MolNFT v1 · #91656 · protein
Crystal structure of human OTUBAIN2 and ubiquitin complex
4FJV · Ubiquitin thioesterase OTUB2: “Crystal structure of human OTUBAIN2 and ubiquitin complex”. X-ray diffraction, 1 ligand (NEH), 4 pockets (best druggability 0.55). MolNFT v1 #91656 on GenesisL1: 3D structure, binding sites and pockets…
- PDB
- 4FJV
- Type
- protein
- Length
- 625 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Ubiquitin thioesterase OTUB2; Polyubiquitin-C
- EC
- 3.4.19.12
- UniProt
- Q96DC9, P0CG48
- Ligands
- NEH
- Pockets
- 4 · best druggability 0.55
Structure
x-ray diffraction · 3 distinct chains · 49% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Ubiquitin thioesterase OTUB2 (EC 3.4.19.12) | protein | 231 | 54% helix, 14% strand | Q96DC9 |
| B, D | Polyubiquitin-C | protein | 82 | 22% helix, 34% strand | P0CG48 |
| C | Ubiquitin thioesterase OTUB2 (EC 3.4.19.12) | protein | 230 | 55% helix, 14% strand | Q96DC9 |
Ligands and binding sites
- NEH · Ethanamine · ligand · 2 copies · chains A, B, C, D
- GOL · Glycerol · additive · 6 copies · chains A, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 142 | 0.55 | 0.82 | 23 | empty |
| 2 | 132 | 0.54 | 0.82 | 22 | empty |
| 3 | 77 | 0.48 | 0.83 | 18 | empty |
| 4 | 65 | 0.48 | 0.84 | 17 | empty |
Interfaces
3 interfaces between chains.
- A–B · 1156 Ų buried · 16 hydrogen bonds · protein-protein
- C–D · 1099 Ų buried · 14 hydrogen bonds · protein-protein
- A–C · 71 Ų buried · 2 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 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 Q96DC9
- Every structure of UniProt P0CG48
- Elsewhere: RCSB PDB 4FJV · PDBe 4FJV · UniProt Q96DC9 · UniProt P0CG48
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