Research workbench
Crystal structure of RAD4-RAD23 crosslinked to an undamaged DNA
Analyse Crystal structure of RAD4-RAD23 crosslinked to an undamaged DNA in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4YIR
- Type
- protein + DNA
- Length
- 598 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
- 7 · best druggability 0.80
Structure
x-ray diffraction · 4 distinct chains · 42% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | DNA repair protein RAD4 | protein | 499 | 38% helix, 20% strand | P14736 |
| X | UV excision repair protein RAD23 | protein | 53 | 81% helix, 0% strand | P32628 |
| W | DNA (5'-D(*TP*TP*GP*AP*CP*TP*CP*(G47) P*AP*CP*AP*TP*CP*CP*CP*CP*CP*GP*CP*TP*AP*CP*AP*A)-3') | dna | 24 | — | — |
| Y | DNA (5'- D(*AP*TP*TP*GP*TP*AP*GP*CP*G*GP*GP*GP*AP*TP*GP*TP*CP*GP*AP*GP*TP*CP*A )-3') | dna | 22 | — | — |
Pockets
7 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1035 | 0.80 | 0.82 | 89 | empty |
| 2 | 299 | 0.68 | 0.83 | 37 | empty |
| 3 | 284 | 0.55 | 0.76 | 24 | empty |
| 4 | 109 | 0.43 | 0.78 | 13 | empty |
| 5 | 93 | 0.41 | 0.78 | 15 | empty |
Interfaces
4 interfaces between chains.
- A–X · 1459 Ų buried · 11 hydrogen bonds · protein-protein
- A–W · 1176 Ų buried · 8 hydrogen bonds · protein-nucleic
- W–Y · 1007 Ų buried · 93 hydrogen bonds · nucleic-nucleic
- A–Y · 705 Ų buried · 9 hydrogen bonds · protein-nucleic
Modifications
Observed in the structure: 1 modified (nucleotide modification).
Compared structures
- 4YIR · Crystal structure of Rad4-Rad23 crosslinked to an undamaged DNA · 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 0.91
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 4YIR · PDBe 4YIR · UniProt P14736 · UniProt P32628
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