MolNFT v1 · #57615 · protein + RNA
Crystal structure of O-phosphoseryl-tRNA kinase complexed with selenocysteine tRNA and amppnp (crystal type 1)
3ADB · L-seryl-TRNA(SEC) kinase: “Crystal structure of O-phosphoseryl-tRNA kinase complexed with selenocysteine tRNA and amppnp (crystal type 1)”. X-ray diffraction, 3 ligands (ANP, MG, PO4), 11 pockets (best druggability 0.76). MolNFT v1…
- PDB
- 3ADB
- Type
- protein + RNA
- Length
- 681 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- L-seryl-TRNA(SEC) kinase; Selenocysteine tRNA
- EC
- 2.7.1.-
- UniProt
- Q58933
- Ligands
- ANP, MG, PO4
- Pockets
- 11 · best druggability 0.76
Structure
x-ray diffraction · 3 distinct chains · 55% helix, 10% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | L-seryl-TRNA(SEC) kinase (EC 2.7.1.-) | protein | 250 | 55% helix, 10% strand | Q58933 |
| B | L-seryl-TRNA(SEC) kinase (EC 2.7.1.-) | protein | 247 | 55% helix, 10% strand | Q58933 |
| C, D | Selenocysteine tRNA | rna | 92 | — | — |
Ligands and binding sites
- ANP · Phosphoaminophosphonic acid-adenylate ester · ligand · chains B
- MG · Magnesium ion · metal · chains B
- PO4 · Phosphate ion · ion · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
11 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1111 | 0.76 | 0.79 | 59 | empty |
| 2 | 730 | 0.73 | 0.80 | 46 | empty |
| 3 | 469 | 0.73 | 0.82 | 43 | PO4 |
| 4 | 329 | 0.66 | 0.81 | 40 | ANP, MG |
| 5 | 500 | 0.66 | 0.78 | 39 | empty |
Interfaces
3 interfaces between chains.
- B–D · 1757 Ų buried · 52 hydrogen bonds · protein-nucleic
- A–C · 1628 Ų buried · 27 hydrogen bonds · protein-nucleic
- A–B · 1157 Ų buried · 10 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 9 modified (engineered).
Compared structures
- 3ADB · Crystal structure of O-phosphoseryl-tRNA kinase complexed with selenocysteine tRNA and… · 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 B 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 3ADB · PDBe 3ADB · UniProt Q58933
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