MolNFT v1 · #157957 · protein
Structure of USP5 zinc-finger ubiquitin binding domain co-crystallized with (4-oxoquinazolin-3(4H)-YL)ACETIC acid
6NFT · Ubiquitin carboxyl-terminal hydrolase 5: “Structure of USP5 zinc-finger ubiquitin binding domain co-crystallized with (4-oxoquinazolin-3(4H)-YL)ACETIC…”. X-ray diffraction, 3 ligands (KKG, ZN, UNX), 3 pockets (best druggability…
- PDB
- 6NFT
- Type
- protein
- Length
- 231 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Ubiquitin carboxyl-terminal hydrolase 5
- EC
- 3.4.19.12
- UniProt
- P45974
- Ligands
- KKG, ZN, UNX
- Pockets
- 3 · best druggability 0.35
Structure
x-ray diffraction · 2 distinct chains · 13% helix, 20% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Ubiquitin carboxyl-terminal hydrolase 5 (EC 3.4.19.12) | protein | 115 | 13% helix, 20% strand | P45974 |
| B | Ubiquitin carboxyl-terminal hydrolase 5 (EC 3.4.19.12) | protein | 116 | 13% helix, 21% strand | P45974 |
Ligands and binding sites
- KKG · (4-oxoquinazolin-3(4H)-yl)acetic acid · ligand · 2 copies · chains A, B
- ZN · Zinc ion · metal · 2 copies · chains A, B
- UNX · Unknown atom or ion · ion · 17 copies · chains A, B
- EDO · 1,2-ethanediol · additive · 3 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 50 | 0.35 | 0.79 | 13 | KKG |
| 2 | 52 | 0.33 | 0.77 | 13 | KKG |
| 3 | 66 | 0.33 | 0.75 | 14 | UNX |
Interfaces
1 interface between chains.
- A–B · 88 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 disulfide (disulfide).
Compared structures
- 6NFT · Structure of USP5 zinc-finger ubiquitin binding domain co-crystallized with… · the same entry in another collection · chain A against A, TM-score 1.00
- P45974 · AlphaFold monomer V2.0 prediction for ubiquitin carboxyl-terminal hydrolase 5 (P45974) · a predicted model of the same protein · chain A 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 P45974
- Elsewhere: RCSB PDB 6NFT · PDBe 6NFT · UniProt P45974
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