MolNFT v1 · #50312 · protein
Crystal structure of oxidoreductase dsba from xylella fastidiosa
2REM · Disulfide oxidoreductase: “Crystal structure of oxidoreductase dsba from xylella fastidiosa”. X-ray diffraction, 6 pockets (best druggability 0.69). MolNFT v1 #50312 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 2REM
- Type
- protein
- Length
- 576 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Disulfide oxidoreductase; 8 residue peptide
- EC
- 1.8.4.2
- UniProt
- Q9PDE3
- Pockets
- 6 · best druggability 0.69
Structure
x-ray diffraction · 4 distinct chains · 50% helix, 14% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Disulfide oxidoreductase (EC 1.8.4.2) | protein | 190 | 51% helix, 13% strand | Q9PDE3 |
| B | Disulfide oxidoreductase (EC 1.8.4.2) | protein | 187 | 50% helix, 13% strand | Q9PDE3 |
| C | Disulfide oxidoreductase (EC 1.8.4.2) | protein | 191 | 50% helix, 14% strand | Q9PDE3 |
| T | 8 residue peptide | protein | 8 | 0% helix, 25% strand | — |
Pockets
6 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 714 | 0.69 | 0.76 | 58 | empty |
| 2 | 502 | 0.62 | 0.75 | 50 | empty |
| 3 | 95 | 0.52 | 0.83 | 15 | empty |
| 4 | 141 | 0.45 | 0.76 | 20 | empty |
| 5 | 63 | 0.40 | 0.80 | 19 | empty |
Interfaces
3 interfaces between chains.
- A–B · 589 Ų buried · 6 hydrogen bonds · protein-protein
- C–T · 424 Ų buried · 7 hydrogen bonds · protein-protein
- A–C · 386 Ų buried · 5 hydrogen bonds · protein-protein
Compared structures
- 2REM · Crystal Structure of oxidoreductase DsbA from Xylella fastidiosa · 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 Q9PDE3
- Elsewhere: RCSB PDB 2REM · PDBe 2REM · UniProt Q9PDE3
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