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Crystal structure of human type-I N-myristoyltransferase with bound myristoyl-CoA and inhibitor DDD90096
Analyse Crystal structure of human type-I N-myristoyltransferase with bound… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3IU2
- Type
- protein
- Length
- 761 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Glycylpeptide N-tetradecanoyltransferase 1
- EC
- 2.3.1.97
- UniProt
- P30419
- Ligands
- MYA, 096
- Pockets
- 5 · best druggability 0.80
Structure
x-ray diffraction · 2 distinct chains · 27% helix, 29% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Glycylpeptide N-tetradecanoyltransferase 1 (EC 2.3.1.97) | protein | 382 | 27% helix, 29% strand | P30419 |
| B | Glycylpeptide N-tetradecanoyltransferase 1 (EC 2.3.1.97) | protein | 379 | 27% helix, 29% strand | P30419 |
Ligands and binding sites
- MYA · Tetradecanoyl-coa · ligand · 2 copies · chains A, B
- 096 · (2R)-2-{4-hydroxy-5-methoxy-2-[3-(4-methylpiperazin-1-yl)propyl]phenyl}-3-pyridin-3-yl-1,3-thiazolidin-4-one · ligand · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1030 | 0.80 | 0.81 | 104 | MYA, 096 |
| 2 | 1036 | 0.80 | 0.81 | 98 | MYA, 096 |
| 3 | 898 | 0.80 | 0.82 | 84 | empty |
| 4 | 50 | 0.32 | 0.78 | 15 | empty |
| 5 | 59 | 0.31 | 0.76 | 14 | empty |
Interfaces
1 interface between chains.
- A–B · 932 Ų buried · 20 hydrogen bonds · protein-protein
Compared structures
- 3IU2 · Crystal Structure of human type-I N-myristoyltransferase with bound myristoyl-CoA and… · 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 3IU2 · PDBe 3IU2 · UniProt P30419
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