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
- 6QRD
- Type
- protein
- Length
- 414 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
- JEH, SO4
- Pockets
- 4 · best druggability 0.72
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, 21% strand | B1MDI3 |
| B | TRNA (guanine-N(1)-)-methyltransferase (EC 2.1.1.228) | protein | 202 | 36% helix, 22% strand | B1MDI3 |
Ligands and binding sites
- JEH · 5-azanyl-3-[1-[[4-[(4-propan-2-ylpiperazin-1-yl) methyl]phenyl]methyl]indol-6-yl]-1~{H}-pyrazole-4-carbonitrile · ligand · 2 copies · chains A, B
- SO4 · Sulfate ion · ion · 3 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 370 | 0.72 | 0.83 | 57 | JEH |
| 2 | 341 | 0.71 | 0.84 | 55 | JEH |
| 3 | 163 | 0.52 | 0.79 | 27 | empty |
| 4 | 81 | 0.35 | 0.75 | 13 | empty |
Interfaces
1 interface between chains.
- A–B · 3498 Ų buried · 77 hydrogen bonds · protein-protein
Compared structures
- 6QRD · Crystal structure of TrmD, a tRNA-(N1G37) methyltransferase, from Mycobacterium abscessus… · the same entry in another collection · chain B against B, 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 6QRD · PDBe 6QRD · UniProt B1MDI3
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