MolNFT v1 · #138082 · protein
Crystal structure of fha domain of human aplf in complex with XRCC1 bisphospho peptide
5W7X · Aprataxin and pnk-like factor: “Crystal structure of fha domain of human aplf in complex with XRCC1 bisphospho peptide”. X-ray diffraction, 3 pockets (best druggability 0.69). MolNFT v1 #138082 on GenesisL1: 3D structure, binding…
- PDB
- 5W7X
- Type
- protein
- Length
- 437 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Aprataxin and pnk-like factor; DNA repair protein XRCC1
- EC
- 4.2.99.18
- UniProt
- Q8IW19, P18887
- Pockets
- 3 · best druggability 0.69
Structure
x-ray diffraction · 4 distinct chains · 0% helix, 44% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| D, B, C | Aprataxin and pnk-like factor (EC 4.2.99.18) | protein | 102 | 0% helix, 46% strand | Q8IW19 |
| A | Aprataxin and pnk-like factor (EC 4.2.99.18) | protein | 101 | 0% helix, 49% strand | Q8IW19 |
| H, F | DNA repair protein XRCC1 | protein | 7 | 0% helix, 0% strand | P18887 |
| E, G | DNA repair protein XRCC1 | protein | 8 | 0% helix, 0% strand | P18887 |
Pockets
3 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 838 | 0.69 | 0.75 | 93 | empty |
| 2 | 442 | 0.60 | 0.75 | 42 | empty |
| 3 | 100 | 0.40 | 0.77 | 20 | empty |
Interfaces
14 interfaces between chains.
- A–E · 469 Ų buried · 14 hydrogen bonds · protein-protein
- D–H · 441 Ų buried · 17 hydrogen bonds · protein-protein
- B–F · 404 Ų buried · 16 hydrogen bonds · protein-protein
- C–G · 395 Ų buried · 13 hydrogen bonds · protein-protein
- D–A · 340 Ų buried · 9 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 8 modified (phosphorylation).
Compared structures
- 5W7X · Crystal Structure of FHA domain of human APLF in complex with XRCC1 bisphospho peptide · the same entry in another collection · chain G against G, TM-score 1.00
- Q8IW19 · AlphaFold monomer V2.0 prediction for aprataxin and pnk-like factor (Q8IW19) · a predicted model of the same protein · chain B against A, TM-score 0.98
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 Q8IW19
- Every structure of UniProt P18887
- Elsewhere: RCSB PDB 5W7X · PDBe 5W7X · UniProt Q8IW19 · UniProt P18887
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