Research workbench
Human porcn in complex with palmitoleoyl-CoA
Analyse Human porcn in complex with palmitoleoyl-CoA in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7URA
- Type
- protein
- Length
- 658 residues
- Chains
- 3
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Isoform 2 of protein-serine O-palmitoleoyltransferase porcupine; 2C11 light chain; 2C11…
- EC
- 2.3.1.250
- UniProt
- Q9H237
- Ligands
- CLR, OH6, AJP, OLA, ZN
- Pockets
- 8 · best druggability 0.78
Structure
electron microscopy · 3 distinct chains · 48% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Isoform 2 of protein-serine O-palmitoleoyltransferase porcupine (EC 2.3.1.250) | protein | 432 | 70% helix, 1% strand | Q9H237 |
| L | 2C11 light chain | protein | 107 | 3% helix, 49% strand | — |
| H | 2C11 heavy chain | protein | 119 | 8% helix, 50% strand | — |
Ligands and binding sites
- CLR · Cholesterol · ligand · 2 copies · chains A
- OH6 · ~{S}-[2-[3-[[(2~{R})-4-[[[(2~{R},3~{R},4~{R},5~{R})-5-(6-aminopurin-9-yl)-4-oxidanyl-3-phosphonooxy-oxolan-2-yl]methoxy-oxidanyl-phosphoryl]oxy-oxidanyl-phosphoryl]oxy-3,3-dimethyl-2-oxidanyl-butanoyl]amino]propanoylamino]ethyl] (~{Z})-hexadec-9-enethioate · ligand · chains A
- AJP · Digitonin · ligand · chains A, H
- OLA · Oleic acid · ligand · chains A
- ZN · Zinc ion · metal · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 836 | 0.78 | 0.81 | 63 | OH6 |
| 2 | 236 | 0.59 | 0.79 | 25 | AJP |
| 3 | 347 | 0.55 | 0.75 | 32 | empty |
| 4 | 133 | 0.38 | 0.73 | 24 | empty |
| 5 | 78 | 0.33 | 0.74 | 21 | OLA |
Interfaces
3 interfaces between chains.
- L–H · 813 Ų buried · 8 hydrogen bonds · protein-protein
- A–H · 614 Ų buried · 8 hydrogen bonds · protein-protein
- A–L · 470 Ų buried · 6 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 3 disulfide (disulfide).
Compared structures
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 Q9H237
- Elsewhere: RCSB PDB 7URA · PDBe 7URA · UniProt Q9H237
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