Research workbench
Crystal structure of trmd, a tRNA-(N1G37) methyltransferase, from mycobacterium abscessus in complex with fragment 21 (2-amino-3- nitrophenol)
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
- 6QOR
- Type
- protein
- Length
- 421 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
- JBK, SO4
- Pockets
- 5 · best druggability 0.71
Structure
x-ray diffraction · 2 distinct chains · 38% helix, 21% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | TRNA (guanine-N(1)-)-methyltransferase (EC 2.1.1.228) | protein | 214 | 38% helix, 21% strand | B1MDI3 |
| B | TRNA (guanine-N(1)-)-methyltransferase (EC 2.1.1.228) | protein | 207 | 37% helix, 21% strand | B1MDI3 |
Ligands and binding sites
- JBK · 2-azanyl-3-nitro-phenol · ligand · 2 copies · chains A, B
- SO4 · Sulfate ion · ion · chains A, B
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 | 393 | 0.71 | 0.82 | 58 | JBK |
| 2 | 378 | 0.69 | 0.82 | 59 | JBK |
| 3 | 149 | 0.62 | 0.85 | 22 | empty |
| 4 | 216 | 0.54 | 0.78 | 25 | empty |
| 5 | 88 | 0.48 | 0.81 | 19 | empty |
Interfaces
1 interface between chains.
- A–B · 3458 Ų buried · 75 hydrogen bonds · protein-protein
Compared structures
- 6QOR · 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 6QOR · PDBe 6QOR · UniProt B1MDI3
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