Research workbench
Crystal structure of O-phosphoseryl-tRNA kinase complexed with selenocysteine tRNA and amppnp (crystal type 3)
Analyse Crystal structure of O-phosphoseryl-tRNA kinase complexed with selenocysteine… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3ADD
- Type
- protein + RNA
- Length
- 666 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
- Pockets
- 11 · best druggability 0.73
Structure
x-ray diffraction · 4 distinct chains · 55% helix, 11% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | L-seryl-TRNA(SEC) kinase (EC 2.7.1.-) | protein | 251 | 54% helix, 10% strand | Q58933 |
| B | L-seryl-TRNA(SEC) kinase (EC 2.7.1.-) | protein | 239 | 56% helix, 11% strand | Q58933 |
| C | Selenocysteine tRNA | rna | 88 | — | — |
| D | Selenocysteine tRNA | rna | 88 | — | — |
Ligands and binding sites
- ANP · Phosphoaminophosphonic acid-adenylate ester · ligand · 2 copies · chains A, B
- MG · Magnesium ion · metal · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
11 pockets found on a 1 Å grid, 9 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 716 | 0.73 | 0.80 | 43 | empty |
| 2 | 504 | 0.71 | 0.81 | 42 | MG |
| 3 | 620 | 0.67 | 0.77 | 66 | ANP, MG |
| 4 | 787 | 0.66 | 0.75 | 45 | empty |
| 5 | 475 | 0.65 | 0.78 | 37 | empty |
Interfaces
3 interfaces between chains.
- A–C · 1592 Ų buried · 22 hydrogen bonds · protein-nucleic
- B–D · 1347 Ų buried · 36 hydrogen bonds · protein-nucleic
- A–B · 1154 Ų buried · 11 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 8 modified (engineered).
Compared structures
- 3ADD · 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 0.77
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 3ADD · PDBe 3ADD · UniProt Q58933
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