MolNFT v1 · #160111 · protein
Structure of human NMT1 with products CoA and myristoyl-lysine peptide with acetylated N-terminus
6PAV · Glycylpeptide N-tetradecanoyltransferase 1: “Structure of human NMT1 with products CoA and myristoyl-lysine peptide with acetylated N-terminus”. X-ray diffraction, 3 ligands (COA, MYR, ACE), 7 pockets (best druggability 0.78).…
- PDB
- 6PAV
- Type
- protein
- Length
- 771 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Glycylpeptide N-tetradecanoyltransferase 1; Acetyl-ARF6 peptide; ARF6 peptide
- EC
- 2.3.1.97
- UniProt
- P30419
- Ligands
- COA, MYR, ACE
- Pockets
- 7 · best druggability 0.78
Structure
x-ray diffraction · 4 distinct chains · 27% helix, 29% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| B | Glycylpeptide N-tetradecanoyltransferase 1 (EC 2.3.1.97) | protein | 379 | 29% helix, 29% strand | P30419 |
| D | Acetyl-ARF6 peptide | protein | 7 | 0% helix, 14% strand | — |
| A | Glycylpeptide N-tetradecanoyltransferase 1 (EC 2.3.1.97) | protein | 377 | 27% helix, 29% strand | P30419 |
| C | ARF6 peptide | protein | 8 | 0% helix, 13% strand | — |
Ligands and binding sites
- COA · Coenzyme A · ligand · 2 copies · chains B, D, A, C
- MYR · Myristic acid · ligand · 2 copies · chains B, D, A, C
- ACE · Acetyl group · ligand · chains B, D
- GOL · Glycerol · additive · 4 copies · chains B, A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 856 | 0.78 | 0.81 | 79 | empty |
| 2 | 53 | 0.71 | 0.98 | 18 | GOL |
| 3 | 486 | 0.68 | 0.78 | 46 | COA, MYR |
| 4 | 449 | 0.67 | 0.78 | 49 | COA, MYR |
| 5 | 70 | 0.38 | 0.78 | 20 | empty |
Interfaces
3 interfaces between chains.
- B–A · 929 Ų buried · 22 hydrogen bonds · protein-protein
- A–C · 858 Ų buried · 13 hydrogen bonds · protein-protein
- B–D · 832 Ų buried · 12 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 lipid, 1 covalent (myristoylation, covalent ligand).
Compared structures
- 6PAV · Structure of Human NMT1 with products CoA and myristoyl-lysine peptide with acetylated… · the same entry in another collection · chain B against B, 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 6PAV · PDBe 6PAV · UniProt P30419
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