MolNFT v1 · #161862 · protein
Crystal structure of trmd, a tRNA-(N1G37) methyltransferase, from mycobacterium abscessus in complex with inhibitor
6QRA · TRNA (guanine-N(1)-)-methyltransferase: “Crystal structure of trmd, a tRNA-(N1G37) methyltransferase, from mycobacterium abscessus in complex with…”. X-ray diffraction, 2 ligands (JDK, SO4), 7 pockets (best druggability 0.73).…
- PDB
- 6QRA
- Type
- protein
- Length
- 418 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
- JDK, SO4
- Pockets
- 7 · best druggability 0.73
Structure
x-ray diffraction · 2 distinct chains · 36% helix, 22% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | TRNA (guanine-N(1)-)-methyltransferase (EC 2.1.1.228) | protein | 212 | 38% helix, 21% strand | B1MDI3 |
| B | TRNA (guanine-N(1)-)-methyltransferase (EC 2.1.1.228) | protein | 206 | 34% helix, 22% strand | B1MDI3 |
Ligands and binding sites
- JDK · 3-[1-[[4-(piperidin-1-ylmethyl)phenyl]methyl]indol-6-yl]-1~{H}-pyrazol-5-amine · 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
7 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 209 | 0.73 | 0.89 | 38 | JDK |
| 2 | 435 | 0.73 | 0.83 | 58 | JDK |
| 3 | 176 | 0.50 | 0.78 | 26 | empty |
| 4 | 76 | 0.45 | 0.81 | 16 | empty |
| 5 | 101 | 0.41 | 0.77 | 21 | empty |
Interfaces
1 interface between chains.
- A–B · 3526 Ų buried · 74 hydrogen bonds · protein-protein
Compared structures
- 6QRA · 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 6QRA · PDBe 6QRA · UniProt B1MDI3
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