MolNFT v1 · #107599 · protein
Uch-L5 in complex with ubiquitin-propargyl bound to an activating fragment of INO80G
4UF6 · Ubiquitin carboxyl-terminal hydrolase isozyme L5: “Uch-L5 in complex with ubiquitin-propargyl bound to an activating fragment of INO80G”. X-ray diffraction, 1 ligand (AYE), 20 pockets (best druggability 0.79). MolNFT v1 #107599 on…
- PDB
- 4UF6
- Type
- protein
- Length
- 1,666 residues
- Chains
- 12
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Ubiquitin carboxyl-terminal hydrolase isozyme L5; Polyubiquitin-B; Nuclear factor related…
- EC
- 3.4.19.12
- UniProt
- Q9Y5K5, P0CG47, Q6P4R8
- Ligands
- AYE
- Pockets
- 20 · best druggability 0.79
Structure
x-ray diffraction · 7 distinct chains · 48% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Ubiquitin carboxyl-terminal hydrolase isozyme L5 (EC 3.4.19.12) | protein | 292 | 48% helix, 16% strand | Q9Y5K5 |
| B, E, H, K | Polyubiquitin-B | protein | 75 | 24% helix, 36% strand | P0CG47 |
| C, F | Nuclear factor related to kappa-B-binding protein | protein | 50 | 68% helix, 0% strand | Q6P4R8 |
| D | Ubiquitin carboxyl-terminal hydrolase isozyme L5 (EC 3.4.19.12) | protein | 295 | 48% helix, 16% strand | Q9Y5K5 |
| G | Ubiquitin carboxyl-terminal hydrolase isozyme L5 (EC 3.4.19.12) | protein | 287 | 49% helix, 17% strand | Q9Y5K5 |
| I, L | Nuclear factor related to kappa-B-binding protein | protein | 49 | 67% helix, 0% strand | Q6P4R8 |
| J | Ubiquitin carboxyl-terminal hydrolase isozyme L5 (EC 3.4.19.12) | protein | 294 | 48% helix, 16% strand | Q9Y5K5 |
Ligands and binding sites
- AYE · prop-2-en-1-amine · ligand · 4 copies · chains A, B, D, E, G, H, J, K
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 15 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1138 | 0.79 | 0.81 | 91 | empty |
| 2 | 819 | 0.79 | 0.82 | 68 | empty |
| 3 | 670 | 0.77 | 0.82 | 59 | empty |
| 4 | 907 | 0.77 | 0.79 | 85 | empty |
| 5 | 713 | 0.75 | 0.81 | 69 | empty |
Interfaces
24 interfaces between chains.
- J–K · 1206 Ų buried · 13 hydrogen bonds · protein-protein
- D–E · 1205 Ų buried · 16 hydrogen bonds · protein-protein
- G–H · 1201 Ų buried · 16 hydrogen bonds · protein-protein
- A–B · 1189 Ų buried · 17 hydrogen bonds · protein-protein
- D–F · 1135 Ų buried · 4 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 8 covalent (covalent ligand).
Compared structures
- 4UF6 · UCH-L5 in complex with ubiquitin-propargyl bound to an activating fragment of INO80G · the same entry in another collection · chain L against L, TM-score 1.00
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 Q9Y5K5
- Every structure of UniProt P0CG47
- Every structure of UniProt Q6P4R8
- Elsewhere: RCSB PDB 4UF6 · PDBe 4UF6 · UniProt Q9Y5K5 · UniProt P0CG47 · UniProt Q6P4R8
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