MolNFT v1 · #164000 · protein
C-terminal HSNMT1 DELTAC3 truncation in complex with both myrcoa and gncfskpr substrates
6SK3 · Glycylpeptide N-tetradecanoyltransferase 1: “C-terminal HSNMT1 DELTAC3 truncation in complex with both myrcoa and gncfskpr substrates”. X-ray diffraction, 2 ligands (MYA, MG), 10 pockets (best druggability 0.85). MolNFT v1 #164000…
- PDB
- 6SK3
- Type
- protein
- Length
- 793 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, MG
- Pockets
- 10 · best druggability 0.85
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 | 387 | 28% helix, 28% strand | P30419 |
| B | Glycylpeptide N-tetradecanoyltransferase 1 (EC 2.3.1.97) | protein | 390 | 27% helix, 28% strand | P30419 |
| C, D | Apoptosis-inducing factor 3 | protein | 8 | 0% helix, 13% strand | — |
Ligands and binding sites
- MYA · Tetradecanoyl-coa · ligand · 2 copies · chains A, C, B, D
- MG · Magnesium ion · metal · chains B
- GOL · Glycerol · additive · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
10 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 300 | 0.85 | 0.95 | 43 | empty |
| 2 | 295 | 0.84 | 0.95 | 42 | empty |
| 3 | 825 | 0.78 | 0.81 | 70 | empty |
| 4 | 713 | 0.77 | 0.82 | 59 | MYA |
| 5 | 626 | 0.73 | 0.80 | 57 | MYA |
Interfaces
3 interfaces between chains.
- A–B · 927 Ų buried · 25 hydrogen bonds · protein-protein
- B–D · 873 Ų buried · 20 hydrogen bonds · protein-protein
- A–C · 854 Ų buried · 15 hydrogen bonds · protein-protein
Compared structures
- 6SK3 · C-terminal HsNMT1 deltaC3 truncation in complex with both MyrCoA and GNCFSKPR 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 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 6SK3 · PDBe 6SK3 · UniProt P30419
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