Research workbench
Crystal structure of trmd from pseudomonas aeruginosa in complex with active-site inhibitor
Analyse Crystal structure of trmd from pseudomonas aeruginosa 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
- 6AFK
- Type
- protein
- Length
- 482 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
- Q02RL6
- Ligands
- SAM, 9WO
- Pockets
- 4 · best druggability 0.81
Structure
x-ray diffraction · 2 distinct chains · 42% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | TRNA (guanine-N(1)-)-methyltransferase (EC 2.1.1.228) | protein | 237 | 42% helix, 17% strand | Q02RL6 |
| B | TRNA (guanine-N(1)-)-methyltransferase (EC 2.1.1.228) | protein | 245 | 42% helix, 18% strand | Q02RL6 |
Ligands and binding sites
- SAM · S-adenosylmethionine · ligand · chains A, B
- 9WO · N-{(3S)-1-[3-(pyridin-4-yl)-1H-pyrazol-5-yl]piperidin-3-yl}-1H-indole-2-carboxamide · ligand · 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, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 165 | 0.81 | 0.96 | 36 | SAM |
| 2 | 491 | 0.71 | 0.81 | 60 | 9WO |
| 3 | 135 | 0.50 | 0.80 | 23 | empty |
| 4 | 88 | 0.36 | 0.75 | 14 | empty |
Interfaces
1 interface between chains.
- A–B · 3720 Ų buried · 63 hydrogen bonds · protein-protein
Compared structures
- 6AFK · Crystal structure of TrmD from Pseudomonas aeruginosa in complex with active-site… · the same entry in another collection · chain A against A, TM-score 1.00
- Q02RL6 · AlphaFold monomer V2.0 prediction for tRNA (guanine-N(1)-)-methyltransferase (Q02RL6) · a predicted model of the same protein · chain A against A, TM-score 0.98
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 Q02RL6
- Elsewhere: RCSB PDB 6AFK · PDBe 6AFK · UniProt Q02RL6
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