Research workbench
Crystal structure of human UBA5 in complex with UFM1 and AMP
Analyse Crystal structure of human UBA5 in complex with UFM1 and AMP in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5L95
- Type
- protein
- Length
- 654 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Ubiquitin-like modifier-activating enzyme 5; Ubiquitin-fold modifier 1
- UniProt
- Q9GZZ9, P61960
- Ligands
- AMP, ZN
- Pockets
- 4 · best druggability 0.70
Structure
x-ray diffraction · 3 distinct chains · 38% helix, 21% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Ubiquitin-like modifier-activating enzyme 5 | protein | 255 | 39% helix, 18% strand | Q9GZZ9 |
| B | Ubiquitin-like modifier-activating enzyme 5 | protein | 239 | 41% helix, 20% strand | Q9GZZ9 |
| C, D | Ubiquitin-fold modifier 1 | protein | 80 | 25% helix, 35% strand | P61960 |
Ligands and binding sites
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 598 | 0.70 | 0.79 | 66 | AMP |
| 2 | 238 | 0.59 | 0.80 | 39 | empty |
| 3 | 177 | 0.59 | 0.82 | 36 | empty |
| 4 | 93 | 0.41 | 0.78 | 23 | empty |
Interfaces
5 interfaces between chains.
- A–C · 1455 Ų buried · 27 hydrogen bonds · protein-protein
- B–D · 1446 Ų buried · 28 hydrogen bonds · protein-protein
- A–B · 1197 Ų buried · 16 hydrogen bonds · protein-protein
- A–D · 654 Ų buried · 5 hydrogen bonds · protein-protein
- B–C · 565 Ų buried · 6 hydrogen bonds · protein-protein
Compared structures
- 5L95 · Crystal structure of human UBA5 in complex with UFM1 and AMP · the same entry in another collection · chain A against A, TM-score 1.00
- Q9GZZ9 · AlphaFold monomer V2.0 prediction for ubiquitin-like modifier- activating enzyme 5… · a predicted model of the same protein · chain B against A, TM-score 0.99
- P61960 · AlphaFold monomer V2.0 prediction for ubiquitin-fold modifier 1 (P61960) · a predicted model of the same protein · chain C against A, TM-score 0.94
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 Q9GZZ9
- Every structure of UniProt P61960
- Elsewhere: RCSB PDB 5L95 · PDBe 5L95 · UniProt Q9GZZ9 · UniProt P61960
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