Research workbench
Crystal structure of THG1 like protein (tlp) with TRNA(PHE) and gdpnp
Analyse Crystal structure of THG1 like protein (tlp) with TRNA(PHE) and gdpnp in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5AXN
- Type
- protein + RNA
- Length
- 524 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
- GNP, MG
- Pockets
- 9 · best druggability 0.78
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 | 219 | 47% helix, 15% strand | — |
| B | TRNA(HIS)-5'-guanylyltransferase (THG1) like protein | protein | 239 | 47% helix, 22% strand | — |
| P | RNA (75-mer) | rna | 66 | — | — |
Ligands and binding sites
- GNP · Phosphoaminophosphonic acid-guanylate ester · ligand · 2 copies · chains A, B, P
- MG · Magnesium ion · metal · 5 copies · chains A, P, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1175 | 0.78 | 0.80 | 87 | MG, GNP |
| 2 | 255 | 0.67 | 0.83 | 38 | GNP, MG |
| 3 | 129 | 0.49 | 0.80 | 19 | empty |
| 4 | 228 | 0.45 | 0.74 | 18 | empty |
| 5 | 108 | 0.45 | 0.79 | 19 | empty |
Interfaces
3 interfaces between chains.
- A–B · 2031 Ų buried · 38 hydrogen bonds · protein-protein
- A–P · 854 Ų buried · 28 hydrogen bonds · protein-nucleic
- B–P · 750 Ų buried · 20 hydrogen bonds · protein-nucleic
Modifications
Observed in the structure: 1 modified (nucleotide modification).
Compared structures
- 5AXN · Crystal structure of Thg1 like protein (TLP) with tRNA(Phe) and GDPNP · 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 5AXN · PDBe 5AXN
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