Research workbench
Crystal structure of tRNA (guanine-N1)-methyltransferase from Anaplasma phagocytophilum
Analyse Crystal structure of tRNA (guanine-N1)-methyltransferase from Anaplasma… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3KNU
- Type
- protein
- Length
- 785 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 2.25
- Source
- Anaplasma phagocytophilum
- Molecule
- tRNA (guanine-N(1)-)-methyltransferase
- EC
- 2.1.1.31
- UniProt
- Q2GIL5
- Pockets
- 5 · best druggability 0.67
Structure
x-ray diffraction · resolution 2.25 · 4 distinct chains · 39% helix, 22% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | tRNA (guanine-N(1)-)-methyltransferase (EC 2.1.1.31) | protein | 192 | 40% helix, 23% strand | Q2GIL5 |
| B | tRNA (guanine-N(1)-)-methyltransferase (EC 2.1.1.31) | protein | 197 | 40% helix, 22% strand | Q2GIL5 |
| C | tRNA (guanine-N(1)-)-methyltransferase (EC 2.1.1.31) | protein | 199 | 39% helix, 22% strand | Q2GIL5 |
| D | tRNA (guanine-N(1)-)-methyltransferase (EC 2.1.1.31) | protein | 197 | 38% helix, 21% strand | Q2GIL5 |
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 | 356 | 0.67 | 0.81 | 42 | empty |
| 2 | 386 | 0.66 | 0.80 | 41 | empty |
| 3 | 272 | 0.62 | 0.80 | 31 | empty |
| 4 | 282 | 0.61 | 0.80 | 31 | empty |
| 5 | 209 | 0.46 | 0.74 | 21 | empty |
Interfaces
3 interfaces between chains.
- C–D · 3107 Ų buried · 58 hydrogen bonds · protein-protein
- A–B · 3088 Ų buried · 60 hydrogen bonds · protein-protein
- A–D · 40 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 3KNU · Crystal structure of tRNA (guanine-N1)-methyltransferase from anaplasma phagocytophilum · the same entry in another collection · chain D against D, TM-score 1.00
- Q2GIL5 · AlphaFold monomer V2.0 prediction for tRNA (guanine-N(1)-)-methyltransferase (Q2GIL5) · a predicted model of the same protein · chain A against A, TM-score 0.94
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 Q2GIL5
- Elsewhere: RCSB PDB 3KNU · PDBe 3KNU · UniProt Q2GIL5
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