MolNFT v1 · #37521 · protein
Co-crystal structure of znf ubp domain from the deubiquitinating enzyme isopeptidase T (isot) in complex with ubiquitin
2G45 · Ubiquitin carboxyl-terminal hydrolase 5: “Co-crystal structure of znf ubp domain from the deubiquitinating enzyme isopeptidase T (isot) in complex with…”. X-ray diffraction, 2 ligands (ZN, CL), 1 pocket (best druggability 0.66).…
- PDB
- 2G45
- Type
- protein
- Length
- 386 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Ubiquitin carboxyl-terminal hydrolase 5; Ubiquitin
- EC
- 3.1.2.15
- UniProt
- P45974, P62988
- Ligands
- ZN, CL
- Pockets
- 1 · best druggability 0.66
Structure
x-ray diffraction · 2 distinct chains · 17% helix, 26% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, D | Ubiquitin carboxyl-terminal hydrolase 5 (EC 3.1.2.15) | protein | 117 | 13% helix, 21% strand | P45974 |
| B, E | Ubiquitin | protein | 76 | 24% helix, 33% strand | P62988 |
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, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 561 | 0.66 | 0.76 | 61 | CL |
Interfaces
3 interfaces between chains.
- A–D · 2073 Ų buried · 29 hydrogen bonds · protein-protein
- A–B · 532 Ų buried · 12 hydrogen bonds · protein-protein
- D–E · 532 Ų buried · 11 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 disulfide (disulfide).
Compared structures
- 2G45 · Co-crystal structure of znf ubp domain from the deubiquitinating enzyme isopeptidase T… · the same entry in another collection · chain A against A, TM-score 1.00
- P45974 · AlphaFold monomer V2.0 prediction for ubiquitin carboxyl-terminal hydrolase 5 (P45974) · a predicted model of the same protein · chain A against A, TM-score 0.78
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 P45974
- Every structure of UniProt P62988
- Elsewhere: RCSB PDB 2G45 · PDBe 2G45 · UniProt P45974 · UniProt P62988
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