Research workbench
Structure of sulfolobus solfataricus trxr-B3
Analyse Structure of sulfolobus solfataricus trxr-B3 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3F8P
- Type
- protein
- Length
- 1,231 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Thioredoxin reductase (trxb-3)
- EC
- 1.6.4.5
- UniProt
- Q97W27
- Ligands
- NAD, SO4
- Pockets
- 12 · best druggability 0.81
Structure
x-ray diffraction · 4 distinct chains · 28% helix, 29% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Thioredoxin reductase (trxb-3) (EC 1.6.4.5) | protein | 307 | 28% helix, 30% strand | Q97W27 |
| B | Thioredoxin reductase (trxb-3) (EC 1.6.4.5) | protein | 306 | 27% helix, 29% strand | Q97W27 |
| C | Thioredoxin reductase (trxb-3) (EC 1.6.4.5) | protein | 308 | 28% helix, 30% strand | Q97W27 |
| D | Thioredoxin reductase (trxb-3) (EC 1.6.4.5) | protein | 310 | 27% helix, 29% strand | Q97W27 |
Ligands and binding sites
- NAD · Nicotinamide-adenine-dinucleotide · ligand · 4 copies · chains A, B, C, D
- SO4 · Sulfate ion · ion · 6 copies · chains A, B, D
- ACY · Acetic acid · additive · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
12 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 676 | 0.81 | 0.85 | 85 | NAD |
| 2 | 1002 | 0.80 | 0.82 | 113 | NAD, SO4 |
| 3 | 885 | 0.80 | 0.82 | 98 | ACY, NAD, SO4 |
| 4 | 814 | 0.79 | 0.83 | 85 | NAD |
| 5 | 77 | 0.45 | 0.81 | 16 | empty |
Interfaces
2 interfaces between chains.
- C–D · 2573 Ų buried · 34 hydrogen bonds · protein-protein
- A–B · 2565 Ų buried · 35 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 disulfide (disulfide).
Compared structures
- 3F8P · Structure of Sulfolobus solfataricus TrxR-B3 · the same entry in another collection · chain A 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 Q97W27
- Elsewhere: RCSB PDB 3F8P · PDBe 3F8P · UniProt Q97W27
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