Research workbench
Human hedgehog acyltransferase (hhat) in complex with a palmitoylated hedgehog peptide product and a Fab antibody fragment
Analyse Human hedgehog acyltransferase (hhat) in complex with a palmitoylated hedgehog… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7MHZ
- Type
- protein
- Length
- 723 residues
- Chains
- 4
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Sonic hedgehog protein N-product peptide; Protein-cysteine N-palmitoyltransferase hhat…
- EC
- 2.3.1.-
- UniProt
- Q15465, Q5VTY9
- Ligands
- AJP, PKZ, PLM, HEM
- Pockets
- 10 · best druggability 0.81
Structure
electron microscopy · 4 distinct chains · 54% helix, 15% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| B | Sonic hedgehog protein N-product peptide | protein | 8 | 0% helix, 0% strand | Q15465 |
| A | Protein-cysteine N-palmitoyltransferase hhat (EC 2.3.1.-) | protein | 491 | 79% helix, 1% strand | Q5VTY9 |
| O | 3H02 Fab heavy chain | protein | 113 | 3% helix, 53% strand | — |
| P | 3H02 Fab light chain | protein | 111 | 0% helix, 40% strand | — |
Ligands and binding sites
- AJP · Digitonin · ligand · 10 copies · chains A
- PKZ · Palmitoyl-CoA · ligand · 3 copies · chains A
- PLM · Palmitic acid · ligand · chains B, A
- HEM · Protoporphyrin IX containing Fe · ligand · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
10 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 165 | 0.81 | 0.96 | 30 | PLM |
| 2 | 162 | 0.75 | 0.92 | 22 | PKZ |
| 3 | 291 | 0.70 | 0.84 | 26 | empty |
| 4 | 468 | 0.65 | 0.77 | 50 | PKZ |
| 5 | 180 | 0.63 | 0.84 | 25 | empty |
Interfaces
4 interfaces between chains.
- O–P · 845 Ų buried · 11 hydrogen bonds · protein-protein
- B–A · 632 Ų buried · 5 hydrogen bonds · protein-protein
- A–O · 530 Ų buried · 5 hydrogen bonds · protein-protein
- A–P · 261 Ų buried · 2 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 disulfide, 1 lipid (disulfide, palmitoylation).
Compared structures
- 7MHZ · Human Hedgehog acyltransferase (HHAT) in complex with a palmitoylated Hedgehog peptide… · the same entry in another collection · chain B against B, TM-score 1.00
- Q5VTY9 · AlphaFold monomer V2.0 prediction for protein-cysteine N-palmitoyltransferase hhat… · a predicted model of the same protein · chain A against A, TM-score 0.99
- Q15465 · AlphaFold monomer V2.0 prediction for sonic hedgehog protein (Q15465) · a predicted model of the same protein · chain B against A, TM-score 0.33
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 Q15465
- Every structure of UniProt Q5VTY9
- Elsewhere: RCSB PDB 7MHZ · PDBe 7MHZ · UniProt Q15465 · UniProt Q5VTY9
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