Research workbench
Sequence impact in DNA duplex opening by the RAD4/XPC nucleotide excision repair complex
Analyse Sequence impact in DNA duplex opening by the RAD4/XPC nucleotide excision… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6UG1
- Type
- protein + DNA
- Length
- 576 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 (5'…
- UniProt
- P14736, P32628
- Pockets
- 8 · best druggability 0.75
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 | 477 | 39% helix, 18% strand | P14736 |
| X | UV excision repair protein RAD23 | protein | 57 | 75% helix, 0% strand | P32628 |
| Y | DNA (5'- D(*AP*TP*TP*GP*TP*AP*GP*GP*GP*AP*TP*GP*TP*CP*GP*AP*GP*TP*CP*A)-3') | dna | 21 | — | — |
| W | DNA (5'-D(*TP*TP*GP*AP*CP*TP*CP*(G47) P*AP*CP*AP*TP*CP*CP*CP*CP*TP*AP*CP*AP*A)-3') | dna | 21 | — | — |
Pockets
8 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1010 | 0.75 | 0.78 | 69 | empty |
| 2 | 356 | 0.64 | 0.79 | 40 | empty |
| 3 | 470 | 0.61 | 0.76 | 41 | empty |
| 4 | 249 | 0.56 | 0.78 | 25 | empty |
| 5 | 131 | 0.39 | 0.75 | 19 | empty |
Interfaces
4 interfaces between chains.
- A–X · 1427 Ų buried · 10 hydrogen bonds · protein-protein
- Y–W · 982 Ų buried · 90 hydrogen bonds · nucleic-nucleic
- A–Y · 611 Ų buried · 7 hydrogen bonds · protein-nucleic
- A–W · 534 Ų buried · 4 hydrogen bonds · protein-nucleic
Modifications
Observed in the structure: 1 modified (nucleotide modification).
Compared structures
- 6UG1 · Sequence impact in DNA duplex opening by the Rad4/XPC nucleotide excision repair complex · 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 0.87
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 6UG1 · PDBe 6UG1 · UniProt P14736 · UniProt P32628
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