Research workbench
Crystal structure of RAD5 and REV1
Analyse Crystal structure of RAD5 and REV1 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5YRQ
- Type
- protein
- Length
- 489 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- DNA repair protein RAD5,DNA repair protein REV1
- EC
- 3.6.4.-, 2.7.7.-
- UniProt
- P32849, P12689
- Pockets
- 6 · best druggability 0.70
Structure
x-ray diffraction · 4 distinct chains · 62% helix, 5% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | DNA repair protein RAD5,DNA repair protein REV1 (EC 3.6.4.-, 2.7.7.-) | protein | 125 | 59% helix, 2% strand | P32849, P12689 |
| B | DNA repair protein RAD5,DNA repair protein REV1 (EC 3.6.4.-, 2.7.7.-) | protein | 120 | 65% helix, 9% strand | P32849, P12689 |
| D | DNA repair protein RAD5,DNA repair protein REV1 (EC 3.6.4.-, 2.7.7.-) | protein | 123 | 64% helix, 9% strand | P32849, P12689 |
| E | DNA repair protein RAD5,DNA repair protein REV1 (EC 3.6.4.-, 2.7.7.-) | protein | 121 | 61% helix, 2% strand | P32849, P12689 |
Pockets
6 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 572 | 0.70 | 0.79 | 64 | empty |
| 2 | 146 | 0.52 | 0.80 | 26 | empty |
| 3 | 120 | 0.51 | 0.80 | 22 | empty |
| 4 | 67 | 0.33 | 0.76 | 15 | empty |
| 5 | 53 | 0.30 | 0.76 | 13 | empty |
Interfaces
6 interfaces between chains.
- B–D · 1139 Ų buried · 29 hydrogen bonds · protein-protein
- B–E · 1121 Ų buried · 15 hydrogen bonds · protein-protein
- A–D · 1089 Ų buried · 16 hydrogen bonds · protein-protein
- A–E · 813 Ų buried · 14 hydrogen bonds · protein-protein
- A–B · 507 Ų buried · 8 hydrogen bonds · protein-protein
Compared structures
- 5YRQ · Crystal structure of Rad5 and Rev1 · the same entry in another collection · chain A against A, TM-score 1.00
- P12689 · AlphaFold monomer V2.0 prediction for DNA repair protein REV1 (P12689) · a predicted model of the same protein · chain B against A, TM-score 0.75
- P32849 · AlphaFold monomer V2.0 prediction for DNA repair protein RAD5 (P32849) · a predicted model of the same protein · chain D against A, TM-score 0.41
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 P32849
- Every structure of UniProt P12689
- Elsewhere: RCSB PDB 5YRQ · PDBe 5YRQ · UniProt P32849 · UniProt P12689
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