MolNFT v1 · #172308 · protein
NOTUM_GHRELIN complex
6ZYF · Palmitoleoyl-protein carboxylesterase notum: “NOTUM_GHRELIN complex”. X-ray diffraction, 2 ligands (K4Q, NAG), 8 pockets (best druggability 0.75). MolNFT v1 #172308 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 6ZYF
- Type
- protein
- Length
- 701 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Palmitoleoyl-protein carboxylesterase notum
- EC
- 3.1.1.98
- UniProt
- Q6P988
- Ligands
- K4Q, NAG
- Pockets
- 8 · best druggability 0.75
Structure
x-ray diffraction · 2 distinct chains · 34% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Palmitoleoyl-protein carboxylesterase notum (EC 3.1.1.98) | protein | 352 | 33% helix, 16% strand | Q6P988 |
| B | Palmitoleoyl-protein carboxylesterase notum (EC 3.1.1.98) | protein | 349 | 35% helix, 17% strand | Q6P988 |
Ligands and binding sites
- K4Q · [(2~{S})-2-azanyl-3-oxidanylidene-propyl] octanoate · ligand · 2 copies · chains A, B
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 2 copies · chains A, B
- EDO · 1,2-ethanediol · additive · 2 copies · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 109 | 0.75 | 0.95 | 20 | K4Q |
| 2 | 148 | 0.71 | 0.90 | 31 | K4Q |
| 3 | 70 | 0.43 | 0.81 | 19 | EDO |
| 4 | 127 | 0.41 | 0.75 | 27 | empty |
| 5 | 57 | 0.39 | 0.80 | 11 | empty |
Interfaces
1 interface between chains.
- A–B · 449 Ų buried · 9 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 14 disulfide, 2 glycan (disulfide, N-glycosylation).
Compared structures
- 6ZYF · Notum_Ghrelin complex · 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 6ZYF · PDBe 6ZYF · UniProt Q6P988
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