Research workbench
Crystal structure of SLX1-SLX4 in complex with 5'FLAP DNA
Analyse Crystal structure of SLX1-SLX4 in complex with 5'FLAP DNA in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7CQ4
- Type
- protein + DNA
- Length
- 461 residues
- Chains
- 5
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- DNA (5'-D(*GP*GP*AP*TP*TP*AP*CP*AP*AP*CP*AP*GP*AP*T)-3'); DNA…
- EC
- 3.1.-.-
- UniProt
- A6ZLG6, A0A6A5PU22
- Ligands
- ZN
- Pockets
- 6 · best druggability 0.71
Structure
x-ray diffraction · 5 distinct chains · 47% helix, 14% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| H | DNA (5'-D(*GP*GP*AP*TP*TP*AP*CP*AP*AP*CP*AP*GP*AP*T)-3') | dna | 14 | — | — |
| K | DNA (5'-D(*AP*GP*GP*AP*CP*AP*TP*CP*TP*TP*TP*GP*CP*C)-3') | dna | 14 | — | — |
| L | DNA (27-mer) | dna | 27 | — | — |
| A | Structure-specific endonuclease subunit SLX1 (EC 3.1.-.-) | protein | 291 | 40% helix, 18% strand | A6ZLG6 |
| B | SLX4 isoform 1 | protein | 115 | 65% helix, 5% strand | A0A6A5PU22 |
Ligands and binding sites
- ZN · Zinc ion · metal · 2 copies · chains A
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 | 829 | 0.71 | 0.77 | 71 | empty |
| 2 | 156 | 0.51 | 0.79 | 30 | empty |
| 3 | 137 | 0.51 | 0.80 | 21 | empty |
| 4 | 98 | 0.43 | 0.79 | 14 | empty |
| 5 | 64 | 0.39 | 0.79 | 18 | empty |
Interfaces
8 interfaces between chains.
- A–B · 1138 Ų buried · 9 hydrogen bonds · protein-protein
- K–L · 697 Ų buried · 61 hydrogen bonds · nucleic-nucleic
- H–L · 586 Ų buried · 50 hydrogen bonds · nucleic-nucleic
- L–A · 408 Ų buried · 5 hydrogen bonds · protein-nucleic
- L–B · 384 Ų buried · 11 hydrogen bonds · protein-nucleic
Compared structures
- 7CQ4 · Crystal structure of Slx1-Slx4 in complex with 5'flap DNA · the same entry in another collection · chain H against H, TM-score 1.00
- A6ZLG6 · AlphaFold monomer V2.0 prediction for structure-specific endonuclease subunit SLX1… · a predicted model of the same protein · chain A against A, TM-score 0.94
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 A6ZLG6
- Every structure of UniProt A0A6A5PU22
- Elsewhere: RCSB PDB 7CQ4 · PDBe 7CQ4 · UniProt A6ZLG6 · UniProt A0A6A5PU22
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