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Crystal structure of archaeal O-phosphoseryl-TRNA(SEC) selenium transferase (sepsecs)
Analyse Crystal structure of archaeal O-phosphoseryl-TRNA(SEC) selenium transferase… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2Z67
- Type
- protein
- Length
- 1,736 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- O-phosphoseryl-TRNA(SEC) selenium transferase
- EC
- 2.9.1.-
- UniProt
- Q6LZM9
- Ligands
- PLP, SO4
- Pockets
- 14 · best druggability 0.85
Structure
x-ray diffraction · 1 distinct chain · 47% helix, 15% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | O-phosphoseryl-TRNA(SEC) selenium transferase (EC 2.9.1.-) | protein | 434 | 47% helix, 15% strand | Q6LZM9 |
Ligands and binding sites
- PLP · Pyridoxal-5'-phosphate · ligand · 4 copies · chains A, B, C, D
- SO4 · Sulfate ion · ion · 2 copies · chains B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
14 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1185 | 0.85 | 0.85 | 91 | empty |
| 2 | 516 | 0.72 | 0.81 | 47 | SO4, PLP |
| 3 | 608 | 0.71 | 0.79 | 49 | PLP |
| 4 | 484 | 0.70 | 0.80 | 52 | PLP |
| 5 | 468 | 0.67 | 0.79 | 32 | SO4 |
Interfaces
6 interfaces between chains.
- A–B · 4086 Ų buried · 55 hydrogen bonds · protein-protein
- C–D · 4052 Ų buried · 56 hydrogen bonds · protein-protein
- B–C · 2267 Ų buried · 16 hydrogen bonds · protein-protein
- A–D · 2162 Ų buried · 17 hydrogen bonds · protein-protein
- A–C · 406 Ų buried · 1 hydrogen bond · protein-protein
Modifications
Observed in the structure: 40 modified, 4 cofactor (engineered, pyridoxal phosphate Schiff base).
Compared structures
- 2Z67 · Crystal structure of archaeal O-phosphoseryl-tRNA(Sec) selenium transferase (SepSecS) · the same entry in another collection · chain A against A, TM-score 1.00
- Q6LZM9 · AlphaFold monomer V2.0 prediction for O-phosphoseryl-TRNA(SEC) selenium transferase… · a predicted model of the same protein · chain A against A, TM-score 0.99
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 Q6LZM9
- Elsewhere: RCSB PDB 2Z67 · PDBe 2Z67 · UniProt Q6LZM9
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