MolNFT v1 · #161149 · protein
Crystal structure of the B. subtilis M1A22 tRNA methyltransferase trmk
6Q56 · TRNA (ADENINE(22)-N(1))-methyltransferase: “Crystal structure of the B. subtilis M1A22 tRNA methyltransferase trmk”. X-ray diffraction, 1 ligand (NI), 13 pockets (best druggability 0.79). MolNFT v1 #161149 on GenesisL1: 3D…
- PDB
- 6Q56
- Type
- protein
- Length
- 936 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- TRNA (ADENINE(22)-N(1))-methyltransferase
- EC
- 2.1.1.217
- UniProt
- P54471
- Ligands
- NI
- Pockets
- 13 · best druggability 0.79
Structure
x-ray diffraction · 1 distinct chain · 48% helix, 22% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | TRNA (ADENINE(22)-N(1))-methyltransferase (EC 2.1.1.217) | protein | 234 | 48% helix, 22% strand | P54471 |
Ligands and binding sites
- NI · Nickel (II) ion · metal · 4 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
13 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 862 | 0.79 | 0.82 | 108 | empty |
| 2 | 293 | 0.69 | 0.83 | 46 | NI |
| 3 | 186 | 0.65 | 0.85 | 28 | empty |
| 4 | 150 | 0.58 | 0.83 | 36 | empty |
| 5 | 100 | 0.52 | 0.83 | 21 | empty |
Interfaces
4 interfaces between chains.
- C–D · 981 Ų buried · 14 hydrogen bonds · protein-protein
- A–B · 976 Ų buried · 15 hydrogen bonds · protein-protein
- A–C · 310 Ų buried · 2 hydrogen bonds · protein-protein
- B–C · 31 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 6Q56 · Crystal structure of the B. subtilis M1A22 tRNA methyltransferase TrmK · the same entry in another collection · chain A against A, TM-score 1.00
- P54471 · AlphaFold monomer V2.0 prediction for tRNA (ADENINE(22)-N(1))-methyltransferase (P54471) · a predicted model of the same protein · chain A 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 P54471
- Elsewhere: RCSB PDB 6Q56 · PDBe 6Q56 · UniProt P54471
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