MolNFT v1 · #164005 · protein
DELTAC3 C-terminal truncation of HSNMT1 in complex with myrcoa and gdcfskpr substrates
6SK8 · Glycylpeptide N-tetradecanoyltransferase 1: “DELTAC3 C-terminal truncation of HSNMT1 in complex with myrcoa and gdcfskpr substrates”. X-ray diffraction, 2 ligands (MYA, CL), 9 pockets (best druggability 0.85). MolNFT v1 #164005 on…
- PDB
- 6SK8
- Type
- protein
- Length
- 794 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Glycylpeptide N-tetradecanoyltransferase 1; Apoptosis-inducing factor 3
- EC
- 2.3.1.97
- UniProt
- P30419
- Ligands
- MYA, CL
- Pockets
- 9 · best druggability 0.85
Structure
x-ray diffraction · 4 distinct chains · 27% helix, 28% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Glycylpeptide N-tetradecanoyltransferase 1 (EC 2.3.1.97) | protein | 392 | 28% helix, 28% strand | P30419 |
| B | Glycylpeptide N-tetradecanoyltransferase 1 (EC 2.3.1.97) | protein | 387 | 27% helix, 28% strand | P30419 |
| C | Apoptosis-inducing factor 3 | protein | 7 | 0% helix, 14% strand | — |
| D | Apoptosis-inducing factor 3 | protein | 8 | 0% helix, 13% strand | — |
Ligands and binding sites
- MYA · Tetradecanoyl-coa · ligand · 2 copies · chains A, B
- CL · Chloride ion · ion · chains A
- GOL · Glycerol · additive · 6 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 284 | 0.85 | 0.95 | 43 | empty |
| 2 | 322 | 0.84 | 0.94 | 42 | empty |
| 3 | 842 | 0.78 | 0.81 | 64 | MYA |
| 4 | 795 | 0.77 | 0.81 | 80 | GOL |
| 5 | 756 | 0.75 | 0.80 | 61 | MYA |
Interfaces
3 interfaces between chains.
- A–B · 912 Ų buried · 26 hydrogen bonds · protein-protein
- B–D · 858 Ų buried · 16 hydrogen bonds · protein-protein
- A–C · 742 Ų buried · 13 hydrogen bonds · protein-protein
Compared structures
- 6SK8 · DeltaC3 C-terminal truncation of HsNMT1 in complex with MyrCoA and GDCFSKPR substrates · 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
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 6SK8 · PDBe 6SK8 · UniProt P30419
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