MolNFT v1 · #141740 · protein
Crystal structure of trmd from pseudomonas aeruginosa in complex with active-site inhibitor
5ZHN · TRNA (guanine-N(1)-)-methyltransferase: “Crystal structure of trmd from pseudomonas aeruginosa in complex with active-site inhibitor”. X-ray diffraction, 1 ligand (9D0), 3 pockets (best druggability 0.72). MolNFT v1 #141740 on…
- PDB
- 5ZHN
- Type
- protein
- Length
- 474 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
- 9D0
- Pockets
- 3 · best druggability 0.72
Structure
x-ray diffraction · 2 distinct chains · 43% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | TRNA (guanine-N(1)-)-methyltransferase (EC 2.1.1.228) | protein | 236 | 43% helix, 18% strand | Q02RL6 |
| B | TRNA (guanine-N(1)-)-methyltransferase (EC 2.1.1.228) | protein | 238 | 42% helix, 18% strand | Q02RL6 |
Ligands and binding sites
- 9D0 · N-({4-[(octylamino)methyl]phenyl}methyl)-4-oxo-3,4-dihydrothieno[2,3-d]pyrimidine-5-carboxamide · ligand · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 516 | 0.72 | 0.81 | 67 | 9D0 |
| 2 | 527 | 0.71 | 0.80 | 60 | 9D0 |
| 3 | 111 | 0.39 | 0.75 | 18 | empty |
Interfaces
1 interface between chains.
- A–B · 3599 Ų buried · 68 hydrogen bonds · protein-protein
Compared structures
- 5ZHN · 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 5ZHN · PDBe 5ZHN · UniProt Q02RL6
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