MolNFT v1 · #87493 · protein
Human N-myristoyltransferase (NMT1) with myristoyl-CoA and inhibitor bound
4C2Z · Glycylpeptide N-tetradecanoyltransferase 1: “Human N-myristoyltransferase (NMT1) with myristoyl-CoA and inhibitor bound”. X-ray diffraction, 4 ligands (MYA, 646, MG), 5 pockets (best druggability 0.79). MolNFT v1 #87493 on…
- PDB
- 4C2Z
- Type
- protein
- Length
- 764 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
- MYA, 646, MG, CL
- Pockets
- 5 · best druggability 0.79
Structure
x-ray diffraction · 1 distinct chain · 27% helix, 29% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Glycylpeptide N-tetradecanoyltransferase 1 (EC 2.3.1.97) | protein | 382 | 27% helix, 29% strand | P30419 |
Ligands and binding sites
- MYA · Tetradecanoyl-coa · ligand · 2 copies · chains A, B
- 646 · 2,6-dichloro-4-(2-piperazin-1-ylpyridin-4-yl)-N-(1,3,5-trimethyl-1H-pyrazol-4-yl)benzenesulfonamide · ligand · 2 copies · chains A, B
- MG · Magnesium ion · metal · 2 copies · chains A, B
- CL · Chloride ion · ion · 8 copies · chains A, B
- GOL · Glycerol · additive · 4 copies · chains A, B
- CIT · Citric acid · additive · 2 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, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 990 | 0.79 | 0.80 | 90 | MYA, 646, MG, CL |
| 2 | 1036 | 0.78 | 0.80 | 92 | MYA, 646, MG, CL |
| 3 | 888 | 0.77 | 0.80 | 75 | empty |
| 4 | 69 | 0.35 | 0.77 | 14 | CIT |
| 5 | 58 | 0.33 | 0.77 | 15 | empty |
Interfaces
1 interface between chains.
- A–B · 873 Ų buried · 20 hydrogen bonds · protein-protein
Compared structures
- 4C2Z · Human N-myristoyltransferase (NMT1) with Myristoyl-CoA and inhibitor 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 A against A, TM-score 1.00
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 4C2Z · PDBe 4C2Z · UniProt P30419
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