Research workbench
Crystal structure of TrmD, a tRNA-(N1G37) methyltransferase, from Mycobacterium abscessus in complex with inhibitor
Analyse Crystal structure of TrmD, a tRNA-(N1G37) methyltransferase, from Mycobacterium… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6QRB
- Type
- protein
- Length
- 425 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 1.66
- Source
- Mycobacterium abscessus
- Molecule
- tRNA (guanine-N(1)-)-methyltransferase
- EC
- 2.1.1.228
- UniProt
- B1MDI3
- Ligands
- JEQ
- Pockets
- 5 · best druggability 0.76
Structure
x-ray diffraction · resolution 1.66 · 2 distinct chains · 36% helix, 21% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | tRNA (guanine-N(1)-)-methyltransferase (EC 2.1.1.228) | protein | 220 | 37% helix, 20% strand | B1MDI3 |
| B | tRNA (guanine-N(1)-)-methyltransferase (EC 2.1.1.228) | protein | 205 | 35% helix, 22% strand | B1MDI3 |
Ligands and binding sites
- JEQ · 5-azanyl-3-[1-[[(3~{R})-1-(phenylmethyl)piperidin-3-yl]methyl]indol-6-yl]-1~{H}-pyrazole-4-carbonitrile · ligand · 2 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, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 669 | 0.76 | 0.82 | 80 | JEQ |
| 2 | 329 | 0.72 | 0.84 | 50 | JEQ |
| 3 | 188 | 0.52 | 0.78 | 28 | empty |
| 4 | 142 | 0.51 | 0.79 | 16 | empty |
| 5 | 55 | 0.28 | 0.75 | 13 | empty |
Interfaces
1 interface between chains.
- A–B · 3603 Ų buried · 76 hydrogen bonds · protein-protein
Compared structures
- 6QRB · Crystal structure of trmd, a tRNA-(N1G37) methyltransferase, from mycobacterium abscessus… · the same entry in another collection · 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 B1MDI3
- Elsewhere: RCSB PDB 6QRB · PDBe 6QRB · UniProt B1MDI3
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