Research workbench
Crystal structure of RAD7 and ELC1 complex in yeast
Analyse Crystal structure of RAD7 and ELC1 complex in yeast in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5ZB2
- Type
- protein
- Length
- 480 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- DNA repair protein RAD7; Elongin-C
- UniProt
- P06779, Q03071
- Ligands
- 9FO, NA
- Pockets
- 1 · best druggability 0.30
Structure
x-ray diffraction · 2 distinct chains · 43% helix, 14% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | DNA repair protein RAD7 | protein | 402 | 43% helix, 14% strand | P06779 |
| B | Elongin-C | protein | 78 | 45% helix, 17% strand | Q03071 |
Ligands and binding sites
- 9FO · 3,6,9,12,15,18,21,24,27,30,33,36,39,42,45,48,51,54,57-nonadecaoxanonapentacontane-1,59-diol · ligand · chains A
- NA · Sodium ion · metal
- GOL · Glycerol · additive · 5 copies · chains A
- PG0 · 2-(2-methoxyethoxy)ethanol · additive · chains A
- P33 · 3,6,9,12,15,18-hexaoxaicosane-1,20-diol · additive · chains A
- P6G · Hexaethylene glycol · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
1 pocket found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 67 | 0.30 | 0.75 | 15 | empty |
Interfaces
1 interface between chains.
- A–B · 628 Ų buried · 4 hydrogen bonds · protein-protein
Compared structures
- 5ZB2 · Crystal structure of Rad7 and Elc1 complex in yeast · the same entry in another collection · chain A against A, TM-score 1.00
- P06779 · AlphaFold monomer V2.0 prediction for DNA repair protein RAD7 (P06779) · a predicted model of the same protein · chain A against A, TM-score 1.00
- Q03071 · AlphaFold monomer V2.0 prediction for elongin-C (Q03071) · a predicted model of the same protein · chain B against A, TM-score 0.95
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 P06779
- Every structure of UniProt Q03071
- Elsewhere: RCSB PDB 5ZB2 · PDBe 5ZB2 · UniProt P06779 · UniProt Q03071
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