Research workbench
X-ray crystal structure of C118A rlmn with cross-linked tRNA purified from escherichia COLI
Analyse X-ray crystal structure of C118A rlmn with cross-linked tRNA purified from… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5HR6
- Type
- protein + RNA
- Length
- 842 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Rlmn methylase; TRNA glu
- UniProt
- A7ZPW0
- Ligands
- MET, SF4, 5AD, MG
- Pockets
- 14 · best druggability 0.85
Structure
x-ray diffraction · 3 distinct chains · 38% helix, 20% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Rlmn methylase | protein | 354 | 38% helix, 20% strand | A7ZPW0 |
| C | TRNA glu | rna | 68 | — | — |
| D | TRNA glu | rna | 66 | — | — |
Ligands and binding sites
- MET · Methionine · ligand · 2 copies · chains A, B
- SF4 · Iron/sulfur cluster · ligand · 2 copies · chains A, B
- 5AD · 5'-deoxyadenosine · ligand · 2 copies · chains A, B
- MG · Magnesium ion · metal · 6 copies · chains A, C, B, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
14 pockets found on a 1 Å grid, 10 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 213 | 0.85 | 0.98 | 32 | MET, SF4, 5AD |
| 2 | 200 | 0.83 | 0.97 | 31 | MET, SF4, 5AD |
| 3 | 547 | 0.72 | 0.81 | 53 | MG |
| 4 | 147 | 0.69 | 0.89 | 26 | empty |
| 5 | 878 | 0.68 | 0.75 | 41 | empty |
Interfaces
3 interfaces between chains.
- A–C · 1871 Ų buried · 46 hydrogen bonds · protein-nucleic
- B–D · 1806 Ų buried · 52 hydrogen bonds · protein-nucleic
- C–B · 586 Ų buried · 8 hydrogen bonds · protein-nucleic
Modifications
Observed in the structure: 2 modified (methylation).
Compared structures
- 5HR6 · X-ray crystal structure of C118A RlmN with cross-linked tRNA purified from Escherichia… · the same entry in another collection · chain A against A, TM-score 1.00
- A7ZPW0 · AlphaFold monomer V2.0 prediction for dual-specificity RNA methyltransferase rlmn (A7ZPW0) · a predicted model of the same protein · chain A against A, TM-score 1.00
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 A7ZPW0
- Elsewhere: RCSB PDB 5HR6 · PDBe 5HR6 · UniProt A7ZPW0
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