Research workbench
Crystal structure of the selenocysteine synthase sela from aquifex aeolicus
Analyse Crystal structure of the selenocysteine synthase sela from aquifex aeolicus in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3W1H
- Type
- protein
- Length
- 2,141 residues
- Chains
- 5
- 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
- Pockets
- 20 · best druggability 0.59
Structure
x-ray diffraction · 4 distinct chains · 40% helix, 19% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C | L-seryl-TRNA(SEC) selenium transferase (EC 2.9.1.1) | protein | 452 | 41% helix, 17% strand | O67140 |
| B | L-seryl-TRNA(SEC) selenium transferase (EC 2.9.1.1) | protein | 443 | 42% helix, 18% strand | O67140 |
| D | L-seryl-TRNA(SEC) selenium transferase (EC 2.9.1.1) | protein | 395 | 38% helix, 21% strand | O67140 |
| E | L-seryl-TRNA(SEC) selenium transferase (EC 2.9.1.1) | protein | 399 | 37% helix, 21% strand | O67140 |
Pockets
20 pockets found on a 1 Å grid, 12 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 362 | 0.59 | 0.76 | 49 | empty |
| 2 | 313 | 0.59 | 0.77 | 40 | empty |
| 3 | 273 | 0.58 | 0.78 | 37 | empty |
| 4 | 273 | 0.57 | 0.77 | 40 | empty |
| 5 | 165 | 0.56 | 0.81 | 24 | empty |
Interfaces
4 interfaces between chains.
- A–B · 4249 Ų buried · 85 hydrogen bonds · protein-protein
- C–D · 4041 Ų buried · 71 hydrogen bonds · protein-protein
- B–C · 1213 Ų buried · 32 hydrogen bonds · protein-protein
- D–E · 1194 Ų buried · 33 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 5 modified (cofactor).
Compared structures
- 3W1H · Crystal structure of the selenocysteine synthase SelA from Aquifex aeolicus · the same entry in another collection · chain E against E, 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 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 O67140
- Elsewhere: RCSB PDB 3W1H · PDBe 3W1H · UniProt O67140
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