Research workbench
Crystal structure of H. influenzae trmd in complex with sinefungin and tRNA
Analyse Crystal structure of H. influenzae trmd in complex with sinefungin and tRNA in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4YVI
- 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 | 43% helix, 19% 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, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 164 | 0.81 | 0.97 | 35 | SFG |
| 2 | 309 | 0.74 | 0.86 | 48 | SFG |
| 3 | 555 | 0.68 | 0.79 | 40 | empty |
| 4 | 195 | 0.58 | 0.81 | 28 | empty |
| 5 | 380 | 0.56 | 0.75 | 22 | empty |
Interfaces
3 interfaces between chains.
- A–B · 3908 Ų buried · 67 hydrogen bonds · protein-protein
- B–C · 756 Ų buried · 21 hydrogen bonds · protein-nucleic
- A–C · 750 Ų buried · 17 hydrogen bonds · protein-nucleic
Compared structures
- 4YVI · Crystal Structure of H. influenzae TrmD in complex with sinefungin and tRNA · 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 4YVI · PDBe 4YVI · UniProt P43912
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