Research workbench
Human hhat H379C in complex with shh N-terminal peptide
Analyse Human hhat H379C in complex with shh N-terminal peptide in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7URF
- Type
- protein
- Length
- 722 residues
- Chains
- 4
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Protein-cysteine N-palmitoyltransferase hhat; Shh-N peptide; 3H02 heavy chain; 3H02 light…
- EC
- 2.3.1.-
- UniProt
- Q5VTY9
- Ligands
- AJP, PKZ, HEM
- Pockets
- 8 · best druggability 0.84
Structure
electron microscopy · 4 distinct chains · 53% helix, 15% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Protein-cysteine N-palmitoyltransferase hhat (EC 2.3.1.-) | protein | 491 | 78% helix, 0% strand | Q5VTY9 |
| B | Shh-N peptide | protein | 7 | 0% helix, 0% strand | — |
| O | 3H02 heavy chain | protein | 113 | 3% helix, 50% strand | — |
| P | 3H02 light chain | protein | 111 | 0% helix, 42% strand | — |
Ligands and binding sites
- AJP · Digitonin · ligand · 5 copies · chains A
- PKZ · Palmitoyl-CoA · ligand · 2 copies · chains A, B
- HEM · Protoporphyrin IX containing Fe · ligand · 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, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 983 | 0.84 | 0.85 | 97 | PKZ |
| 2 | 328 | 0.72 | 0.84 | 27 | empty |
| 3 | 490 | 0.63 | 0.76 | 49 | empty |
| 4 | 205 | 0.62 | 0.82 | 30 | empty |
| 5 | 121 | 0.57 | 0.84 | 17 | empty |
Interfaces
4 interfaces between chains.
- O–P · 852 Ų buried · 7 hydrogen bonds · protein-protein
- A–B · 557 Ų buried · 3 hydrogen bonds · protein-protein
- A–O · 525 Ų buried · 6 hydrogen bonds · protein-protein
- A–P · 233 Ų buried · 3 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 disulfide (disulfide).
Compared structures
- 7URF · Human HHAT H379C in complex with SHH N-terminal peptide · 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 7URF · PDBe 7URF · UniProt Q5VTY9
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