MolNFT v1 · #126067 · protein
Structure of the deamidase-depupylase dop of the prokaryotic ubiquitin-like modification pathway in complex with ADP and phosphate
5LRT: “Structure of the deamidase-depupylase dop of the prokaryotic ubiquitin-like modification pathway in complex…”. X-ray diffraction, 4 ligands (ADP, MG, NA), 4 pockets (best druggability 0.73). MolNFT v1 #126067 on GenesisL1: 3D…
- PDB
- 5LRT
- Type
- protein
- Length
- 464 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Depupylase
- EC
- 3.4.-.-
- UniProt
- A0LU48
- Ligands
- ADP, MG, NA, PO4
- Pockets
- 4 · best druggability 0.73
Structure
x-ray diffraction · 1 distinct chain · 45% helix, 19% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Depupylase (EC 3.4.-.-) | protein | 464 | 45% helix, 19% strand | A0LU48 |
Ligands and binding sites
- ADP · Adenosine-5'-diphosphate · ligand · chains A
- MG · Magnesium ion · metal · 4 copies · chains A
- NA · Sodium ion · metal · chains A
- PO4 · Phosphate ion · ion · chains A
- PGE · Triethylene glycol · additive · 2 copies · chains A
- P6G · Hexaethylene glycol · additive · chains A
- PEG · Di(hydroxyethyl)ether · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 112 | 0.73 | 0.94 | 26 | ADP, MG |
| 2 | 157 | 0.49 | 0.77 | 23 | empty |
| 3 | 129 | 0.42 | 0.75 | 27 | empty |
| 4 | 52 | 0.28 | 0.75 | 19 | MG, PO4, NA |
Compared structures
- 5LRT · 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 1.00
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 5LRT · PDBe 5LRT · UniProt A0LU48
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