Research workbench
Human ubiquitin-activating enzyme 5 in complex with amppnp
Analyse Human ubiquitin-activating enzyme 5 in complex with amppnp in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3GUC
- Type
- protein
- Length
- 463 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Ubiquitin-like modifier-activating enzyme 5
- EC
- 2.7.7.-
- UniProt
- Q9GZZ9
- Ligands
- ANP, ZN
- Pockets
- 5 · best druggability 0.64
Structure
x-ray diffraction · 2 distinct chains · 41% helix, 19% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Ubiquitin-like modifier-activating enzyme 5 (EC 2.7.7.-) | protein | 242 | 42% helix, 18% strand | Q9GZZ9 |
| B | Ubiquitin-like modifier-activating enzyme 5 (EC 2.7.7.-) | protein | 221 | 40% helix, 19% strand | Q9GZZ9 |
Ligands and binding sites
- ANP · Phosphoaminophosphonic acid-adenylate ester · ligand · chains A
- 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
5 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 427 | 0.64 | 0.77 | 42 | empty |
| 2 | 234 | 0.61 | 0.80 | 34 | empty |
| 3 | 138 | 0.51 | 0.80 | 28 | ANP |
| 4 | 90 | 0.46 | 0.81 | 24 | empty |
| 5 | 111 | 0.42 | 0.77 | 27 | empty |
Interfaces
1 interface between chains.
- A–B · 1188 Ų buried · 25 hydrogen bonds · protein-protein
Compared structures
- 3GUC · Human Ubiquitin-activating Enzyme 5 in Complex with AMPPNP · 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 0.95
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
- Elsewhere: RCSB PDB 3GUC · PDBe 3GUC · UniProt Q9GZZ9
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