Research workbench
Crystal structure of the covalent complex between tribolium castaneum deubiquitinase zup and ubiquitin-pa
Analyse Crystal structure of the covalent complex between tribolium castaneum… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7OJE
- Type
- protein
- Length
- 876 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Lys-63-specific deubiquitinase zufsp; Polyubiquitin-B
- UniProt
- D6WWN1, P0CG47
- Ligands
- AYE, NA, ZN
- Pockets
- 12 · best druggability 0.68
Structure
x-ray diffraction · 3 distinct chains · 41% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Lys-63-specific deubiquitinase zufsp | protein | 365 | 43% helix, 16% strand | D6WWN1 |
| B, D | Polyubiquitin-B | protein | 75 | 20% helix, 36% strand | P0CG47 |
| C | Lys-63-specific deubiquitinase zufsp | protein | 361 | 44% helix, 16% strand | D6WWN1 |
Ligands and binding sites
- AYE · prop-2-en-1-amine · ligand · 2 copies · chains A, B, C, D
- NA · Sodium ion · metal · 3 copies · chains A, C
- ZN · Zinc ion · metal · 2 copies · chains A, C
- EDO · 1,2-ethanediol · additive · 4 copies · chains A, B, C, D
- CIT · Citric acid · additive · 2 copies · chains A, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
12 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 511 | 0.68 | 0.79 | 56 | empty |
| 2 | 667 | 0.68 | 0.76 | 81 | AYE |
| 3 | 128 | 0.59 | 0.85 | 25 | empty |
| 4 | 112 | 0.59 | 0.85 | 28 | EDO |
| 5 | 144 | 0.56 | 0.82 | 23 | empty |
Interfaces
5 interfaces between chains.
- C–D · 1561 Ų buried · 37 hydrogen bonds · protein-protein
- A–B · 1463 Ų buried · 30 hydrogen bonds · protein-protein
- A–C · 1317 Ų buried · 18 hydrogen bonds · protein-protein
- B–C · 134 Ų buried · 0 hydrogen bonds · protein-protein
- A–D · 134 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 covalent (covalent ligand).
Compared structures
- 7OJE · Crystal structure of the covalent complex between Tribolium castaneum deubiquitinase ZUP… · the same entry in another collection · chain A against A, 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 D6WWN1
- Every structure of UniProt P0CG47
- Elsewhere: RCSB PDB 7OJE · PDBe 7OJE · UniProt D6WWN1 · UniProt P0CG47
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.