MolNFT v1 · #147577 · protein
Human N-myristoyltransferase (NMT1) with myristoyl-CoA and peptide bound
6EHJ · Glycylpeptide N-tetradecanoyltransferase 1: “Human N-myristoyltransferase (NMT1) with myristoyl-CoA and peptide bound”. X-ray diffraction, 3 ligands (MYR, COA, MYA), 5 pockets (best druggability 0.69). MolNFT v1 #147577 on…
- PDB
- 6EHJ
- Type
- protein
- Length
- 763 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Glycylpeptide N-tetradecanoyltransferase 1
- EC
- 2.3.1.97
- UniProt
- P30419
- Ligands
- MYR, COA, MYA
- Pockets
- 5 · best druggability 0.69
Structure
x-ray diffraction · 2 distinct chains · 27% helix, 29% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Glycylpeptide N-tetradecanoyltransferase 1 (EC 2.3.1.97) | protein | 379 | 27% helix, 29% strand | P30419 |
| B | Glycylpeptide N-tetradecanoyltransferase 1 (EC 2.3.1.97) | protein | 384 | 27% helix, 29% strand | P30419 |
Ligands and binding sites
- MYR · Myristic acid · ligand · 2 copies · chains A, B
- COA · Coenzyme A · ligand · 2 copies · chains A, B
- MYA · Tetradecanoyl-coa · ligand · chains A
- GOL · Glycerol · additive · 4 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 463 | 0.69 | 0.80 | 46 | COA, MYR |
| 2 | 464 | 0.68 | 0.79 | 44 | MYA, MYR, COA |
| 3 | 93 | 0.41 | 0.78 | 21 | empty |
| 4 | 57 | 0.31 | 0.76 | 12 | empty |
| 5 | 55 | 0.29 | 0.75 | 14 | empty |
Modifications
Observed in the structure: 2 lipid, 1 covalent (myristoylation, covalent ligand).
Compared structures
- 6EHJ · Human N-myristoyltransferase (NMT1) with Myristoyl-CoA and peptide bound · the same entry in another collection · chain A against A, TM-score 1.00
- P30419 · AlphaFold monomer V2.0 prediction for glycylpeptide N-tetradecanoyltransferase 1 (P30419) · a predicted model of the same protein · chain B against A, TM-score 0.98
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 P30419
- Elsewhere: RCSB PDB 6EHJ · PDBe 6EHJ · UniProt P30419
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