Research workbench
HSNMT1 in complex with CoA and acetylated-ncfskpk peptide
Analyse HSNMT1 in complex with CoA and acetylated-ncfskpk peptide in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5O9T
- Type
- protein
- Length
- 799 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Glycylpeptide N-tetradecanoyltransferase 1; 1IP-cys-phe-ser-lys-pro-arg
- EC
- 2.3.1.97
- UniProt
- P30419
- Ligands
- MYA, CL
- Pockets
- 7 · best druggability 0.77
Structure
x-ray diffraction · 3 distinct chains · 27% helix, 28% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Glycylpeptide N-tetradecanoyltransferase 1 (EC 2.3.1.97) | protein | 392 | 28% helix, 28% strand | P30419 |
| B | Glycylpeptide N-tetradecanoyltransferase 1 (EC 2.3.1.97) | protein | 393 | 27% helix, 28% strand | P30419 |
| C, D | 1IP-cys-phe-ser-lys-pro-arg | protein | 7 | 0% helix, 14% strand | — |
Ligands and binding sites
- MYA · Tetradecanoyl-coa · ligand · 2 copies · chains A, C, B, D
- CL · Chloride ion · ion · 2 copies · chains A, B
- GOL · Glycerol · additive · 4 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 854 | 0.77 | 0.80 | 79 | empty |
| 2 | 703 | 0.76 | 0.81 | 54 | MYA |
| 3 | 722 | 0.75 | 0.80 | 57 | MYA |
| 4 | 107 | 0.45 | 0.79 | 19 | empty |
| 5 | 131 | 0.45 | 0.77 | 23 | empty |
Interfaces
3 interfaces between chains.
- A–B · 892 Ų buried · 19 hydrogen bonds · protein-protein
- B–D · 854 Ų buried · 26 hydrogen bonds · protein-protein
- A–C · 826 Ų buried · 16 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 modified (nonstandard).
Compared structures
- 5O9T · HsNMT1 in complex with CoA and acetylated-NCFSKPK peptide · 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 5O9T · PDBe 5O9T · UniProt P30419
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