Research workbench
Crystal structure of CHLADUB2 dub domain
Analyse Crystal structure of CHLADUB2 dub domain in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6OAM
- Type
- protein
- Length
- 628 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Deubiquitinase and deneddylase DUB2; Ubiquitin
- EC
- 3.4.22.-
- UniProt
- B0B999, J3QS39
- Ligands
- AYE
- Pockets
- 5 · best druggability 0.86
Structure
x-ray diffraction · 3 distinct chains · 39% helix, 14% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Deubiquitinase and deneddylase DUB2 (EC 3.4.22.-) | protein | 239 | 44% helix, 12% strand | B0B999 |
| D, C | Ubiquitin | protein | 75 | 16% helix, 31% strand | J3QS39 |
| B | Deubiquitinase and deneddylase DUB2 (EC 3.4.22.-) | protein | 239 | 42% helix, 11% strand | B0B999 |
Ligands and binding sites
- AYE · prop-2-en-1-amine · ligand · 2 copies · chains A, D, B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1014 | 0.86 | 0.87 | 108 | empty |
| 2 | 64 | 0.51 | 0.85 | 14 | empty |
| 3 | 65 | 0.37 | 0.78 | 15 | empty |
| 4 | 60 | 0.34 | 0.77 | 20 | empty |
| 5 | 52 | 0.31 | 0.76 | 17 | AYE |
Interfaces
5 interfaces between chains.
- A–D · 1205 Ų buried · 13 hydrogen bonds · protein-protein
- B–C · 1127 Ų buried · 12 hydrogen bonds · protein-protein
- A–B · 830 Ų buried · 6 hydrogen bonds · protein-protein
- A–C · 252 Ų buried · 4 hydrogen bonds · protein-protein
- D–B · 202 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 B0B999
- Every structure of UniProt J3QS39
- Elsewhere: RCSB PDB 6OAM · PDBe 6OAM · UniProt B0B999 · UniProt J3QS39
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