MolNFT v1 · #82910 · protein + RNA
Crystal structure of the selenocysteine synthase sela and trnasec complex
3W1K · L-seryl-TRNA(SEC) selenium transferase: “Crystal structure of the selenocysteine synthase sela and trnasec complex”. X-ray diffraction, 20 pockets (best druggability 0.75). MolNFT v1 #82910 on GenesisL1: 3D structure, binding sites…
- PDB
- 3W1K
- Type
- protein + RNA
- Length
- 2,720 residues
- Chains
- 10
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- L-seryl-TRNA(SEC) selenium transferase; Selenocysteine tRNA
- EC
- 2.9.1.1
- UniProt
- O67140
- Pockets
- 20 · best druggability 0.75
Structure
x-ray diffraction · 2 distinct chains · 40% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D, E | L-seryl-TRNA(SEC) selenium transferase (EC 2.9.1.1) | protein | 452 | 40% helix, 17% strand | O67140 |
| F, G, H, I, J | Selenocysteine tRNA | rna | 92 | — | — |
Pockets
20 pockets found on a 1 Å grid, 20 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 93 | 0.75 | 0.96 | 24 | empty |
| 2 | 777 | 0.75 | 0.81 | 44 | empty |
| 3 | 1056 | 0.74 | 0.78 | 58 | empty |
| 4 | 1048 | 0.74 | 0.78 | 58 | empty |
| 5 | 1031 | 0.74 | 0.78 | 55 | empty |
Interfaces
17 interfaces between chains.
- C–D · 4273 Ų buried · 74 hydrogen bonds · protein-protein
- A–B · 4218 Ų buried · 78 hydrogen bonds · protein-protein
- D–E · 1208 Ų buried · 32 hydrogen bonds · protein-protein
- B–C · 1204 Ų buried · 34 hydrogen bonds · protein-protein
- D–H · 677 Ų buried · 17 hydrogen bonds · protein-nucleic
Modifications
Observed in the structure: 5 modified (cofactor).
Compared structures
- 3W1K · Crystal structure of the selenocysteine synthase SelA and tRNASec complex · the same entry in another collection · chain J against J, TM-score 1.00
- O67140 · AlphaFold monomer V2.0 prediction for L-seryl-TRNA(SEC) selenium transferase (O67140) · a predicted model of the same protein · chain A against A, TM-score 0.97
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 O67140
- Elsewhere: RCSB PDB 3W1K · PDBe 3W1K · UniProt O67140
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