Research workbench
Covalent fragment group deposition -- crystal structure of OUTB2 in complex with pcm-0102998
Analyse Covalent fragment group deposition -- crystal structure of OUTB2 in complex… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5QIV
- Type
- protein
- Length
- 225 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Ubiquitin thioesterase OTUB2
- EC
- 3.4.19.12
- UniProt
- Q96DC9
- Ligands
- J5P, UNL
- Pockets
- 1 · best druggability 0.52
Structure
x-ray diffraction · 1 distinct chain · 56% helix, 12% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Ubiquitin thioesterase OTUB2 (EC 3.4.19.12) | protein | 225 | 56% helix, 12% strand | Q96DC9 |
Ligands and binding sites
- J5P · N'-acetyl-2-[(3R)-1,1-dioxo-1lambda~6~-thiolan-3-yl]acetohydrazide · ligand · chains A
- UNL · Unknown ligand · ion · 5 copies · chains A
- EDO · 1,2-ethanediol · additive · 5 copies · chains A
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 | 81 | 0.52 | 0.84 | 17 | empty |
Modifications
Observed in the structure: 1 covalent (covalent ligand).
Compared structures
- 5QIV · Covalent fragment group deposition -- Crystal Structure of OUTB2 in complex with… · the same entry in another collection · chain A against A, TM-score 1.00
- Q96DC9 · AlphaFold monomer V2.0 prediction for ubiquitin thioesterase OTUB2 (Q96DC9) · a predicted model of the same protein · chain A against A, TM-score 0.98
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
- Elsewhere: RCSB PDB 5QIV · PDBe 5QIV · UniProt Q96DC9
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