MolNFT v1 · #113193 · protein
Crystal structure of sulfolobus acidocaldarius TRM10 in complex with S-adenosylhomocysteine
5A7Y · TRNA (ADENINE(9)-N1)-methyltransferase: “Crystal structure of sulfolobus acidocaldarius TRM10 in complex with S-adenosylhomocysteine”. X-ray diffraction, 1 ligand (SAH), 7 pockets (best druggability 0.75). MolNFT v1 #113193 on…
- PDB
- 5A7Y
- Type
- protein
- Length
- 548 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- TRNA (ADENINE(9)-N1)-methyltransferase
- EC
- 2.1.1.218
- UniProt
- Q4J894
- Ligands
- SAH
- Pockets
- 7 · best druggability 0.75
Structure
x-ray diffraction · 2 distinct chains · 40% helix, 22% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | TRNA (ADENINE(9)-N1)-methyltransferase (EC 2.1.1.218) | protein | 270 | 42% helix, 24% strand | Q4J894 |
| B | TRNA (ADENINE(9)-N1)-methyltransferase (EC 2.1.1.218) | protein | 278 | 39% helix, 21% strand | Q4J894 |
Ligands and binding sites
- SAH · S-adenosyl-L-homocysteine · ligand · 2 copies · chains A, B
- PEG · Di(hydroxyethyl)ether · additive · 2 copies · chains A, B
- ACT · Acetate ion · additive · 2 copies · chains A, B
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 | 620 | 0.75 | 0.81 | 65 | SAH |
| 2 | 137 | 0.55 | 0.82 | 20 | empty |
| 3 | 93 | 0.55 | 0.85 | 16 | SAH |
| 4 | 269 | 0.54 | 0.76 | 25 | empty |
| 5 | 63 | 0.35 | 0.77 | 16 | ACT |
Interfaces
1 interface between chains.
- A–B · 1217 Ų buried · 11 hydrogen bonds · protein-protein
Compared structures
- 5A7Y · Crystal structure of Sulfolobus acidocaldarius Trm10 in complex with… · the same entry in another collection · chain B against B, TM-score 1.00
- Q4J894 · AlphaFold monomer V2.0 prediction for tRNA (ADENINE(9)-N1)-methyltransferase (Q4J894) · a predicted model of the same protein · chain B against A, TM-score 0.93
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 Q4J894
- Elsewhere: RCSB PDB 5A7Y · PDBe 5A7Y · UniProt Q4J894
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