MolNFT v1 · #70330 · protein
Crystal structure of P. abyssi tRNA M1A58 methyltransferase in complex with S-adenosyl-L-homocysteine
3LHD · SAM-dependent methyltransferase, putative: “Crystal structure of P. abyssi tRNA M1A58 methyltransferase in complex with S-adenosyl-L-homocysteine”. X-ray diffraction, 1 ligand (SAH), 15 pockets (best druggability 0.74). MolNFT v1…
- PDB
- 3LHD
- Type
- protein
- Length
- 1,012 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- SAM-dependent methyltransferase, putative
- EC
- 2.1.1.36
- UniProt
- Q9V1J7
- Ligands
- SAH
- Pockets
- 15 · best druggability 0.74
Structure
x-ray diffraction · 1 distinct chain · 29% helix, 33% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| C, A, B, D | SAM-dependent methyltransferase, putative (EC 2.1.1.36) | protein | 253 | 29% helix, 33% strand | Q9V1J7 |
Ligands and binding sites
- SAH · S-adenosyl-L-homocysteine · ligand · 4 copies · chains C, A, B, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
15 pockets found on a 1 Å grid, 11 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 57 | 0.74 | 0.99 | 16 | empty |
| 2 | 59 | 0.73 | 0.98 | 15 | empty |
| 3 | 327 | 0.62 | 0.78 | 36 | empty |
| 4 | 288 | 0.60 | 0.78 | 35 | empty |
| 5 | 279 | 0.58 | 0.78 | 33 | empty |
Interfaces
6 interfaces between chains.
- C–D · 2332 Ų buried · 37 hydrogen bonds · protein-protein
- A–B · 2321 Ų buried · 33 hydrogen bonds · protein-protein
- B–D · 808 Ų buried · 15 hydrogen bonds · protein-protein
- C–A · 807 Ų buried · 14 hydrogen bonds · protein-protein
- A–D · 146 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 disulfide (disulfide).
Compared structures
- 3LHD · Crystal structure of P. abyssi tRNA m1A58 methyltransferase in complex with… · the same entry in another collection · chain B against B, TM-score 1.00
- Q9V1J7 · AlphaFold monomer V2.0 prediction for tRNA (ADENINE(57)-N(1)/ADENINE(58)-N(1))-methyltrans… · a predicted model of the same protein · chain D against A, TM-score 0.99
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 Q9V1J7
- Elsewhere: RCSB PDB 3LHD · PDBe 3LHD · UniProt Q9V1J7
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