MolNFT v1 · #151136 · protein
Structure of human USP28 bound to ubiquitin-pa
6HEK · Ubiquitin carboxyl-terminal hydrolase 28: “Structure of human USP28 bound to ubiquitin-pa”. X-ray diffraction, 2 ligands (AYE, CL), 15 pockets (best druggability 0.73). MolNFT v1 #151136 on GenesisL1: 3D structure, binding sites and…
- PDB
- 6HEK
- Type
- protein
- Length
- 1,063 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Ubiquitin carboxyl-terminal hydrolase 28; Polyubiquitin-B
- EC
- 3.4.19.12
- UniProt
- Q96RU2, P0CG47
- Ligands
- AYE, CL
- Pockets
- 15 · best druggability 0.73
Structure
x-ray diffraction · 4 distinct chains · 44% helix, 24% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Ubiquitin carboxyl-terminal hydrolase 28 (EC 3.4.19.12) | protein | 453 | 48% helix, 23% strand | Q96RU2 |
| B | Polyubiquitin-B | protein | 77 | 23% helix, 32% strand | P0CG47 |
| C | Ubiquitin carboxyl-terminal hydrolase 28 (EC 3.4.19.12) | protein | 459 | 47% helix, 22% strand | Q96RU2 |
| D | Polyubiquitin-B | protein | 74 | 24% helix, 28% strand | P0CG47 |
Ligands and binding sites
- AYE · prop-2-en-1-amine · ligand · 2 copies · chains A, B, C, D
- CL · Chloride ion · ion · chains A
- PG4 · Tetraethylene glycol · additive · 2 copies · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
15 pockets found on a 1 Å grid, 10 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 54 | 0.73 | 1.00 | 24 | empty |
| 2 | 139 | 0.69 | 0.90 | 26 | empty |
| 3 | 294 | 0.63 | 0.80 | 33 | empty |
| 4 | 195 | 0.61 | 0.82 | 34 | empty |
| 5 | 249 | 0.60 | 0.80 | 39 | empty |
Interfaces
3 interfaces between chains.
- A–C · 1746 Ų buried · 16 hydrogen bonds · protein-protein
- C–D · 1506 Ų buried · 19 hydrogen bonds · protein-protein
- A–B · 1446 Ų buried · 17 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 Q96RU2
- Every structure of UniProt P0CG47
- Elsewhere: RCSB PDB 6HEK · PDBe 6HEK · UniProt Q96RU2 · UniProt P0CG47
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