Research workbench
Xpf-ERCC1 cryo-EM structure, DNA-bound form
Analyse Xpf-ERCC1 cryo-EM structure, DNA-bound form in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6SXB
- Type
- protein + DNA
- Length
- 912 residues
- Chains
- 4
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- DNA repair endonuclease xpf; DNA excision repair protein ercc-1; DNA…
- EC
- 3.1.-.-
- UniProt
- Q92889, P07992
- Pockets
- 16 · best druggability 0.78
Structure
electron microscopy · 4 distinct chains · 45% helix, 11% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| F | DNA repair endonuclease xpf (EC 3.1.-.-) | protein | 701 | 47% helix, 11% strand | Q92889 |
| G | DNA excision repair protein ercc-1 | protein | 191 | 40% helix, 14% strand | P07992 |
| C | DNA (5'-D(P*CP*AP*GP*AP*TP*GP*CP*TP*GP*A)-3') | dna | 10 | — | — |
| D | DNA (5'-D(*TP*CP*AP*GP*CP*AP*TP*CP*TP*G)-3') | dna | 10 | — | — |
Pockets
16 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 621 | 0.78 | 0.83 | 59 | empty |
| 2 | 451 | 0.77 | 0.85 | 61 | empty |
| 3 | 126 | 0.73 | 0.92 | 30 | empty |
| 4 | 148 | 0.61 | 0.84 | 26 | empty |
| 5 | 140 | 0.60 | 0.84 | 26 | empty |
Interfaces
4 interfaces between chains.
- F–G · 3158 Ų buried · 31 hydrogen bonds · protein-protein
- C–D · 502 Ų buried · 30 hydrogen bonds · nucleic-nucleic
- G–C · 283 Ų buried · 2 hydrogen bonds · protein-nucleic
- G–D · 141 Ų buried · 0 hydrogen bonds · protein-nucleic
Compared structures
- 6SXB · XPF-ERCC1 Cryo-EM Structure, DNA-Bound 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 0.81
- 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 0.62
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 6SXB · PDBe 6SXB · UniProt Q92889 · UniProt P07992
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