Research workbench
HSNMT1 in complex with both myrcoa and acetylated-gncfskpr substrates
Analyse HSNMT1 in complex with both myrcoa and acetylated-gncfskpr substrates in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6SJZ
- Type
- protein
- Length
- 795 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Glycylpeptide N-tetradecanoyltransferase 1; Apoptosis-inducing factor 3
- EC
- 2.3.1.97, 1.-.-.-
- UniProt
- P30419, Q96NN9
- Ligands
- ACE, MYA, CL
- Pockets
- 5 · best druggability 0.77
Structure
x-ray diffraction · 4 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 | 391 | 27% helix, 28% strand | P30419 |
| B | Glycylpeptide N-tetradecanoyltransferase 1 (EC 2.3.1.97) | protein | 389 | 28% helix, 28% strand | P30419 |
| E | Apoptosis-inducing factor 3 (EC 1.-.-.-) | protein | 8 | 0% helix, 13% strand | Q96NN9 |
| F | Apoptosis-inducing factor 3 (EC 1.-.-.-) | protein | 7 | 0% helix, 0% strand | Q96NN9 |
Ligands and binding sites
- ACE · Acetyl group · ligand · 2 copies · chains B, E, A, F
- MYA · Tetradecanoyl-coa · ligand · 2 copies · chains A, F, B, E
- 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
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 | 857 | 0.77 | 0.80 | 76 | empty |
| 2 | 722 | 0.76 | 0.81 | 56 | MYA |
| 3 | 686 | 0.75 | 0.81 | 56 | MYA |
| 4 | 84 | 0.41 | 0.78 | 20 | empty |
| 5 | 63 | 0.34 | 0.77 | 15 | empty |
Interfaces
3 interfaces between chains.
- A–B · 897 Ų buried · 20 hydrogen bonds · protein-protein
- B–E · 800 Ų buried · 19 hydrogen bonds · protein-protein
- A–F · 756 Ų buried · 15 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 covalent (covalent ligand).
Compared structures
- 6SJZ · HsNMT1 in complex with both MyrCoA and Acetylated-GNCFSKPR substrates · the same entry in another collection · chain F against F, TM-score 1.00
- P30419 · AlphaFold monomer V2.0 prediction for glycylpeptide N-tetradecanoyltransferase 1 (P30419) · a predicted model of the same protein · chain B against A, TM-score 1.00
- Q96NN9 · AlphaFold monomer V2.0 prediction for apoptosis-inducing factor 3 (Q96NN9) · a predicted model of the same protein · chain E against A, TM-score 0.53
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
- Every structure of UniProt Q96NN9
- Elsewhere: RCSB PDB 6SJZ · PDBe 6SJZ · UniProt P30419 · UniProt Q96NN9
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