Research workbench
Crystal structure of MINDY1 mutant (P138A) in complex with LYS48 linked di-ubiquitin
Analyse Crystal structure of MINDY1 mutant (P138A) in complex with LYS48 linked… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6TXB
- Type
- protein
- Length
- 456 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Ubiquitin carboxyl-terminal hydrolase mindy-1; Polyubiquitin-C
- EC
- 3.4.19.12
- UniProt
- Q8N5J2, P0CG48
- Ligands
- NA, CL
- Pockets
- 5 · best druggability 0.72
Structure
x-ray diffraction · 4 distinct chains · 33% helix, 26% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Ubiquitin carboxyl-terminal hydrolase mindy-1 (EC 3.4.19.12) | protein | 263 | 38% helix, 21% strand | Q8N5J2 |
| D | Polyubiquitin-C | protein | 76 | 24% helix, 37% strand | P0CG48 |
| H | Polyubiquitin-C | protein | 74 | 23% helix, 34% strand | P0CG48 |
| L | Polyubiquitin-C | protein | 43 | 33% helix, 21% strand | P0CG48 |
Ligands and binding sites
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 | 643 | 0.72 | 0.79 | 55 | empty |
| 2 | 268 | 0.59 | 0.79 | 33 | empty |
| 3 | 155 | 0.43 | 0.75 | 29 | empty |
| 4 | 79 | 0.39 | 0.78 | 16 | NA |
| 5 | 57 | 0.31 | 0.76 | 17 | NA |
Interfaces
5 interfaces between chains.
- A–H · 1146 Ų buried · 17 hydrogen bonds · protein-protein
- A–D · 808 Ų buried · 14 hydrogen bonds · protein-protein
- A–L · 801 Ų buried · 8 hydrogen bonds · protein-protein
- D–L · 202 Ų buried · 4 hydrogen bonds · protein-protein
- D–H · 70 Ų buried · 2 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 isopeptide (isopeptide).
Compared structures
- 6TXB · Crystal structure of Mindy1 mutant (P138A) in complex with Lys48 linked di-ubiquitin · the same entry in another collection · chain A against A, TM-score 1.00
- Q8N5J2 · AlphaFold monomer V2.0 prediction for ubiquitin carboxyl-terminal hydrolase mindy-1… · 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 Q8N5J2
- Every structure of UniProt P0CG48
- Elsewhere: RCSB PDB 6TXB · PDBe 6TXB · UniProt Q8N5J2 · UniProt P0CG48
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