MolNFT v1 · #121297 · protein + RNA
X-ray crystal structure of C118A rlmn from escherichia COLI with cross-linked in vitro transcribed tRNA
5HR7 · TRNA glu: “X-ray crystal structure of C118A rlmn from escherichia COLI with cross-linked in vitro transcribed tRNA”. X-ray diffraction, 4 ligands (SF4, 5AD, MET), 12 pockets (best druggability 0.85). MolNFT v1 #121297 on GenesisL1…
- PDB
- 5HR7
- Type
- protein + RNA
- Length
- 860 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- TRNA glu; Dual-specificity RNA methyltransferase rlmn
- EC
- 2.1.1.192
- UniProt
- A7ZPW0
- Ligands
- SF4, 5AD, MET, MG
- Pockets
- 12 · best druggability 0.85
Structure
x-ray diffraction · 2 distinct chains · 39% helix, 20% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| D, C | TRNA glu | rna | 70 | — | — |
| B, A | Dual-specificity RNA methyltransferase rlmn (EC 2.1.1.192) | protein | 360 | 39% helix, 20% strand | A7ZPW0 |
Ligands and binding sites
- SF4 · Iron/sulfur cluster · ligand · 2 copies · chains B, A
- 5AD · 5'-deoxyadenosine · ligand · 2 copies · chains B, A
- MET · Methionine · ligand · 2 copies · chains B, A
- MG · Magnesium ion · metal · 7 copies · chains D, A, C, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
12 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 214 | 0.85 | 0.98 | 31 | SF4, 5AD, MET |
| 2 | 221 | 0.84 | 0.97 | 32 | SF4, 5AD, MET |
| 3 | 701 | 0.70 | 0.78 | 54 | MG |
| 4 | 638 | 0.69 | 0.78 | 54 | MG |
| 5 | 979 | 0.69 | 0.75 | 41 | MG |
Interfaces
3 interfaces between chains.
- C–B · 1802 Ų buried · 51 hydrogen bonds · protein-nucleic
- D–A · 1775 Ų buried · 50 hydrogen bonds · protein-nucleic
- C–A · 584 Ų buried · 12 hydrogen bonds · protein-nucleic
Modifications
Observed in the structure: 4 modified (artifact, methylation).
Compared structures
- 5HR7 · X-ray crystal structure of C118A RlmN from Escherichia coli with cross-linked in vitro… · the same entry in another collection · chain D against D, 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 B against A, TM-score 0.98
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 5HR7 · PDBe 5HR7 · UniProt A7ZPW0
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