MolNFT v1 · #66258 · protein + RNA
The crystal structure of the human sepsecs-trnasec complex
3HL2 · O-phosphoseryl-TRNA(SEC) selenium transferase: “The crystal structure of the human sepsecs-trnasec complex”. X-ray diffraction, 3 ligands (PLR, SEP, TS6), 20 pockets (best druggability 0.70). MolNFT v1 #66258 on GenesisL1: 3D…
- PDB
- 3HL2
- Type
- protein + RNA
- Length
- 1,852 residues
- Chains
- 5
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- O-phosphoseryl-TRNA(SEC) selenium transferase; Trnasec
- EC
- 2.9.1.1
- UniProt
- Q9HD40
- Ligands
- PLR, SEP, TS6
- Pockets
- 20 · best druggability 0.70
Structure
x-ray diffraction · 4 distinct chains · 46% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, D | O-phosphoseryl-TRNA(SEC) selenium transferase (EC 2.9.1.1) | protein | 441 | 46% helix, 16% strand | Q9HD40 |
| B | O-phosphoseryl-TRNA(SEC) selenium transferase (EC 2.9.1.1) | protein | 443 | 45% helix, 16% strand | Q9HD40 |
| C | O-phosphoseryl-TRNA(SEC) selenium transferase (EC 2.9.1.1) | protein | 445 | 46% helix, 15% strand | Q9HD40 |
| E | Trnasec | rna | 82 | — | — |
Ligands and binding sites
- PLR · (5-hydroxy-4,6-dimethylpyridin-3-yl)methyl dihydrogen phosphate · ligand · 4 copies · chains A, B, C, D
- SEP · Phosphoserine · ligand · 4 copies · chains B, D
- TS6 · Monothiophosphate · ligand · 3 copies · chains A, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 531 | 0.70 | 0.80 | 33 | empty |
| 2 | 424 | 0.69 | 0.81 | 45 | empty |
| 3 | 290 | 0.59 | 0.79 | 24 | empty |
| 4 | 284 | 0.59 | 0.78 | 45 | PLR |
| 5 | 225 | 0.55 | 0.79 | 23 | empty |
Interfaces
6 interfaces between chains.
- A–E · 643 Ų buried · 16 hydrogen bonds · protein-nucleic
- C–E · 524 Ų buried · 5 hydrogen bonds · protein-nucleic
- B–E · 410 Ų buried · 13 hydrogen bonds · protein-nucleic
- A–B · 154 Ų buried · 1 hydrogen bond · protein-protein
- C–D · 133 Ų buried · 5 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 covalent (covalent ligand).
Compared structures
- 3HL2 · The crystal structure of the human SepSecS-tRNASec complex · the same entry in another collection · chain E against E, 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 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 Q9HD40
- Elsewhere: RCSB PDB 3HL2 · PDBe 3HL2 · UniProt Q9HD40
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