Research workbench
Crystal structure of the DNA repair protein uvrb in complex with ATP
Analyse Crystal structure of the DNA repair protein uvrb in complex with ATP in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1D9Z
- Type
- protein
- Length
- 590 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Excinuclease uvrabc component uvrb
- UniProt
- P56981
- Ligands
- ATP, ZN, MG
- Pockets
- 5 · best druggability 0.78
Structure
x-ray diffraction · 1 distinct chain · 36% helix, 13% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Excinuclease uvrabc component uvrb | protein | 590 | 36% helix, 13% strand | P56981 |
Ligands and binding sites
- ATP · Adenosine-5'-triphosphate · ligand · chains A
- ZN · Zinc ion · metal · 2 copies · chains A
- MG · Magnesium ion · metal · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 723 | 0.78 | 0.83 | 68 | empty |
| 2 | 702 | 0.71 | 0.78 | 70 | MG, ATP |
| 3 | 395 | 0.71 | 0.82 | 63 | empty |
| 4 | 122 | 0.68 | 0.90 | 25 | empty |
| 5 | 60 | 0.31 | 0.75 | 12 | empty |
Compared structures
- 1D9Z · Crystal structure of the DNA repair protein uvrb in complex with ATP · the same entry in another collection · chain A against A, TM-score 1.00
- P56981 · AlphaFold monomer V2.0 prediction for uvrabc system protein B (P56981) · a predicted model of the same protein · chain A against A, TM-score 0.94
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 P56981
- Elsewhere: RCSB PDB 1D9Z · PDBe 1D9Z · UniProt P56981
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.