MolNFT v1 · #129080 · protein
HSNMT1 in complex with CoA and myristoylated-gksnsklk octapeptide
5O9S · Glycylpeptide N-tetradecanoyltransferase 1: “HSNMT1 in complex with CoA and myristoylated-gksnsklk octapeptide”. X-ray diffraction, 2 ligands (MYR, CL), 6 pockets (best druggability 0.77). MolNFT v1 #129080 on GenesisL1: 3D…
- PDB
- 5O9S
- Type
- protein
- Length
- 775 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Glycylpeptide N-tetradecanoyltransferase 1; Neuronal calcium sensor 1
- EC
- 2.3.1.97
- UniProt
- P30419, P62166
- Ligands
- MYR, CL
- Pockets
- 6 · best druggability 0.77
Structure
x-ray diffraction · 3 distinct chains · 26% helix, 29% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Glycylpeptide N-tetradecanoyltransferase 1 (EC 2.3.1.97) | protein | 378 | 27% helix, 29% strand | P30419 |
| B | Glycylpeptide N-tetradecanoyltransferase 1 (EC 2.3.1.97) | protein | 381 | 25% helix, 29% strand | P30419 |
| C, D | Neuronal calcium sensor 1 | protein | 8 | 0% helix, 13% strand | P62166 |
Ligands and binding sites
- MYR · Myristic acid · ligand · 2 copies · chains A, C, B, D
- CL · Chloride ion · ion · 3 copies · chains A, B
- GOL · Glycerol · additive · 4 copies · chains A, B
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 | 837 | 0.77 | 0.81 | 76 | empty |
| 2 | 459 | 0.68 | 0.79 | 48 | MYR |
| 3 | 417 | 0.66 | 0.79 | 49 | MYR |
| 4 | 61 | 0.33 | 0.76 | 14 | empty |
| 5 | 53 | 0.32 | 0.77 | 15 | empty |
Interfaces
3 interfaces between chains.
- A–B · 945 Ų buried · 19 hydrogen bonds · protein-protein
- A–C · 849 Ų buried · 17 hydrogen bonds · protein-protein
- B–D · 828 Ų buried · 19 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 lipid (myristoylation).
Compared structures
- 5O9S · HsNMT1 in complex with CoA and Myristoylated-GKSNSKLK octapeptide · 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 1.00
- P62166 · AlphaFold monomer V2.0 prediction for neuronal calcium sensor 1 (P62166) · a predicted model of the same protein · chain C against A, TM-score 0.34
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
- Every structure of UniProt P62166
- Elsewhere: RCSB PDB 5O9S · PDBe 5O9S · UniProt P30419 · UniProt P62166
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