MolNFT v1 · #171512 · protein
Crystal structure of MINDY2 (C266A) in complex with LYS48 linked di- ubiquitin (K48-UB2)
6Z7V · Ubiquitin carboxyl-terminal hydrolase mindy-2: “Crystal structure of MINDY2 (C266A) in complex with LYS48 linked di- ubiquitin (K48-UB2)”. X-ray diffraction, 1 ligand (K), 17 pockets (best druggability 0.75). MolNFT v1 #171512 on…
- PDB
- 6Z7V
- Type
- protein
- Length
- 1,036 residues
- Chains
- 9
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Ubiquitin carboxyl-terminal hydrolase mindy-2; Polyubiquitin-C
- EC
- 3.4.19.12
- UniProt
- Q8NBR6, P0CG48
- Ligands
- K
- Pockets
- 17 · best druggability 0.75
Structure
x-ray diffraction · 6 distinct chains · 34% helix, 27% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Ubiquitin carboxyl-terminal hydrolase mindy-2 (EC 3.4.19.12) | protein | 260 | 40% helix, 21% strand | Q8NBR6 |
| B | Ubiquitin carboxyl-terminal hydrolase mindy-2 (EC 3.4.19.12) | protein | 259 | 40% helix, 21% strand | Q8NBR6 |
| C, D | Polyubiquitin-C | protein | 76 | 25% helix, 38% strand | P0CG48 |
| E, F, G | Polyubiquitin-C | protein | 73 | 21% helix, 36% strand | P0CG48 |
| H | Polyubiquitin-C | protein | 72 | 24% helix, 36% strand | P0CG48 |
| I | Polyubiquitin-C | protein | 74 | 20% helix, 36% strand | P0CG48 |
Ligands and binding sites
- K · Potassium ion · metal · 4 copies · chains A, B, G
- PG4 · Tetraethylene glycol · additive · 3 copies · chains A, B, C, E
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
17 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 591 | 0.75 | 0.82 | 50 | empty |
| 2 | 614 | 0.70 | 0.78 | 47 | empty |
| 3 | 260 | 0.67 | 0.83 | 34 | empty |
| 4 | 345 | 0.61 | 0.78 | 38 | empty |
| 5 | 237 | 0.55 | 0.78 | 35 | empty |
Interfaces
14 interfaces between chains.
- A–H · 1107 Ų buried · 20 hydrogen bonds · protein-protein
- B–E · 1101 Ų buried · 21 hydrogen bonds · protein-protein
- A–B · 859 Ų buried · 3 hydrogen bonds · protein-protein
- B–F · 824 Ų buried · 19 hydrogen bonds · protein-protein
- A–G · 818 Ų buried · 16 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 isopeptide (isopeptide).
Compared structures
- 6Z7V · Crystal structure of Mindy2 (C266A) in complex with Lys48 linked di-ubiquitin (K48-Ub2) · the same entry in another collection · chain I against I, TM-score 1.00
- Q8NBR6 · AlphaFold monomer V2.0 prediction for ubiquitin carboxyl-terminal hydrolase mindy-2… · a predicted model of the same protein · chain B against A, TM-score 0.99
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
- Every structure of UniProt P0CG48
- Elsewhere: RCSB PDB 6Z7V · PDBe 6Z7V · UniProt Q8NBR6 · UniProt P0CG48
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