, 17% strand | G2QV68 |
| D | Structure-specific endonuclease subunit SLX4 | protein | 82 | 55% helix, 5% strand | A0A3S4CYR8 |
| A | Structure-specific endonuclease subunit SLX1 (EC 3.1.-.-) | protein | 249 | 37% helix, 17% strand | G2QV68 |
| B | Structure-specific endonuclease subunit SLX4 | protein | 77 | 52% helix, 5% strand | A0A3S4CYR8 |
Ligands and binding sites
- ZN · Zinc ion · metal · 4 copies · chains C, D, A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
11 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 242 | 0.65 | 0.83 | 33 | empty |
| 2 | 171 | 0.62 | 0.84 | 31 | empty |
| 3 | 237 | 0.60 | 0.80 | 27 | empty |
| 4 | 124 | 0.39 | 0.74 | 25 | empty |
| 5 | 110 | 0.39 | 0.75 | 21 | empty |
Interfaces
4 interfaces between chains.
- C–D · 1306 Ų buried · 15 hydrogen bonds · protein-protein
- A–B · 1228 Ų buried · 13 hydrogen bonds · protein-protein
- C–A · 356 Ų buried · 4 hydrogen bonds · protein-protein
- C–B · 20 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 6SEH · Recognition and processing of branched DNA substrates by Slx1-Slx4 nuclease · the same entry in another collection · chain C against C, 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 G2QV68
- Every structure of UniProt A0A3S4CYR8
- Elsewhere: RCSB PDB 6SEH · PDBe 6SEH · UniProt G2QV68 · UniProt A0A3S4CYR8
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