MolNFT v1 · #27244 · protein
Structural and biochemical identification of a novel bacterial oxidoreductase, W-containing cofactor
1XDY · Bacterial sulfite oxidase: “Structural and biochemical identification of a novel bacterial oxidoreductase, W-containing cofactor”. X-ray diffraction, 2 ligands (MTE, W), 20 pockets (best druggability 0.81). MolNFT v1 #27244 on…
- PDB
- 1XDY
- Type
- protein
- Length
- 2,625 residues
- Chains
- 10
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Bacterial sulfite oxidase
- UniProt
- P76342
- Ligands
- MTE, W
- Pockets
- 20 · best druggability 0.81
Structure
x-ray diffraction · 7 distinct chains · 23% helix, 27% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Bacterial sulfite oxidase | protein | 263 | 24% helix, 28% strand | P76342 |
| B | Bacterial sulfite oxidase | protein | 262 | 23% helix, 28% strand | P76342 |
| C, H | Bacterial sulfite oxidase | protein | 264 | 24% helix, 28% strand | P76342 |
| D | Bacterial sulfite oxidase | protein | 263 | 23% helix, 27% strand | P76342 |
| E, I, J | Bacterial sulfite oxidase | protein | 262 | 24% helix, 27% strand | P76342 |
| F | Bacterial sulfite oxidase | protein | 262 | 23% helix, 27% strand | P76342 |
| G | Bacterial sulfite oxidase | protein | 261 | 23% helix, 28% strand | P76342 |
Ligands and binding sites
- MTE · Phosphonic acidmono-(2-amino-5,6-dimercapto-4-oxo-3,7,8A,9,10,10A-hexahydro-4H-8-oxa-1,3,9,10-tetraaza-anthracen-7-ylmethyl)ester · ligand · 10 copies · chains A, B, C, D, E, F, G, H, I, J
- W · Tungsten ion · metal · 10 copies · chains A, B, C, D, E, F, G, H, I, J
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 20 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 179 | 0.81 | 0.95 | 37 | W, MTE |
| 2 | 167 | 0.80 | 0.95 | 30 | W, MTE |
| 3 | 158 | 0.80 | 0.96 | 27 | W, MTE |
| 4 | 166 | 0.80 | 0.95 | 30 | W, MTE |
| 5 | 159 | 0.80 | 0.95 | 30 | W, MTE |
Interfaces
12 interfaces between chains.
- F–H · 661 Ų buried · 9 hydrogen bonds · protein-protein
- B–E · 627 Ų buried · 5 hydrogen bonds · protein-protein
- G–J · 623 Ų buried · 5 hydrogen bonds · protein-protein
- A–D · 605 Ų buried · 6 hydrogen bonds · protein-protein
- A–C · 599 Ų buried · 7 hydrogen bonds · protein-protein
Compared structures
- 1XDY · Structural and Biochemical Identification of a Novel Bacterial Oxidoreductase… · the same entry in another collection · chain J against J, TM-score 1.00
- P76342 · AlphaFold monomer V2.0 prediction for protein-methionine-sulfoxide reductase catalytic… · a predicted model of the same protein · 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 P76342
- Elsewhere: RCSB PDB 1XDY · PDBe 1XDY · UniProt P76342
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