MolNFT v1 · #111600 · protein + RNA
Crystal structure of H. influenzae trmd in complex with sinefungin and tRNA variant (G36U)
4YVJ · TRNA (guanine-N(1)-)-methyltransferase: “Crystal structure of H. influenzae trmd in complex with sinefungin and tRNA variant (G36U)”. X-ray diffraction, 1 ligand (SFG), 7 pockets (best druggability 0.81). MolNFT v1 #111600 on…
- PDB
- 4YVJ
- 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
- 7 · best druggability 0.81
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 | 43% helix, 17% 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
7 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 149 | 0.81 | 0.98 | 35 | SFG |
| 2 | 447 | 0.73 | 0.83 | 67 | SFG |
| 3 | 729 | 0.73 | 0.80 | 45 | empty |
| 4 | 362 | 0.56 | 0.75 | 18 | empty |
| 5 | 149 | 0.47 | 0.77 | 24 | empty |
Interfaces
3 interfaces between chains.
- A–B · 3825 Ų buried · 67 hydrogen bonds · protein-protein
- B–C · 742 Ų buried · 22 hydrogen bonds · protein-nucleic
- A–C · 618 Ų buried · 13 hydrogen bonds · protein-nucleic
Compared structures
- 4YVJ · Crystal Structure of H. influenzae TrmD in complex with sinefungin and tRNA variant (G36U) · the same entry in another collection · chain A against A, 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 4YVJ · PDBe 4YVJ · UniProt P43912
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