Research workbench
Structure of the pup ligase pafa of the prokaryotic ubiquitin-like modification pathway in complex with ADP
Analyse Structure of the pup ligase pafa of the prokaryotic ubiquitin-like modification… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4B0T
- Type
- protein
- Length
- 942 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Pup--protein ligase
- EC
- 6.3.2.-
- UniProt
- Q8NQE1
- Ligands
- ADP, MG
- Pockets
- 12 · best druggability 0.85
Structure
x-ray diffraction · 2 distinct chains · 44% helix, 15% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Pup--protein ligase (EC 6.3.2.-) | protein | 470 | 44% helix, 15% strand | Q8NQE1 |
| B | Pup--protein ligase (EC 6.3.2.-) | protein | 472 | 43% helix, 15% strand | Q8NQE1 |
Ligands and binding sites
- ADP · Adenosine-5'-diphosphate · ligand · 2 copies · chains A, B
- MG · Magnesium ion · metal · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
12 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1157 | 0.85 | 0.86 | 119 | ADP, MG |
| 2 | 693 | 0.78 | 0.83 | 70 | ADP, MG |
| 3 | 381 | 0.59 | 0.76 | 47 | empty |
| 4 | 156 | 0.57 | 0.82 | 20 | empty |
| 5 | 171 | 0.55 | 0.80 | 17 | empty |
Interfaces
1 interface between chains.
- A–B · 6700 Ų buried · 102 hydrogen bonds · protein-protein
Compared structures
- 4B0T · Structure of the Pup Ligase PafA of the Prokaryotic Ubiquitin-like Modification Pathway… · the same entry in another collection · chain A against A, TM-score 1.00
- Q8NQE1 · AlphaFold monomer V2.0 prediction for pup--protein ligase (Q8NQE1) · a predicted model of the same protein · chain A against A, TM-score 0.90
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 Q8NQE1
- Elsewhere: RCSB PDB 4B0T · PDBe 4B0T · UniProt Q8NQE1
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