Research workbench
Crystal structure of human UBA5 in complex with UFM1
Analyse Crystal structure of human UBA5 in complex with UFM1 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5IAA
- Type
- protein
- Length
- 659 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
- ZN
- Pockets
- 6 · best druggability 0.67
Structure
x-ray diffraction · 3 distinct chains · 37% helix, 21% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Ubiquitin-like modifier-activating enzyme 5 | protein | 260 | 38% helix, 18% strand | Q9GZZ9 |
| B | Ubiquitin-like modifier-activating enzyme 5 | protein | 239 | 41% helix, 21% strand | Q9GZZ9 |
| C, D | Ubiquitin-fold modifier 1 | protein | 80 | 24% helix, 35% strand | P61960 |
Ligands and binding sites
- ZN · Zinc ion · metal · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 367 | 0.67 | 0.81 | 48 | empty |
| 2 | 247 | 0.64 | 0.82 | 32 | empty |
| 3 | 207 | 0.57 | 0.80 | 41 | empty |
| 4 | 138 | 0.54 | 0.81 | 26 | empty |
| 5 | 83 | 0.45 | 0.81 | 19 | empty |
Interfaces
5 interfaces between chains.
- A–C · 1437 Ų buried · 24 hydrogen bonds · protein-protein
- B–D · 1398 Ų buried · 25 hydrogen bonds · protein-protein
- A–B · 1325 Ų buried · 22 hydrogen bonds · protein-protein
- A–D · 656 Ų buried · 5 hydrogen bonds · protein-protein
- B–C · 540 Ų buried · 5 hydrogen bonds · protein-protein
Compared structures
- 5IAA · Crystal structure of human UBA5 in complex with UFM1 · 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 5IAA · PDBe 5IAA · UniProt Q9GZZ9 · UniProt P61960
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