Research workbench
Human NMT1 in complex with myristoyl-CoA and inhibitor IMP-917
Analyse Human NMT1 in complex with myristoyl-CoA and inhibitor IMP-917 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5O6H
- Type
- protein
- Length
- 764 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 1.29
- Source
- Homo sapiens
- Molecule
- Glycylpeptide N-tetradecanoyltransferase 1
- EC
- 2.3.1.97
- UniProt
- P30419
- Ligands
- MYA, 9M2, MG, PO4
- Pockets
- 6 · best druggability 0.80
Structure
x-ray diffraction · resolution 1.29 · 1 distinct chain · 26% helix, 29% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Glycylpeptide N-tetradecanoyltransferase 1 (EC 2.3.1.97) | protein | 382 | 26% helix, 29% strand | P30419 |
Ligands and binding sites
- MYA · Tetradecanoyl-coa · ligand · 2 copies · chains A, B
- 9M2 · 1-[5-[4-fluoranyl-2-[2-(1,3,5-trimethylpyrazol-4-yl)ethoxy]phenyl]-2~{H}-indazol-3-yl]-~{N},~{N}-dimethyl-methanamine · ligand · 2 copies · chains A, B
- MG · Magnesium ion · metal · 2 copies · chains A, B
- PO4 · Phosphate ion · ion · 8 copies · chains A, B
- GOL · Glycerol · additive · 3 copies · chains A, B
- DMS · Dimethyl sulfoxide · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 905 | 0.80 | 0.82 | 83 | MYA, 9M2, MG |
| 2 | 908 | 0.80 | 0.82 | 73 | MYA, 9M2, MG |
| 3 | 802 | 0.76 | 0.80 | 73 | empty |
| 4 | 85 | 0.39 | 0.77 | 20 | empty |
| 5 | 89 | 0.36 | 0.75 | 18 | empty |
Interfaces
1 interface between chains.
- A–B · 935 Ų buried · 24 hydrogen bonds · protein-protein
Compared structures
- 5O6H · Human NMT1 in complex with myristoyl-CoA and inhibitor imp-917 · 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 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 P30419
- Elsewhere: RCSB PDB 5O6H · PDBe 5O6H · UniProt P30419
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