MolNFT v1 · #125586 · protein
Structure of deubiquitinating enzyme homolog (pyrococcus furiosus JAMM1) in complex with ubiquitin-like SAMP2.
5LDA: “Structure of deubiquitinating enzyme homolog (pyrococcus furiosus JAMM1) in complex with ubiquitin-like SAMP2.”. X-ray diffraction, 1 ligand (ZN), 1 pocket (best druggability 0.49). MolNFT v1 #125586 on GenesisL1: 3D structure…
- PDB
- 5LDA
- Type
- protein
- Length
- 187 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- JAMM1; SAMP2
- UniProt
- Q8U1Y4, Q8U1Z3
- Ligands
- ZN
- Pockets
- 1 · best druggability 0.49
Structure
x-ray diffraction · 2 distinct chains · 22% helix, 39% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | JAMM1 | protein | 130 | 26% helix, 40% strand | Q8U1Y4 |
| B | SAMP2 | protein | 57 | 14% helix, 37% strand | Q8U1Z3 |
Ligands and binding sites
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
1 pocket found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 149 | 0.49 | 0.78 | 19 | GOL |
Interfaces
1 interface between chains.
- A–B · 915 Ų buried · 16 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 5 modified (engineered).
Compared structures
- 5LDA · Structure of deubiquitinating enzyme homolog (Pyrococcus furiosus JAMM1) in complex with… · the same entry in another collection · chain A against A, TM-score 1.00
- Q8U1Y4 · AlphaFold monomer V2.0 prediction for desampylase (Q8U1Y4) · a predicted model of the same protein · chain A against A, TM-score 0.99
- Q8U1Z3 · AlphaFold monomer V2.0 prediction for small archaeal modifier protein 2 (Q8U1Z3) · a predicted model of the same protein · chain B against A, TM-score 0.92
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 Q8U1Y4
- Every structure of UniProt Q8U1Z3
- Elsewhere: RCSB PDB 5LDA · PDBe 5LDA · UniProt Q8U1Y4 · UniProt Q8U1Z3
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