Research workbench
Crystal structure of trmd, a tRNA-(N1G37) methyltransferase, from mycobacterium abscessus in complex with fragment 9 (adenine)
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
- 6QOF
- Type
- protein
- Length
- 429 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
- ADE
- Pockets
- 6 · best druggability 0.71
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 | 214 | 35% helix, 22% strand | B1MDI3 |
| B | TRNA (guanine-N(1)-)-methyltransferase (EC 2.1.1.228) | protein | 215 | 37% helix, 22% strand | B1MDI3 |
Ligands and binding sites
- ADE · Adenine · ligand · 2 copies · chains A, B
- EDO · 1,2-ethanediol · additive · 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, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 100 | 0.71 | 0.93 | 34 | empty |
| 2 | 264 | 0.64 | 0.82 | 50 | empty |
| 3 | 299 | 0.62 | 0.79 | 52 | empty |
| 4 | 93 | 0.49 | 0.82 | 23 | EDO |
| 5 | 148 | 0.48 | 0.78 | 27 | empty |
Interfaces
1 interface between chains.
- A–B · 3708 Ų buried · 78 hydrogen bonds · protein-protein
Compared structures
- 6QOF · 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 6QOF · PDBe 6QOF · UniProt B1MDI3
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