MolNFT v1 · #163694 · protein
Structure of the otulincat C129A - SNX27 PDZ domain complex.
6SAK · Ubiquitin thioesterase otulin: “Structure of the otulincat C129A - SNX27 PDZ domain complex.”. X-ray diffraction, 1 ligand (SO4), 8 pockets (best druggability 0.68). MolNFT v1 #163694 on GenesisL1: 3D structure, binding sites and…
- PDB
- 6SAK
- Type
- protein
- Length
- 729 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Ubiquitin thioesterase otulin; Sorting nexin-27
- EC
- 3.4.19.12
- UniProt
- Q96BN8, Q96L92
- Ligands
- SO4
- Pockets
- 8 · best druggability 0.68
Structure
x-ray diffraction · 4 distinct chains · 44% helix, 22% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Ubiquitin thioesterase otulin (EC 3.4.19.12) | protein | 274 | 54% helix, 15% strand | Q96BN8 |
| B | Ubiquitin thioesterase otulin (EC 3.4.19.12) | protein | 264 | 55% helix, 15% strand | Q96BN8 |
| C | Sorting nexin-27 | protein | 95 | 16% helix, 43% strand | Q96L92 |
| D | Sorting nexin-27 | protein | 96 | 16% helix, 42% strand | Q96L92 |
Ligands and binding sites
- SO4 · Sulfate ion · ion · 6 copies · chains A, B
- GOL · Glycerol · additive · 9 copies · chains A, D, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 552 | 0.68 | 0.78 | 62 | GOL |
| 2 | 169 | 0.53 | 0.79 | 22 | empty |
| 3 | 145 | 0.51 | 0.80 | 22 | empty |
| 4 | 165 | 0.51 | 0.78 | 23 | empty |
| 5 | 188 | 0.50 | 0.77 | 20 | empty |
Interfaces
4 interfaces between chains.
- A–C · 1071 Ų buried · 27 hydrogen bonds · protein-protein
- B–D · 1062 Ų buried · 30 hydrogen bonds · protein-protein
- A–D · 306 Ų buried · 4 hydrogen bonds · protein-protein
- A–B · 184 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 6SAK · Structure of the OTULINcat C129A - SNX27 PDZ domain complex. · the same entry in another collection · chain D against D, TM-score 1.00
- Q96BN8 · AlphaFold monomer V2.0 prediction for ubiquitin thioesterase otulin (Q96BN8) · a predicted model of the same protein · chain A against A, TM-score 0.98
- Q96L92 · AlphaFold monomer V2.0 prediction for sorting nexin-27 (Q96L92) · a predicted model of the same protein · chain C against A, TM-score 0.97
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 Q96BN8
- Every structure of UniProt Q96L92
- Elsewhere: RCSB PDB 6SAK · PDBe 6SAK · UniProt Q96BN8 · UniProt Q96L92
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