Research workbench
The crystal structure of the T325S mutant of the human holo sepsecs
Analyse The crystal structure of the T325S mutant of the human holo sepsecs in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4ZDL
- Type
- protein
- Length
- 888 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- O-phosphoseryl-TRNA(SEC) selenium transferase
- EC
- 2.9.1.2
- UniProt
- Q9HD40
- Ligands
- PLR
- Pockets
- 4 · best druggability 0.58
Structure
x-ray diffraction · 1 distinct chain · 45% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | O-phosphoseryl-TRNA(SEC) selenium transferase (EC 2.9.1.2) | protein | 444 | 45% helix, 16% strand | Q9HD40 |
Ligands and binding sites
- PLR · (5-hydroxy-4,6-dimethylpyridin-3-yl)methyl dihydrogen phosphate · ligand · 2 copies · chains A, B
- FLC · Citrate anion · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 300 | 0.58 | 0.77 | 49 | PLR |
| 2 | 279 | 0.57 | 0.78 | 48 | PLR |
| 3 | 88 | 0.40 | 0.77 | 19 | empty |
| 4 | 73 | 0.35 | 0.76 | 16 | empty |
Interfaces
1 interface between chains.
- A–B · 199 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 covalent (covalent ligand).
Compared structures
- 4ZDL · The crystal structure of the T325S mutant of the human holo SepSecS · the same entry in another collection · chain A against A, TM-score 1.00
- Q9HD40 · 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 1.00
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 Q9HD40
- Elsewhere: RCSB PDB 4ZDL · PDBe 4ZDL · UniProt Q9HD40
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