Research workbench
Crystal structure of pyridine nucleotide disulfide oxidoreductase from pyrococcus horikoshii
Analyse Crystal structure of pyridine nucleotide disulfide oxidoreductase from… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3KD9
- Type
- protein
- Length
- 1,254 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Coenzyme a disulfide reductase
- EC
- 1.8.1.14
- UniProt
- O58308
- Pockets
- 11 · best druggability 0.76
Structure
x-ray diffraction · 1 distinct chain · 25% helix, 31% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C | Coenzyme a disulfide reductase (EC 1.8.1.14) | protein | 418 | 25% helix, 31% strand | O58308 |
Ligands and binding sites
- GOL · Glycerol · additive · chains A, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
11 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1107 | 0.76 | 0.78 | 110 | empty |
| 2 | 1184 | 0.76 | 0.78 | 112 | empty |
| 3 | 897 | 0.70 | 0.76 | 91 | empty |
| 4 | 196 | 0.51 | 0.77 | 21 | empty |
| 5 | 125 | 0.47 | 0.79 | 26 | empty |
Interfaces
2 interfaces between chains.
- A–B · 2387 Ų buried · 18 hydrogen bonds · protein-protein
- A–C · 664 Ų buried · 18 hydrogen bonds · protein-protein
Compared structures
- 3KD9 · Crystal structure of pyridine nucleotide disulfide oxidoreductase from Pyrococcus… · the same entry in another collection · chain A against A, TM-score 1.00
- O58308 · AlphaFold monomer V2.0 prediction for NAD(P)H coenzyme a POLYSULFIDE/PERSULFIDE reductase… · a predicted model of the same protein · chain A 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 O58308
- Elsewhere: RCSB PDB 3KD9 · PDBe 3KD9 · UniProt O58308
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