Research workbench
Recognition and processing of branched DNA substrates by SLX1-SLX4 nuclease
Analyse Recognition and processing of branched DNA substrates by SLX1-SLX4 nuclease in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6SEI
- Type
- protein + DNA
- Length
- 746 residues
- Chains
- 5
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Structure-specific endonuclease subunit SLX1; Structure-specific endonuclease subunit…
- EC
- 3.1.-.-
- UniProt
- G2QV68, A0A3S4CYR8
- Ligands
- ZN, CA
- Pockets
- 14 · best druggability 0.64
Structure
x-ray diffraction · 4 distinct chains · 38% helix, 14% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Structure-specific endonuclease subunit SLX1 (EC 3.1.-.-) | protein | 276 | 34% helix, 16% strand | G2QV68 |
| B, D | Structure-specific endonuclease subunit SLX4 | protein | 84 | 58% helix, 5% strand | A0A3S4CYR8 |
| C | Structure-specific endonuclease subunit SLX1 (EC 3.1.-.-) | protein | 270 | 36% helix, 16% strand | G2QV68 |
| E | DNA (32-mer) | dna | 32 | — | — |
Ligands and binding sites
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
14 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 222 | 0.64 | 0.83 | 34 | empty |
| 2 | 240 | 0.60 | 0.81 | 29 | empty |
| 3 | 190 | 0.60 | 0.82 | 24 | empty |
| 4 | 158 | 0.58 | 0.83 | 18 | empty |
| 5 | 210 | 0.58 | 0.80 | 26 | empty |
Interfaces
4 interfaces between chains.
- A–B · 1607 Ų buried · 23 hydrogen bonds · protein-protein
- C–D · 1540 Ų buried · 19 hydrogen bonds · protein-protein
- C–E · 650 Ų buried · 19 hydrogen bonds · protein-nucleic
- A–E · 497 Ų buried · 9 hydrogen bonds · protein-nucleic
Compared structures
- 6SEI · Recognition and processing of branched DNA substrates by Slx1-Slx4 nuclease · 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 G2QV68
- Every structure of UniProt A0A3S4CYR8
- Elsewhere: RCSB PDB 6SEI · PDBe 6SEI · UniProt G2QV68 · UniProt A0A3S4CYR8
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