Research workbench
Human NMT1 in complex with myristoyl-CoA and inhibitor imp-1031
Analyse Human NMT1 in complex with myristoyl-CoA and inhibitor imp-1031 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5O6J
- Type
- protein
- Length
- 765 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, 9M8, MG, PO4
- Pockets
- 5 · best druggability 0.81
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 | 382 | 27% helix, 29% strand | P30419 |
| B | Glycylpeptide N-tetradecanoyltransferase 1 (EC 2.3.1.97) | protein | 383 | 27% helix, 28% strand | P30419 |
Ligands and binding sites
- MYA · Tetradecanoyl-coa · ligand · 2 copies · chains A, B
- 9M8 · 1-[5-[3-fluoranyl-2-[2-(1,3,5-trimethylpyrazol-4-yl) ethoxy]phenyl]-1-methyl-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 · 6 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 | 984 | 0.81 | 0.82 | 102 | MYA, MG, 9M8 |
| 2 | 984 | 0.80 | 0.81 | 94 | MYA, MG, 9M8 |
| 3 | 872 | 0.77 | 0.80 | 72 | empty |
| 4 | 59 | 0.33 | 0.77 | 14 | PO4 |
| 5 | 51 | 0.30 | 0.76 | 15 | empty |
Interfaces
1 interface between chains.
- A–B · 914 Ų buried · 20 hydrogen bonds · protein-protein
Compared structures
- 5O6J · Human NMT1 in complex with myristoyl-CoA and inhibitor IMP-1031 · 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 5O6J · PDBe 5O6J · UniProt P30419
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