MolNFT v1 · #119627 · protein
Plasmodium vivax N-myristoyltransferase in complex with a quinoline inhibitor (compound 1)
5G1Z · Glycylpeptide N-tetradecanoyltransferase: “Plasmodium vivax N-myristoyltransferase in complex with a quinoline inhibitor (compound 1)”. X-ray diffraction, 5 ligands (NHW, U53, MG), 13 pockets (best druggability 0.82). MolNFT v1…
- PDB
- 5G1Z
- Type
- protein
- Length
- 1,140 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Glycylpeptide N-tetradecanoyltransferase
- EC
- 2.3.1.97
- UniProt
- A5K1A2
- Ligands
- NHW, U53, MG, CL, SO4
- Pockets
- 13 · best druggability 0.82
Structure
x-ray diffraction · 2 distinct chains · 27% helix, 30% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Glycylpeptide N-tetradecanoyltransferase (EC 2.3.1.97) | protein | 385 | 28% helix, 30% strand | A5K1A2 |
| C | Glycylpeptide N-tetradecanoyltransferase (EC 2.3.1.97) | protein | 370 | 27% helix, 30% strand | A5K1A2 |
Ligands and binding sites
- NHW · 2-oxopentadecyl-CoA · ligand · 3 copies · chains A, B, C
- U53 · ethyl 4-(2-cyanoethylsulfanyl)-6-methoxy-quinoline-3-carboxylate · ligand · 3 copies · chains A, B, C
- MG · Magnesium ion · metal · 3 copies · chains A, B, C
- CL · Chloride ion · ion · 3 copies · chains A, B, C
- SO4 · Sulfate ion · ion · 2 copies · chains A, B
- DMS · Dimethyl sulfoxide · additive · 4 copies · chains A, B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
13 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1135 | 0.82 | 0.83 | 110 | empty |
| 2 | 842 | 0.79 | 0.82 | 76 | NHW, U53, MG |
| 3 | 894 | 0.79 | 0.81 | 76 | NHW, U53, DMS, MG |
| 4 | 851 | 0.79 | 0.82 | 68 | NHW, U53, MG |
| 5 | 121 | 0.53 | 0.82 | 27 | empty |
Interfaces
2 interfaces between chains.
- A–B · 602 Ų buried · 6 hydrogen bonds · protein-protein
- A–C · 254 Ų buried · 7 hydrogen bonds · protein-protein
Compared structures
- 5G1Z · Plasmodium vivax N-myristoyltransferase in complex with a quinoline inhibitor (compound 1) · the same entry in another collection · 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 A5K1A2
- Elsewhere: RCSB PDB 5G1Z · PDBe 5G1Z · UniProt A5K1A2
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