Research workbench
Crystal structure of a symmetric dimer of a tRNA (guanine-(N(1)-)- methyltransferase from burkholderia phymatum bound to S-adenosyl homocystein in both half-sites
Analyse Crystal structure of a symmetric dimer of a tRNA (guanine-(N(1)-)… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4H3Z
- Type
- protein
- Length
- 505 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- TRNA (guanine-N(1)-)-methyltransferase
- EC
- 2.1.1.228
- UniProt
- B2JF31
- Ligands
- SAH, CL
- Pockets
- 3 · best druggability 0.77
Structure
x-ray diffraction · 2 distinct chains · 45% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | TRNA (guanine-N(1)-)-methyltransferase (EC 2.1.1.228) | protein | 249 | 45% helix, 17% strand | B2JF31 |
| B | TRNA (guanine-N(1)-)-methyltransferase (EC 2.1.1.228) | protein | 256 | 45% helix, 17% strand | B2JF31 |
Ligands and binding sites
- SAH · S-adenosyl-L-homocysteine · ligand · 2 copies · chains A, B
- CL · Chloride ion · ion · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 514 | 0.77 | 0.85 | 62 | SAH |
| 2 | 521 | 0.76 | 0.84 | 56 | SAH |
| 3 | 50 | 0.24 | 0.73 | 14 | empty |
Interfaces
1 interface between chains.
- A–B · 3710 Ų buried · 66 hydrogen bonds · protein-protein
Compared structures
- 4H3Z · Crystal structure of a symmetric dimer of a tRNA (guanine-(N(1)-)-methyltransferase from… · the same entry in another collection · chain A against A, TM-score 1.00
- B2JF31 · AlphaFold monomer V2.0 prediction for tRNA (guanine-N(1)-)-methyltransferase (B2JF31) · a predicted model of the same protein · chain A against A, TM-score 0.97
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 B2JF31
- Elsewhere: RCSB PDB 4H3Z · PDBe 4H3Z · UniProt B2JF31
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