Research workbench
Crystal structure of the N-terminal truncated selenocysteine synthase sela
Analyse Crystal structure of the N-terminal truncated selenocysteine synthase sela in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3W1I
- Type
- protein
- Length
- 3,901 residues
- Chains
- 10
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- L-seryl-TRNA(SEC) selenium transferase
- EC
- 2.9.1.1
- UniProt
- O67140
- Ligands
- K, PT
- Pockets
- 20 · best druggability 0.65
Structure
x-ray diffraction · 5 distinct chains · 38% helix, 23% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C, F | L-seryl-TRNA(SEC) selenium transferase (EC 2.9.1.1) | protein | 392 | 37% helix, 22% strand | O67140 |
| B | L-seryl-TRNA(SEC) selenium transferase (EC 2.9.1.1) | protein | 388 | 39% helix, 23% strand | O67140 |
| D, G, I, J | L-seryl-TRNA(SEC) selenium transferase (EC 2.9.1.1) | protein | 389 | 39% helix, 23% strand | O67140 |
| E | L-seryl-TRNA(SEC) selenium transferase (EC 2.9.1.1) | protein | 391 | 38% helix, 22% strand | O67140 |
| H | L-seryl-TRNA(SEC) selenium transferase (EC 2.9.1.1) | protein | 390 | 38% helix, 24% strand | O67140 |
Ligands and binding sites
- K · Potassium ion · metal · 5 copies · chains A, B, C, D, E, F, G, H, I, J
- PT · Platinum (II) ion · metal · 2 copies · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
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 | 518 | 0.65 | 0.77 | 62 | empty |
| 2 | 462 | 0.65 | 0.78 | 58 | empty |
| 3 | 439 | 0.63 | 0.77 | 59 | empty |
| 4 | 337 | 0.62 | 0.78 | 59 | empty |
| 5 | 293 | 0.59 | 0.78 | 39 | empty |
Interfaces
11 interfaces between chains.
- E–F · 4136 Ų buried · 65 hydrogen bonds · protein-protein
- G–H · 4120 Ų buried · 77 hydrogen bonds · protein-protein
- C–D · 4021 Ų buried · 65 hydrogen bonds · protein-protein
- A–B · 4013 Ų buried · 67 hydrogen bonds · protein-protein
- I–J · 3932 Ų buried · 70 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 83 modified (engineered, cofactor).
Compared structures
- 3W1I · Crystal structure of the N-terminal truncated selenocysteine synthase SelA · 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 D 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 O67140
- Elsewhere: RCSB PDB 3W1I · PDBe 3W1I · UniProt O67140
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