MolNFT v1 · #188958 · protein
Human porcn in complex with LGK974 and WNT3A peptide
7URD · Isoform 2 of protein-serine O-palmitoleoyltransferase…: “Human porcn in complex with LGK974 and WNT3A peptide”. Electron microscopy, 5 ligands (CLR, O50, AJP), 8 pockets (best druggability 0.80). MolNFT v1 #188958 on GenesisL1: 3D…
- PDB
- 7URD
- Type
- protein
- Length
- 678 residues
- Chains
- 4
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Isoform 2 of protein-serine O-palmitoleoyltransferase porcupine; Isoform 2 of protein…
- EC
- 2.3.1.250
- UniProt
- Q9H237, P56704
- Ligands
- CLR, O50, AJP, OLA, ZN
- Pockets
- 8 · best druggability 0.80
Structure
electron microscopy · 4 distinct chains · 47% helix, 19% 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 | 72% helix, 1% strand | Q9H237 |
| B | Isoform 2 of protein wnt-3A peptide | protein | 20 | 0% helix, 50% strand | P56704 |
| L | 2C11 light chain | protein | 107 | 3% helix, 53% strand | — |
| H | 2C11 heavy chain | protein | 119 | 5% helix, 50% strand | — |
Ligands and binding sites
- CLR · Cholesterol · ligand · 2 copies · chains A
- O50 · 2-[(2P)-2',3-dimethyl[2,4'-bipyridin]-5-yl]-N-[(5P)-5-(pyrazin-2-yl)pyridin-2-yl]acetamide · 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 | 793 | 0.80 | 0.83 | 73 | O50 |
| 2 | 209 | 0.56 | 0.78 | 30 | empty |
| 3 | 303 | 0.54 | 0.75 | 30 | empty |
| 4 | 102 | 0.47 | 0.80 | 23 | empty |
| 5 | 111 | 0.36 | 0.74 | 24 | empty |
Interfaces
4 interfaces between chains.
- A–B · 982 Ų buried · 9 hydrogen bonds · protein-protein
- L–H · 796 Ų buried · 8 hydrogen bonds · protein-protein
- A–H · 628 Ų buried · 9 hydrogen bonds · protein-protein
- A–L · 481 Ų buried · 7 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 5 disulfide (disulfide).
Compared structures
- 7URD · Human PORCN in complex with LGK974 and WNT3A peptide · the same entry in another collection · chain A against A, TM-score 1.00
- Q9H237 · AlphaFold monomer V2.0 prediction for protein-serine O-palmitoleoyltransferase porcupine… · a predicted model of the same protein · chain A against A, TM-score 0.98
- P56704 · AlphaFold monomer V2.0 prediction for protein wnt-3A (P56704) · a predicted model of the same protein · chain B against A, TM-score 0.43
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
- Every structure of UniProt P56704
- Elsewhere: RCSB PDB 7URD · PDBe 7URD · UniProt Q9H237 · UniProt P56704
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