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The crystal structure of Y334C mutant of human sepsecs in complex with selenocysteine tRNA (trnasec)
Analyse The crystal structure of Y334C mutant of human sepsecs in complex with… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4ZDP
- Type
- protein + RNA
- Length
- 1,847 residues
- Chains
- 5
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- O-phosphoseryl-TRNA(SEC) selenium transferase; Selenocysteine tRNA
- EC
- 2.9.1.2
- UniProt
- Q9HD40
- Ligands
- PLR, PO4
- Pockets
- 16 · best druggability 0.72
Structure
x-ray diffraction · 3 distinct chains · 45% helix, 15% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | O-phosphoseryl-TRNA(SEC) selenium transferase (EC 2.9.1.2) | protein | 444 | 45% helix, 15% strand | Q9HD40 |
| B, C, D | O-phosphoseryl-TRNA(SEC) selenium transferase (EC 2.9.1.2) | protein | 443 | 45% helix, 15% strand | Q9HD40 |
| E | Selenocysteine tRNA | rna | 74 | — | — |
Ligands and binding sites
- PLR · (5-hydroxy-4,6-dimethylpyridin-3-yl)methyl dihydrogen phosphate · ligand · 4 copies · chains A, B, C, D
- PO4 · Phosphate ion · ion · 4 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
16 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 939 | 0.72 | 0.77 | 45 | empty |
| 2 | 669 | 0.68 | 0.77 | 45 | empty |
| 3 | 310 | 0.59 | 0.77 | 43 | PLR |
| 4 | 295 | 0.59 | 0.78 | 43 | PLR |
| 5 | 366 | 0.59 | 0.76 | 34 | empty |
Interfaces
6 interfaces between chains.
- A–E · 574 Ų buried · 3 hydrogen bonds · protein-nucleic
- C–E · 415 Ų buried · 6 hydrogen bonds · protein-nucleic
- B–E · 294 Ų buried · 5 hydrogen bonds · protein-nucleic
- D–E · 142 Ų buried · 3 hydrogen bonds · protein-nucleic
- A–B · 125 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 covalent (covalent ligand).
Compared structures
- 4ZDP · The crystal structure of Y334C mutant of human SepSecS in complex with selenocysteine… · the same entry in another collection · chain B against B, 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 B 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 4ZDP · PDBe 4ZDP · UniProt Q9HD40
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