Research workbench
Structure of human NMT2 with myristoyl-lysine peptide and CoA products
Analyse Structure of human NMT2 with myristoyl-lysine peptide and CoA products in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6PAU
- Type
- protein
- Length
- 368 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Glycylpeptide N-tetradecanoyltransferase 2; ARF6 peptide
- EC
- 2.3.1.97
- UniProt
- O60551
- Ligands
- 4PS, MYR, MG, SO4
- Pockets
- 3 · best druggability 0.58
Structure
x-ray diffraction · 2 distinct chains · 27% helix, 30% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Glycylpeptide N-tetradecanoyltransferase 2 (EC 2.3.1.97) | protein | 361 | 28% helix, 30% strand | O60551 |
| C | ARF6 peptide | protein | 7 | 0% helix, 14% strand | — |
Ligands and binding sites
- 4PS · 4'-diphospho pantetheine · ligand · chains A, C
- MYR · Myristic acid · ligand · chains A, C
- MG · Magnesium ion · metal · chains A
- SO4 · Sulfate ion · ion · chains A
- GOL · Glycerol · additive · 9 copies · chains A, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 306 | 0.58 | 0.77 | 36 | MG, GOL, 4PS, MYR |
| 2 | 87 | 0.41 | 0.78 | 20 | empty |
| 3 | 72 | 0.33 | 0.75 | 16 | GOL |
Interfaces
1 interface between chains.
- A–C · 823 Ų buried · 16 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 lipid (myristoylation).
Compared structures
- 6PAU · Structure of Human NMT2 with myristoyl-lysine peptide and CoA products · the same entry in another collection · chain A against A, TM-score 1.00
- O60551 · AlphaFold monomer V2.0 prediction for glycylpeptide N-tetradecanoyltransferase 2 (O60551) · 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 O60551
- Elsewhere: RCSB PDB 6PAU · PDBe 6PAU · UniProt O60551
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