Research workbench
High resolution structure of thioredoxin-disulfide reductase from vibrio vulnificus CMCP6 in complex with NADP and FAD
Analyse High resolution structure of thioredoxin-disulfide reductase from vibrio… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5VT3
- Type
- protein
- Length
- 632 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Thioredoxin reductase
- EC
- 1.8.1.9
- UniProt
- A0A1L9L8C0
- Ligands
- NAP, FAD, K
- Pockets
- 3 · best druggability 0.83
Structure
x-ray diffraction · 2 distinct chains · 30% helix, 28% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Thioredoxin reductase (EC 1.8.1.9) | protein | 313 | 30% helix, 28% strand | A0A1L9L8C0 |
| B | Thioredoxin reductase (EC 1.8.1.9) | protein | 319 | 30% helix, 28% strand | A0A1L9L8C0 |
Ligands and binding sites
- NAP · Nadp nicotinamide-adenine-dinucleotide phosphate · ligand · 2 copies · chains A, B
- FAD · Flavin-adenine dinucleotide · ligand · 2 copies · chains A, B
- K · Potassium ion · metal · 2 copies · chains A, B
- CAC · Cacodylate ion · additive · 2 copies · chains A, B
- GOL · Glycerol · additive · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 207 | 0.83 | 0.97 | 40 | GOL |
| 2 | 1031 | 0.81 | 0.82 | 107 | NAP, FAD, K |
| 3 | 944 | 0.80 | 0.82 | 91 | NAP, FAD, K |
Interfaces
1 interface between chains.
- A–B · 2275 Ų buried · 46 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 disulfide (disulfide).
Compared structures
- 5VT3 · High resolution structure of thioredoxin-disulfide reductase from Vibrio vulnificus CMCP6… · 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 A0A1L9L8C0
- Elsewhere: RCSB PDB 5VT3 · PDBe 5VT3 · UniProt A0A1L9L8C0
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