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
- 6QQZ
- Type
- protein
- Length
- 412 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- TRNA (guanine-N(1)-)-methyltransferase
- EC
- 2.1.1.228
- UniProt
- B1MDI3
- Ligands
- JEB, SO4
- Pockets
- 8 · best druggability 0.73
Structure
x-ray diffraction · 2 distinct chains · 37% helix, 22% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | TRNA (guanine-N(1)-)-methyltransferase (EC 2.1.1.228) | protein | 212 | 39% helix, 22% strand | B1MDI3 |
| B | TRNA (guanine-N(1)-)-methyltransferase (EC 2.1.1.228) | protein | 200 | 36% helix, 23% strand | B1MDI3 |
Ligands and binding sites
- JEB · 5-azanyl-3-[1-(pyridin-3-ylmethyl)indol-6-yl]-1~{H}-pyrazole-4-carbonitrile · ligand · 2 copies · chains A, B
- SO4 · Sulfate ion · ion · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 199 | 0.73 | 0.89 | 37 | JEB |
| 2 | 305 | 0.72 | 0.85 | 45 | JEB |
| 3 | 60 | 0.66 | 0.94 | 15 | empty |
| 4 | 184 | 0.51 | 0.78 | 27 | empty |
| 5 | 92 | 0.39 | 0.77 | 19 | empty |
Interfaces
1 interface between chains.
- A–B · 3574 Ų buried · 76 hydrogen bonds · protein-protein
Compared structures
- 6QQZ · 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 6QQZ · PDBe 6QQZ · UniProt B1MDI3
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