Research workbench
Role of beta-hairpin motifs in the DNA duplex opening by the RAD4/XPC nucleotide excision repair complex
Analyse Role of beta-hairpin motifs in the DNA duplex opening by the RAD4/XPC… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6UBF
- Type
- protein + DNA
- Length
- 575 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 0.79
Structure
x-ray diffraction · 4 distinct chains · 43% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | DNA repair protein RAD4 | protein | 479 | 39% helix, 17% 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*C*GP*CP*TP*AP*CP*AP*A)-3') | dna | 22 | — | — |
| Y | DNA (5'- D(*AP*TP*TP*GP*TP*AP*GP*CP*GP*GP*GP*AP*TP*GP*TP*CP*GP*AP*GP*TP*CP*A)- 3') | dna | 21 | — | — |
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 | 990 | 0.79 | 0.81 | 80 | empty |
| 2 | 160 | 0.58 | 0.82 | 26 | empty |
| 3 | 296 | 0.56 | 0.76 | 24 | empty |
| 4 | 52 | 0.45 | 0.84 | 14 | empty |
| 5 | 64 | 0.44 | 0.82 | 15 | empty |
Interfaces
4 interfaces between chains.
- A–X · 1456 Ų buried · 8 hydrogen bonds · protein-protein
- W–Y · 971 Ų buried · 85 hydrogen bonds · nucleic-nucleic
- A–W · 698 Ų buried · 10 hydrogen bonds · protein-nucleic
- A–Y · 504 Ų buried · 7 hydrogen bonds · protein-nucleic
Modifications
Observed in the structure: 1 modified (nucleotide modification).
Compared structures
- 6UBF · Role of Beta-hairpin motifs in the DNA duplex opening by the Rad4/XPC nucleotide excision… · 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 0.98
- 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 0.87
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 6UBF · PDBe 6UBF · UniProt P14736 · UniProt P32628
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