Research workbench
Structure of the deamidase-depupylase dop of the prokaryotic ubiquitin-like modification pathway in complex with ATP
Analyse Structure of the deamidase-depupylase dop of the prokaryotic ubiquitin-like… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4B0S
- Type
- protein
- Length
- 456 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Deamidase-depupylase dop
- EC
- 3.4.-.-, 3.5.1.-
- UniProt
- A0LU48
- Ligands
- ATP, MG
- Pockets
- 5 · best druggability 0.64
Structure
x-ray diffraction · 1 distinct chain · 45% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Deamidase-depupylase dop (EC 3.4.-.-, 3.5.1.-) | protein | 456 | 45% helix, 17% strand | A0LU48 |
Ligands and binding sites
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 133 | 0.64 | 0.87 | 30 | ATP |
| 2 | 130 | 0.52 | 0.80 | 24 | empty |
| 3 | 68 | 0.33 | 0.76 | 18 | empty |
| 4 | 58 | 0.32 | 0.76 | 12 | empty |
| 5 | 52 | 0.29 | 0.76 | 15 | empty |
Modifications
Observed in the structure: 1 covalent (covalent ligand).
Compared structures
- 4B0S · Structure of the Deamidase-Depupylase Dop of the Prokaryotic Ubiquitin-like Modification… · the same entry in another collection · chain A against A, TM-score 1.00
- A0LU48 · AlphaFold monomer V2.0 prediction for depupylase (A0LU48) · a predicted model of the same protein · chain A against A, TM-score 0.99
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 A0LU48
- Elsewhere: RCSB PDB 4B0S · PDBe 4B0S · UniProt A0LU48
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