MolNFT v1 · #111601 · protein + RNA
Crystal structure of H. influenzae trmd in complex with sinefungin and tRNA variant (G36C)
4YVK · TRNA (guanine-N(1)-)-methyltransferase: “Crystal structure of H. influenzae trmd in complex with sinefungin and tRNA variant (G36C)”. X-ray diffraction, 1 ligand (SFG), 6 pockets (best druggability 0.82). MolNFT v1 #111601 on…
- PDB
- 4YVK
- Type
- protein + RNA
- Length
- 559 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- TRNA (guanine-N(1)-)-methyltransferase; TRNA
- EC
- 2.1.1.228
- UniProt
- P43912
- Ligands
- SFG
- Pockets
- 6 · best druggability 0.82
Structure
x-ray diffraction · 3 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 | 239 | 44% helix, 18% strand | P43912 |
| B | TRNA (guanine-N(1)-)-methyltransferase (EC 2.1.1.228) | protein | 249 | 42% helix, 18% strand | P43912 |
| C | TRNA | rna | 71 | — | — |
Ligands and binding sites
- SFG · Sinefungin · ligand · 2 copies · chains A, B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 155 | 0.82 | 0.98 | 34 | SFG |
| 2 | 856 | 0.75 | 0.80 | 62 | empty |
| 3 | 387 | 0.74 | 0.84 | 62 | SFG |
| 4 | 374 | 0.56 | 0.75 | 22 | empty |
| 5 | 69 | 0.36 | 0.77 | 19 | empty |
Interfaces
3 interfaces between chains.
- A–B · 3818 Ų buried · 68 hydrogen bonds · protein-protein
- B–C · 738 Ų buried · 22 hydrogen bonds · protein-nucleic
- A–C · 609 Ų buried · 10 hydrogen bonds · protein-nucleic
Compared structures
- 4YVK · Crystal Structure of H. influenzae TrmD in complex with sinefungin and tRNA variant (G36C) · the same entry in another collection · chain B against B, TM-score 1.00
- P43912 · AlphaFold monomer V2.0 prediction for tRNA (guanine-N(1)-)-methyltransferase (P43912) · 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 P43912
- Elsewhere: RCSB PDB 4YVK · PDBe 4YVK · UniProt P43912
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