MolNFT v1 · #25387 · protein
Crystal structure of N5-glutamine methyltransferase, HEMK(EC 2.1.1.-) (TM0488) from thermotoga maritima at 2.80 a resolution
1VQ1: “Crystal structure of N5-glutamine methyltransferase, HEMK(EC 2.1.1.-) (TM0488) from thermotoga maritima at…”. X-ray diffraction, 1 ligand (SAM), 6 pockets (best druggability 0.69). MolNFT v1 #25387 on GenesisL1: 3D structure…
- PDB
- 1VQ1
- Type
- protein
- Length
- 530 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- N5-glutamine methyltransferase, hemk
- EC
- 2.1.1.-
- UniProt
- Q9WYV8
- Ligands
- SAM
- Pockets
- 6 · best druggability 0.69
Structure
x-ray diffraction · 2 distinct chains · 43% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | N5-glutamine methyltransferase, hemk (EC 2.1.1.-) | protein | 266 | 43% helix, 17% strand | Q9WYV8 |
| B | N5-glutamine methyltransferase, hemk (EC 2.1.1.-) | protein | 264 | 43% helix, 17% strand | Q9WYV8 |
Ligands and binding sites
- SAM · S-adenosylmethionine · 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 | 257 | 0.69 | 0.85 | 44 | SAM |
| 2 | 285 | 0.68 | 0.83 | 44 | SAM |
| 3 | 280 | 0.49 | 0.73 | 33 | empty |
| 4 | 89 | 0.36 | 0.75 | 15 | empty |
| 5 | 83 | 0.32 | 0.73 | 16 | empty |
Interfaces
1 interface between chains.
- A–B · 25 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 6 modified (engineered).
Compared structures
- 1VQ1 · Crystal structure of N5-glutamine methyltransferase, HemK(EC 2.1.1.-) (TM0488) from… · the same entry in another collection · chain A against A, TM-score 1.00
- Q9WYV8 · AlphaFold monomer V2.0 prediction for release factor glutamine methyltransferase (Q9WYV8) · a predicted model of the same protein · chain A against A, TM-score 0.98
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 1VQ1 · PDBe 1VQ1 · UniProt Q9WYV8
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