Research workbench
Xpf-ERCC1 cryo-EM structure, apo-form
Analyse Xpf-ERCC1 cryo-EM structure, apo-form in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6SXA
- Type
- protein
- Length
- 943 residues
- Chains
- 2
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- DNA repair endonuclease xpf; DNA excision repair protein ercc-1
- EC
- 3.1.-.-
- UniProt
- Q92889, P07992
- Pockets
- 13 · best druggability 0.83
Structure
electron microscopy · 2 distinct chains · 43% helix, 10% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| F | DNA repair endonuclease xpf (EC 3.1.-.-) | protein | 747 | 44% helix, 10% strand | Q92889 |
| G | DNA excision repair protein ercc-1 | protein | 196 | 37% helix, 13% strand | P07992 |
Pockets
13 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 960 | 0.83 | 0.84 | 116 | empty |
| 2 | 246 | 0.80 | 0.92 | 51 | empty |
| 3 | 354 | 0.70 | 0.82 | 39 | empty |
| 4 | 123 | 0.65 | 0.88 | 26 | empty |
| 5 | 198 | 0.55 | 0.79 | 21 | empty |
Interfaces
1 interface between chains.
- F–G · 3098 Ų buried · 18 hydrogen bonds · protein-protein
Compared structures
- 6SXA · XPF-ERCC1 Cryo-EM Structure, Apo-form · the same entry in another collection · chain F against F, TM-score 1.00
- Q92889 · AlphaFold monomer V2.0 prediction for DNA repair endonuclease xpf (Q92889) · a predicted model of the same protein · chain F against A, TM-score 0.84
- P07992 · AlphaFold monomer V2.0 prediction for DNA excision repair protein ercc-1 (P07992) · a predicted model of the same protein · chain G against A, TM-score 0.63
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 Q92889
- Every structure of UniProt P07992
- Elsewhere: RCSB PDB 6SXA · PDBe 6SXA · UniProt Q92889 · UniProt P07992
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