Research workbench
The structure of a probable methylase family protein from haemophilus influenzae rd KW20
Analyse The structure of a probable methylase family protein from haemophilus… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3ILK
- Type
- protein
- Length
- 472 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Uncharacterized TRNA/RRNA methyltransferase HI0380
- EC
- 2.1.1.-
- UniProt
- P44676
- Ligands
- SO4
- Pockets
- 5 · best druggability 0.78
Structure
x-ray diffraction · 2 distinct chains · 52% helix, 13% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Uncharacterized TRNA/RRNA methyltransferase HI0380 (EC 2.1.1.-) | protein | 239 | 52% helix, 13% strand | P44676 |
| B | Uncharacterized TRNA/RRNA methyltransferase HI0380 (EC 2.1.1.-) | protein | 233 | 52% helix, 13% strand | P44676 |
Ligands and binding sites
- SO4 · Sulfate ion · ion · 2 copies · chains A, B
- EDO · 1,2-ethanediol · additive · 5 copies · chains A, B
- ACT · Acetate ion · additive · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 87 | 0.78 | 0.98 | 16 | empty |
| 2 | 231 | 0.66 | 0.84 | 32 | EDO |
| 3 | 195 | 0.66 | 0.85 | 26 | EDO, ACT, SO4 |
| 4 | 190 | 0.50 | 0.77 | 30 | EDO, SO4 |
| 5 | 61 | 0.31 | 0.75 | 11 | empty |
Interfaces
1 interface between chains.
- A–B · 2666 Ų buried · 43 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 14 modified (engineered).
Compared structures
- 3ILK · The structure of a probable methylase family protein from Haemophilus influenzae Rd KW20 · the same entry in another collection · chain A against A, TM-score 1.00
- P44676 · AlphaFold monomer V2.0 prediction for uncharacterized TRNA/RRNA methyltransferase HI_0380… · a predicted model of the same protein · chain A against A, TM-score 0.81
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 P44676
- Elsewhere: RCSB PDB 3ILK · PDBe 3ILK · UniProt P44676
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