MolNFT v1 · #145148 · protein + DNA
Crystal structure of RAD4-RAD23 bound to a 6-4 photoproduct UV lesion
6CFI · DNA repair protein RAD4: “Crystal structure of RAD4-RAD23 bound to a 6-4 photoproduct UV lesion”. X-ray diffraction, 9 pockets (best druggability 0.79). MolNFT v1 #145148 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 6CFI
- Type
- protein + DNA
- Length
- 596 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- DNA repair protein RAD4; UV excision repair protein RAD23; DNA('…
- UniProt
- P14736, P32628
- Pockets
- 9 · best druggability 0.79
Structure
x-ray diffraction · 4 distinct chains · 43% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | DNA repair protein RAD4 | protein | 496 | 39% helix, 19% strand | P14736 |
| X | UV excision repair protein RAD23 | protein | 53 | 81% helix, 0% strand | P32628 |
| W | DNA('- D(*TP*TP*GP*AP*CP*TP*CP*AP*AP*CP*AP*TP*CP*CP*AP*AP*AP*GP*CP*TP*AP*CP* AP*A)-') | dna | 24 | — | — |
| Y | DNA (5'-D(*AP*TP*TP*GP*TP*AP*GP*CP*(T64) P*TP*GP*GP*AP*TP*GP*TP*TP*GP*AP*GP*TP*CP*A)-3') | dna | 23 | — | — |
Pockets
9 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1050 | 0.79 | 0.81 | 100 | empty |
| 2 | 372 | 0.66 | 0.80 | 45 | empty |
| 3 | 267 | 0.53 | 0.76 | 27 | empty |
| 4 | 63 | 0.43 | 0.81 | 13 | empty |
| 5 | 54 | 0.39 | 0.81 | 10 | empty |
Interfaces
4 interfaces between chains.
- A–X · 1502 Ų buried · 13 hydrogen bonds · protein-protein
- A–W · 1063 Ų buried · 17 hydrogen bonds · protein-nucleic
- W–Y · 979 Ų buried · 66 hydrogen bonds · nucleic-nucleic
- A–Y · 593 Ų buried · 10 hydrogen bonds · protein-nucleic
Modifications
Observed in the structure: 1 modified (nucleotide modification).
Compared structures
- 6CFI · Crystal structure of Rad4-Rad23 bound to a 6-4 photoproduct UV lesion · the same entry in another collection · chain A against A, TM-score 1.00
- P14736 · AlphaFold monomer V2.0 prediction for DNA repair protein RAD4 (P14736) · a predicted model of the same protein · chain A against A, TM-score 0.97
- P32628 · AlphaFold monomer V2.0 prediction for UV excision repair protein RAD23 (P32628) · a predicted model of the same protein · chain X against A, TM-score 0.88
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 P14736
- Every structure of UniProt P32628
- Elsewhere: RCSB PDB 6CFI · PDBe 6CFI · UniProt P14736 · UniProt P32628
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