MolNFT v1 · #113957 · protein + RNA
Crystal structure of THG1 like protein (tlp) with TRNA(PHE)
5AXM · TRNA(HIS)-5'-guanylyltransferase (THG1) like protein: “Crystal structure of THG1 like protein (tlp) with TRNA(PHE)”. X-ray diffraction, 1 ligand (MG), 10 pockets (best druggability 0.74). MolNFT v1 #113957 on GenesisL1: 3D…
- PDB
- 5AXM
- Type
- protein + RNA
- Length
- 525 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- TRNA(HIS)-5'-guanylyltransferase (THG1) like protein; RNA (75-mer)
- Ligands
- MG
- Pockets
- 10 · best druggability 0.74
Structure
x-ray diffraction · 3 distinct chains · 47% helix, 19% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | TRNA(HIS)-5'-guanylyltransferase (THG1) like protein | protein | 213 | 48% helix, 15% strand | — |
| B | TRNA(HIS)-5'-guanylyltransferase (THG1) like protein | protein | 239 | 46% helix, 22% strand | — |
| P | RNA (75-mer) | rna | 73 | — | — |
Ligands and binding sites
- MG · Magnesium ion · metal · 4 copies · chains A, P, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
10 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 80 | 0.74 | 0.97 | 21 | empty |
| 2 | 887 | 0.70 | 0.76 | 57 | empty |
| 3 | 465 | 0.70 | 0.80 | 44 | MG |
| 4 | 381 | 0.56 | 0.76 | 22 | empty |
| 5 | 83 | 0.50 | 0.84 | 19 | empty |
Interfaces
3 interfaces between chains.
- A–B · 1953 Ų buried · 36 hydrogen bonds · protein-protein
- A–P · 1032 Ų buried · 33 hydrogen bonds · protein-nucleic
- B–P · 747 Ų buried · 18 hydrogen bonds · protein-nucleic
Modifications
Observed in the structure: 1 modified (nucleotide modification).
Compared structures
- 5AXM · Crystal structure of Thg1 like protein (TLP) with tRNA(Phe) · the same entry in another collection · 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
- Elsewhere: RCSB PDB 5AXM · PDBe 5AXM
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