Research workbench
Crystal structure of the complex between prokaryotic ubiquitin-like protein pup and its ligase pafa
Analyse Crystal structure of the complex between prokaryotic ubiquitin-like protein pup… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4BJR
- Type
- protein
- Length
- 994 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Pup--protein ligase, prokaryotic ubiquitin-like protein pup
- EC
- 6.3.2.-
- UniProt
- Q8NQE1, Q8NQE0
- Ligands
- ATP, MG
- Pockets
- 12 · best druggability 0.67
Structure
x-ray diffraction · 2 distinct chains · 45% helix, 15% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Pup--protein ligase, prokaryotic ubiquitin-like protein pup (EC 6.3.2.-) | protein | 500 | 45% helix, 15% strand | Q8NQE1, Q8NQE0 |
| B | Pup--protein ligase, prokaryotic ubiquitin-like protein pup (EC 6.3.2.-) | protein | 494 | 44% helix, 15% strand | Q8NQE1, Q8NQE0 |
Ligands and binding sites
- ATP · Adenosine-5'-triphosphate · ligand · 2 copies · chains A, B
- MG · Magnesium ion · metal · 3 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, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 231 | 0.67 | 0.85 | 45 | ATP |
| 2 | 218 | 0.67 | 0.85 | 41 | ATP, MG |
| 3 | 524 | 0.66 | 0.77 | 53 | empty |
| 4 | 162 | 0.56 | 0.81 | 31 | empty |
| 5 | 209 | 0.56 | 0.79 | 19 | empty |
Interfaces
1 interface between chains.
- A–B · 3489 Ų buried · 43 hydrogen bonds · protein-protein
Compared structures
- 4BJR · Crystal structure of the complex between Prokaryotic Ubiquitin-like Protein Pup and its… · 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 B against A, TM-score 0.94
- Q8NQE0 · AlphaFold monomer V2.0 prediction for prokaryotic ubiquitin-like protein pup (Q8NQE0) · a predicted model of the same protein · chain A against A, TM-score 0.06
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
- Every structure of UniProt Q8NQE0
- Elsewhere: RCSB PDB 4BJR · PDBe 4BJR · UniProt Q8NQE1 · UniProt Q8NQE0
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