Research workbench
Mutant of human N-myristoyltransferase with bound myristoyl-CoA
Analyse Mutant of human N-myristoyltransferase with bound myristoyl-CoA in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6F56
- Type
- protein
- Length
- 1,528 residues
- Chains
- 4
- 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, MG
- Pockets
- 19 · best druggability 0.81
Structure
x-ray diffraction · 1 distinct chain · 27% helix, 29% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | Glycylpeptide N-tetradecanoyltransferase 1 (EC 2.3.1.97) | protein | 382 | 27% helix, 29% strand | P30419 |
Ligands and binding sites
- MYA · Tetradecanoyl-coa · ligand · 4 copies · chains A, B, C, D
- MG · Magnesium ion · metal · 4 copies · chains A, B, C, D
- GOL · Glycerol · additive · 9 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
19 pockets found on a 1 Å grid, 11 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 972 | 0.81 | 0.82 | 82 | empty |
| 2 | 978 | 0.80 | 0.81 | 85 | MYA, MG |
| 3 | 951 | 0.80 | 0.81 | 80 | MYA, MG |
| 4 | 966 | 0.80 | 0.81 | 78 | MYA, MG |
| 5 | 847 | 0.79 | 0.82 | 76 | MYA, MG |
Interfaces
5 interfaces between chains.
- C–D · 993 Ų buried · 23 hydrogen bonds · protein-protein
- A–B · 922 Ų buried · 20 hydrogen bonds · protein-protein
- A–D · 243 Ų buried · 0 hydrogen bonds · protein-protein
- B–D · 20 Ų buried · 0 hydrogen bonds · protein-protein
- A–C · 11 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 6F56 · Mutant of Human N-myristoyltransferase with bound myristoyl-CoA · 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 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 P30419
- Elsewhere: RCSB PDB 6F56 · PDBe 6F56 · UniProt P30419
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