MolNFT v1 · #165583 · protein
Crystal structure of fungal RNA kinase
6U00 · TRNA ligase: “Crystal structure of fungal RNA kinase”. X-ray diffraction, 1 ligand (PO4), 3 pockets (best druggability 0.68). MolNFT v1 #165583 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 6U00
- Type
- protein
- Length
- 421 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- TRNA ligase
- EC
- 6.5.1.3
- UniProt
- P43075
- Ligands
- PO4
- Pockets
- 3 · best druggability 0.68
Structure
x-ray diffraction · 2 distinct chains · 45% helix, 14% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | TRNA ligase (EC 6.5.1.3) | protein | 211 | 45% helix, 14% strand | P43075 |
| B | TRNA ligase (EC 6.5.1.3) | protein | 210 | 46% helix, 14% strand | P43075 |
Ligands and binding sites
- PO4 · Phosphate 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, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 462 | 0.68 | 0.80 | 58 | empty |
| 2 | 115 | 0.36 | 0.74 | 22 | PO4 |
| 3 | 67 | 0.27 | 0.72 | 20 | PO4 |
Interfaces
1 interface between chains.
- A–B · 557 Ų buried · 5 hydrogen bonds · protein-protein
Compared structures
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 P43075
- Elsewhere: RCSB PDB 6U00 · PDBe 6U00 · UniProt P43075
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