Research workbench
UCHL3 in complex with synthetic, K27-linked diubiquitin
Analyse UCHL3 in complex with synthetic, K27-linked diubiquitin in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6QML
- Type
- protein
- Length
- 758 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Ubiquitin carboxyl-terminal hydrolase isozyme L3; Polyubiquitin-B; Polyubiquitin-C
- EC
- 3.4.19.12
- UniProt
- P15374, P0CG47, P0CG48
- Ligands
- K, BR, CL
- Pockets
- 12 · best druggability 0.60
Structure
x-ray diffraction · 3 distinct chains · 33% helix, 26% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, D | Ubiquitin carboxyl-terminal hydrolase isozyme L3 (EC 3.4.19.12) | protein | 227 | 39% helix, 21% strand | P15374 |
| B, E | Polyubiquitin-B | protein | 76 | 24% helix, 36% strand | P0CG47 |
| C, F | Polyubiquitin-C | protein | 76 | 24% helix, 34% strand | P0CG48 |
Ligands and binding sites
- K · Potassium ion · metal · 5 copies · chains A, D
- BR · Bromide ion · ion · 4 copies · chains A, B, C, F
- CL · Chloride ion · ion · 2 copies · chains A, D
- EDO · 1,2-ethanediol · additive · 15 copies · chains A, B, C, D, F
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
12 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 431 | 0.60 | 0.75 | 45 | K, CL, EDO |
| 2 | 113 | 0.42 | 0.76 | 23 | empty |
| 3 | 106 | 0.41 | 0.76 | 21 | empty |
| 4 | 56 | 0.39 | 0.81 | 17 | empty |
| 5 | 81 | 0.38 | 0.77 | 23 | EDO |
Interfaces
7 interfaces between chains.
- D–E · 1207 Ų buried · 19 hydrogen bonds · protein-protein
- A–B · 1199 Ų buried · 18 hydrogen bonds · protein-protein
- D–F · 596 Ų buried · 13 hydrogen bonds · protein-protein
- A–C · 583 Ų buried · 14 hydrogen bonds · protein-protein
- A–D · 321 Ų buried · 9 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 isopeptide, 2 modified (isopeptide, nonstandard).
Compared structures
- 6QML · UCHL3 in complex with synthetic, K27-linked diubiquitin · the same entry in another collection · chain C against C, TM-score 1.00
- P15374 · AlphaFold monomer V2.0 prediction for ubiquitin carboxyl-terminal hydrolase isozyme L3… · a predicted model of the same protein · chain A 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 P15374
- Every structure of UniProt P0CG47
- Every structure of UniProt P0CG48
- Elsewhere: RCSB PDB 6QML · PDBe 6QML · UniProt P15374 · UniProt P0CG47 · UniProt P0CG48
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