Research workbench
Crystal structure of depupylase dop in complex with pup and ADP/TRIFLUOROMAGNESATE
Analyse Crystal structure of depupylase dop in complex with pup and… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7OYF
- Type
- protein
- Length
- 501 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Depupylase; Prokaryotic ubiquitin-like protein pup
- EC
- 3.4.-.-
- UniProt
- A0LU48, A0LU49
- Ligands
- ADP, KQB, MG
- Pockets
- 5 · best druggability 0.68
Structure
x-ray diffraction · 2 distinct chains · 44% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Depupylase (EC 3.4.-.-) | protein | 473 | 43% helix, 18% strand | A0LU48 |
| B | Prokaryotic ubiquitin-like protein pup | protein | 28 | 57% helix, 0% strand | A0LU49 |
Ligands and binding sites
- ADP · Adenosine-5'-diphosphate · ligand · chains A, B
- KQB · trifluoromagnesate monohydrate · ligand · chains A, B
- MG · Magnesium ion · metal · 3 copies · chains A, B
- EDO · 1,2-ethanediol · additive · 7 copies · chains A, B
- PGE · Triethylene glycol · additive · 3 copies · chains A
- PEG · Di(hydroxyethyl)ether · additive · 2 copies · chains A
- ACT · Acetate ion · additive · 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, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 219 | 0.68 | 0.86 | 34 | ADP, KQB |
| 2 | 147 | 0.49 | 0.78 | 26 | empty |
| 3 | 136 | 0.42 | 0.75 | 23 | empty |
| 4 | 81 | 0.34 | 0.75 | 20 | empty |
| 5 | 62 | 0.34 | 0.77 | 20 | EDO |
Interfaces
1 interface between chains.
- A–B · 1533 Ų buried · 36 hydrogen bonds · protein-protein
Compared structures
- 7OYF · Crystal structure of depupylase Dop in complex with Pup and ADP/trifluoromagnesate · 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 0.98
- A0LU49 · AlphaFold monomer V2.0 prediction for prokaryotic ubiquitin-like protein pup (A0LU49) · a predicted model of the same protein · chain B against A, TM-score 0.36
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
- Every structure of UniProt A0LU49
- Elsewhere: RCSB PDB 7OYF · PDBe 7OYF · UniProt A0LU48 · UniProt A0LU49
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