Research workbench
Structure of the wnt deacylase notum - crystal form II - 2.8A
Analyse Structure of the wnt deacylase notum - crystal form II - 2.8A in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4UYZ
- Type
- protein
- Length
- 1,396 residues
- Chains
- 5
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Protein notum homolog; Poly ala
- EC
- 3.1.1.1
- UniProt
- Q6P988
- Ligands
- NAG, CL
- Pockets
- 16 · best druggability 0.77
Structure
x-ray diffraction · 5 distinct chains · 35% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Protein notum homolog (EC 3.1.1.1) | protein | 345 | 34% helix, 15% strand | Q6P988 |
| B | Protein notum homolog (EC 3.1.1.1) | protein | 335 | 35% helix, 16% strand | Q6P988 |
| C | Protein notum homolog (EC 3.1.1.1) | protein | 337 | 36% helix, 16% strand | Q6P988 |
| D | Protein notum homolog (EC 3.1.1.1) | protein | 369 | 33% helix, 15% strand | Q6P988 |
| E | Poly ala | protein | 10 | 60% helix, 0% strand | — |
Ligands and binding sites
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
16 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 96 | 0.77 | 0.97 | 18 | empty |
| 2 | 88 | 0.77 | 0.98 | 18 | empty |
| 3 | 91 | 0.76 | 0.97 | 16 | empty |
| 4 | 78 | 0.75 | 0.97 | 16 | empty |
| 5 | 1130 | 0.72 | 0.76 | 112 | empty |
Interfaces
6 interfaces between chains.
- C–D · 433 Ų buried · 2 hydrogen bonds · protein-protein
- A–B · 391 Ų buried · 4 hydrogen bonds · protein-protein
- A–D · 207 Ų buried · 1 hydrogen bond · protein-protein
- B–D · 138 Ų buried · 0 hydrogen bonds · protein-protein
- D–E · 86 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 27 disulfide, 1 glycan (disulfide, N-glycosylation).
Compared structures
- 4UYZ · Structure of the wnt deacylase notum - crystal form II - 2.8A · 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 Q6P988
- Elsewhere: RCSB PDB 4UYZ · PDBe 4UYZ · UniProt Q6P988
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