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Crystal structure of deubiquitinase MINDY2
Analyse Crystal structure of deubiquitinase MINDY2 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6Z49
- Type
- protein
- Length
- 1,007 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Ubiquitin carboxyl-terminal hydrolase mindy-2
- EC
- 3.4.19.12
- UniProt
- Q8NBR6
- Ligands
- CL
- Pockets
- 14 · best druggability 0.71
Structure
x-ray diffraction · 4 distinct chains · 38% helix, 20% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Ubiquitin carboxyl-terminal hydrolase mindy-2 (EC 3.4.19.12) | protein | 252 | 38% helix, 20% strand | Q8NBR6 |
| B | Ubiquitin carboxyl-terminal hydrolase mindy-2 (EC 3.4.19.12) | protein | 254 | 40% helix, 21% strand | Q8NBR6 |
| C | Ubiquitin carboxyl-terminal hydrolase mindy-2 (EC 3.4.19.12) | protein | 258 | 36% helix, 20% strand | Q8NBR6 |
| D | Ubiquitin carboxyl-terminal hydrolase mindy-2 (EC 3.4.19.12) | protein | 243 | 36% helix, 20% strand | Q8NBR6 |
Ligands and binding sites
- CL · Chloride ion · ion · 7 copies · chains A, B, C, D
- PEG · Di(hydroxyethyl)ether · additive · 3 copies · chains A, B, D
- PG4 · Tetraethylene glycol · additive · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
14 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 994 | 0.71 | 0.75 | 92 | CL, PEG |
| 2 | 320 | 0.54 | 0.74 | 43 | empty |
| 3 | 186 | 0.53 | 0.78 | 29 | empty |
| 4 | 183 | 0.53 | 0.78 | 29 | empty |
| 5 | 176 | 0.51 | 0.78 | 30 | empty |
Interfaces
4 interfaces between chains.
- A–C · 666 Ų buried · 8 hydrogen bonds · protein-protein
- C–D · 297 Ų buried · 0 hydrogen bonds · protein-protein
- B–C · 119 Ų buried · 0 hydrogen bonds · protein-protein
- A–B · 52 Ų buried · 0 hydrogen bonds · protein-protein
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 Q8NBR6
- Elsewhere: RCSB PDB 6Z49 · PDBe 6Z49 · UniProt Q8NBR6
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