Research workbench
N5-glutamine methyltransferase, hemk
Analyse N5-glutamine methyltransferase, hemk in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1NV8
- Type
- protein
- Length
- 538 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Hemk protein
- EC
- 2.1.1.-
- UniProt
- Q9WYV8
- Ligands
- SAM, MEQ
- Pockets
- 6 · best druggability 0.71
Structure
x-ray diffraction · 2 distinct chains · 42% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Hemk protein (EC 2.1.1.-) | protein | 271 | 41% helix, 17% strand | Q9WYV8 |
| B | Hemk protein (EC 2.1.1.-) | protein | 267 | 43% helix, 17% strand | Q9WYV8 |
Ligands and binding sites
- SAM · S-adenosylmethionine · ligand · 2 copies · chains A, B
- MEQ · N5-methylglutamine · ligand · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 339 | 0.71 | 0.83 | 53 | SAM, MEQ |
| 2 | 296 | 0.69 | 0.83 | 49 | SAM, MEQ |
| 3 | 104 | 0.41 | 0.77 | 18 | empty |
| 4 | 97 | 0.37 | 0.75 | 13 | empty |
| 5 | 113 | 0.35 | 0.73 | 17 | empty |
Interfaces
1 interface between chains.
- A–B · 39 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
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 Q9WYV8
- Elsewhere: RCSB PDB 1NV8 · PDBe 1NV8 · UniProt Q9WYV8
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