MolNFT v1 · #163999 · protein
HSNMT1 in complex with both myrcoa and acetylated-gksfskpr peptide reveals N-terminal lysine myristoylation
6SK2 · Glycylpeptide N-tetradecanoyltransferase 1: “HSNMT1 in complex with both myrcoa and acetylated-gksfskpr peptide reveals N-terminal lysine myristoylation”. X-ray diffraction, 4 ligands (ACE, COA, MYA), 8 pockets (best druggability…
- PDB
- 6SK2
- Type
- protein
- Length
- 798 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, 1.-.-.-
- UniProt
- P30419, Q96NN9
- Ligands
- ACE, COA, MYA, MYR
- Pockets
- 8 · best druggability 0.78
Structure
x-ray diffraction · 3 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 | 27% helix, 28% strand | P30419 |
| B | Glycylpeptide N-tetradecanoyltransferase 1 (EC 2.3.1.97) | protein | 390 | 27% helix, 27% strand | P30419 |
| D, F | Apoptosis-inducing factor 3 (EC 1.-.-.-) | protein | 8 | 0% helix, 25% strand | Q96NN9 |
Ligands and binding sites
- ACE · Acetyl group · ligand · 2 copies · chains A, D, B, F
- COA · Coenzyme A · ligand · chains A, D
- MYA · Tetradecanoyl-coa · ligand · chains B, F
- MYR · Myristic acid · ligand · chains A, D
- GOL · Glycerol · additive · 3 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 770 | 0.78 | 0.82 | 79 | empty |
| 2 | 686 | 0.76 | 0.81 | 55 | MYA |
| 3 | 688 | 0.74 | 0.79 | 57 | COA, MYR |
| 4 | 83 | 0.44 | 0.80 | 22 | empty |
| 5 | 70 | 0.40 | 0.79 | 17 | empty |
Interfaces
3 interfaces between chains.
- A–B · 921 Ų buried · 22 hydrogen bonds · protein-protein
- A–D · 821 Ų buried · 16 hydrogen bonds · protein-protein
- B–F · 767 Ų buried · 13 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 covalent, 1 lipid (covalent ligand, myristoylation).
Compared structures
- 6SK2 · HsNMT1 in complex with both MyrCoA and Acetylated-GKSFSKPR peptide reveals N-terminal… · the same entry in another collection · chain F against F, 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
- Q96NN9 · AlphaFold monomer V2.0 prediction for apoptosis-inducing factor 3 (Q96NN9) · a predicted model of the same protein · chain F against A, TM-score 0.51
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 Q96NN9
- Elsewhere: RCSB PDB 6SK2 · PDBe 6SK2 · UniProt P30419 · UniProt Q96NN9
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