MolNFT v1 · #161767 · protein
Crystal structure of trmd, a tRNA-(N1G37) methyltransferase, from mycobacterium abscessus in complex with fragment 16 (2-amino-3- nitropyridine)
6QOM · TRNA (guanine-N(1)-)-methyltransferase: “Crystal structure of trmd, a tRNA-(N1G37) methyltransferase, from mycobacterium abscessus in complex with…”. X-ray diffraction, 1 ligand (JBE), 5 pockets (best druggability 0.70). MolNFT v1…
- PDB
- 6QOM
- Type
- protein
- Length
- 419 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
- JBE
- Pockets
- 5 · best druggability 0.70
Structure
x-ray diffraction · 2 distinct chains · 34% helix, 22% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | TRNA (guanine-N(1)-)-methyltransferase (EC 2.1.1.228) | protein | 204 | 33% helix, 23% strand | B1MDI3 |
| B | TRNA (guanine-N(1)-)-methyltransferase (EC 2.1.1.228) | protein | 215 | 34% helix, 22% strand | B1MDI3 |
Ligands and binding sites
- JBE · 3-nitropyridin-2-amine · ligand · chains A
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 | 357 | 0.70 | 0.83 | 57 | empty |
| 2 | 324 | 0.70 | 0.83 | 63 | JBE |
| 3 | 263 | 0.59 | 0.78 | 27 | empty |
| 4 | 193 | 0.50 | 0.77 | 25 | empty |
| 5 | 68 | 0.39 | 0.79 | 22 | empty |
Interfaces
1 interface between chains.
- A–B · 3640 Ų buried · 73 hydrogen bonds · protein-protein
Compared structures
- 6QOM · 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 6QOM · PDBe 6QOM · UniProt B1MDI3
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