Research workbench
Human hedgehog acyltransferase (hhat) in complex with palmitoyl-CoA and two Fab antibody fragments
Analyse Human hedgehog acyltransferase (hhat) in complex with palmitoyl-CoA and two Fab… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7MHY
- Type
- protein
- Length
- 912 residues
- Chains
- 5
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Protein-cysteine N-palmitoyltransferase hhat; 1C06 Fab heavy chain; 1C06 Fab light chain…
- EC
- 2.3.1.-
- UniProt
- Q5VTY9
- Ligands
- AJP, PKZ, HEM
- Pockets
- 11 · best druggability 0.86
Structure
electron microscopy · 5 distinct chains · 42% helix, 23% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Protein-cysteine N-palmitoyltransferase hhat (EC 2.3.1.-) | protein | 491 | 76% helix, 1% strand | Q5VTY9 |
| M | 1C06 Fab heavy chain | protein | 118 | 3% helix, 51% strand | — |
| N | 1C06 Fab light chain | protein | 109 | 0% helix, 48% strand | — |
| O | 3H02 Fab heavy chain | protein | 100 | 3% helix, 48% strand | — |
| P | 3H02 Fab light chain | protein | 94 | 0% helix, 43% strand | — |
Ligands and binding sites
- AJP · Digitonin · ligand · 14 copies · chains A
- PKZ · Palmitoyl-CoA · ligand · 3 copies · chains 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
11 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1125 | 0.86 | 0.87 | 109 | PKZ |
| 2 | 195 | 0.77 | 0.91 | 24 | PKZ |
| 3 | 366 | 0.73 | 0.84 | 29 | AJP |
| 4 | 409 | 0.60 | 0.76 | 38 | empty |
| 5 | 181 | 0.51 | 0.77 | 30 | PKZ |
Interfaces
6 interfaces between chains.
- O–P · 844 Ų buried · 8 hydrogen bonds · protein-protein
- M–N · 810 Ų buried · 5 hydrogen bonds · protein-protein
- A–O · 527 Ų buried · 11 hydrogen bonds · protein-protein
- A–M · 523 Ų buried · 4 hydrogen bonds · protein-protein
- A–N · 361 Ų buried · 5 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 disulfide (disulfide).
Compared structures
- 7MHY · Human Hedgehog acyltransferase (HHAT) in complex with palmitoyl-CoA and two Fab antibody… · the same entry in another collection · chain A against A, 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
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 Q5VTY9
- Elsewhere: RCSB PDB 7MHY · PDBe 7MHY · UniProt Q5VTY9
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