MolNFT v1 · #39968 · protein
Covalent ubiquitin-USP2 complex
2IBI · Ubiquitin carboxyl-terminal hydrolase 2: “Covalent ubiquitin-USP2 complex”. X-ray diffraction, 2 ligands (NEH, ZN), 2 pockets (best druggability 0.73). MolNFT v1 #39968 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 2IBI
- Type
- protein
- Length
- 410 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Ubiquitin carboxyl-terminal hydrolase 2; Ubiquitin
- EC
- 3.1.2.15
- UniProt
- O75604, P62988
- Ligands
- NEH, ZN
- Pockets
- 2 · best druggability 0.73
Structure
x-ray diffraction · 2 distinct chains · 29% helix, 28% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Ubiquitin carboxyl-terminal hydrolase 2 (EC 3.1.2.15) | protein | 335 | 30% helix, 28% strand | O75604 |
| B | Ubiquitin | protein | 75 | 20% helix, 31% strand | P62988 |
Ligands and binding sites
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
2 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 548 | 0.73 | 0.81 | 59 | empty |
| 2 | 52 | 0.34 | 0.78 | 17 | empty |
Interfaces
1 interface between chains.
- A–B · 2036 Ų buried · 33 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 covalent (covalent ligand).
Compared structures
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 O75604
- Every structure of UniProt P62988
- Elsewhere: RCSB PDB 2IBI · PDBe 2IBI · UniProt O75604 · UniProt P62988
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