Research workbench
Leismania major N-myristoyltransferase in complex with a peptidomimetic (-oh) molecule
Analyse Leismania major N-myristoyltransferase in complex with a peptidomimetic (-oh)… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4C7I
- Type
- protein
- Length
- 411 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Glycylpeptide N-tetradecanoyltransferase
- EC
- 2.3.1.97
- UniProt
- Q4Q5S8
- Ligands
- MYA, JJ1, MG
- Pockets
- 2 · best druggability 0.80
Structure
x-ray diffraction · 1 distinct chain · 32% helix, 28% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Glycylpeptide N-tetradecanoyltransferase (EC 2.3.1.97) | protein | 411 | 32% helix, 28% strand | Q4Q5S8 |
Ligands and binding sites
- MYA · Tetradecanoyl-coa · ligand · chains A
- JJ1 · N-[(1S)-1-{[(1S)-5-amino-1-[(2-cyclohexylethyl)carbamoyl]pentyl]carbamoyl}-2-hydroxyethyl]-10-hydroxydecanamide · ligand · chains A
- MG · Magnesium ion · metal · chains A
- DMS · Dimethyl sulfoxide · additive · 2 copies · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
2 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 930 | 0.80 | 0.82 | 94 | MYA, MG, JJ1, DMS |
| 2 | 138 | 0.43 | 0.75 | 25 | empty |
Compared structures
- 4C7I · Leismania major N-myristoyltransferase in complex with a peptidomimetic (-OH) molecule · 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 Q4Q5S8
- Elsewhere: RCSB PDB 4C7I · PDBe 4C7I · UniProt Q4Q5S8
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