MolNFT v1 · #10160 · protein
Crystal structure of saccharomyces cerevisiae N- myristoyltransferase with bound S-(2-OXO)PENTADECYLCOA and the octapeptide glyaskla
1IID · Peptide N-myristoyltransferase: “Crystal structure of saccharomyces cerevisiae N- myristoyltransferase with bound S-(2-OXO)PENTADECYLCOA and…”. X-ray diffraction, 2 ligands (NHM, NI), 5 pockets (best druggability 0.75). MolNFT v1…
- PDB
- 1IID
- Type
- protein
- Length
- 430 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Peptide N-myristoyltransferase; Octapeptide glyaskla
- EC
- 2.3.1.97
- UniProt
- P14743
- Ligands
- NHM, NI
- Pockets
- 5 · best druggability 0.75
Structure
x-ray diffraction · 2 distinct chains · 27% helix, 26% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Peptide N-myristoyltransferase (EC 2.3.1.97) | protein | 422 | 27% helix, 26% strand | P14743 |
| O | Octapeptide glyaskla | protein | 8 | 0% helix, 0% strand | — |
Ligands and binding sites
- NHM · S-(2-oxo)pentadecylcoa · ligand · chains A, O
- NI · Nickel (II) ion · metal · 2 copies · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 668 | 0.75 | 0.81 | 57 | NHM |
| 2 | 127 | 0.47 | 0.78 | 24 | empty |
| 3 | 111 | 0.44 | 0.78 | 29 | empty |
| 4 | 115 | 0.43 | 0.78 | 22 | empty |
| 5 | 93 | 0.39 | 0.76 | 20 | empty |
Interfaces
1 interface between chains.
- A–O · 627 Ų buried · 12 hydrogen bonds · protein-protein
Compared structures
- 1IID · Crystal Structure of Saccharomyces cerevisiae N-myristoyltransferase with Bound… · the same entry in another collection · chain A against A, TM-score 1.00
- P14743 · AlphaFold monomer V2.0 prediction for glycylpeptide N-tetradecanoyltransferase (P14743) · 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 P14743
- Elsewhere: RCSB PDB 1IID · PDBe 1IID · UniProt P14743
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