MolNFT v1 · #57891 · protein + RNA
Crystal structure of O-phosphoseryl-tRNA kinase complexed with anticodon-STEM/LOOP truncated TRNA(SEC)
3AM1 · L-seryl-TRNA(SEC) kinase: “Crystal structure of O-phosphoseryl-tRNA kinase complexed with anticodon-STEM/LOOP truncated TRNA(SEC)”. X-ray diffraction, 2 ligands (ATP, MG), 5 pockets (best druggability 0.75). MolNFT v1 #57891 on…
- PDB
- 3AM1
- Type
- protein + RNA
- Length
- 317 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- L-seryl-TRNA(SEC) kinase; Asl-truncated tRNA
- EC
- 2.7.1.164
- UniProt
- Q58933
- Ligands
- ATP, MG
- Pockets
- 5 · best druggability 0.75
Structure
x-ray diffraction · 2 distinct chains · 57% helix, 11% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | L-seryl-TRNA(SEC) kinase (EC 2.7.1.164) | protein | 236 | 57% helix, 11% strand | Q58933 |
| B | Asl-truncated tRNA | rna | 81 | — | — |
Ligands and binding sites
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 975 | 0.75 | 0.79 | 46 | empty |
| 2 | 388 | 0.62 | 0.77 | 46 | empty |
| 3 | 92 | 0.46 | 0.80 | 18 | empty |
| 4 | 143 | 0.43 | 0.76 | 21 | empty |
| 5 | 107 | 0.39 | 0.75 | 23 | empty |
Interfaces
1 interface between chains.
- A–B · 1305 Ų buried · 39 hydrogen bonds · protein-nucleic
Compared structures
- 3AM1 · Crystal structure of O-Phosphoseryl-tRNA kinase complexed with anticodon-stem/loop… · the same entry in another collection · chain A against A, TM-score 1.00
- Q58933 · AlphaFold monomer V2.0 prediction for L-seryl-TRNA(SEC) kinase (Q58933) · a predicted model of the same protein · chain A against A, TM-score 0.75
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 Q58933
- Elsewhere: RCSB PDB 3AM1 · PDBe 3AM1 · UniProt Q58933
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