Research workbench
Crystal structure of trmd from mycobacterium tuberculosis in complex with active-site inhibitor
Analyse Crystal structure of trmd from mycobacterium tuberculosis in complex with… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5ZHK
- Type
- protein
- Length
- 208 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- TRNA (guanine-N(1)-)-methyltransferase
- EC
- 2.1.1.228
- UniProt
- P9WFY7
- Ligands
- 9D6
- Pockets
- 1 · best druggability 0.58
Structure
x-ray diffraction · 1 distinct chain · 41% helix, 21% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | TRNA (guanine-N(1)-)-methyltransferase (EC 2.1.1.228) | protein | 208 | 41% helix, 21% strand | P9WFY7 |
Ligands and binding sites
- 9D6 · N-[(4-{[cyclohexyl(ethyl)amino]methyl}phenyl)methyl]-4-oxo-3,4-dihydrothieno[2,3-d]pyrimidine-5-carboxamide · ligand · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
1 pocket found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 151 | 0.58 | 0.83 | 31 | 9D6 |
Compared structures
- 5ZHK · Crystal structure of TrmD from Mycobacterium tuberculosis in complex with active-site… · the same entry in another collection · chain A against A, TM-score 1.00
- P9WFY7 · AlphaFold monomer V2.0 prediction for tRNA (guanine-N(1)-)-methyltransferase (P9WFY7) · a predicted model of the same protein · chain A against A, TM-score 0.97
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 P9WFY7
- Elsewhere: RCSB PDB 5ZHK · PDBe 5ZHK · UniProt P9WFY7
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