Research workbench
Structural and biochemical identification of a novel bacterial oxidoreductase
Analyse Structural and biochemical identification of a novel bacterial oxidoreductase in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1XDQ
- Type
- protein
- Length
- 1,313 residues
- Chains
- 5
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Bacterial sulfite oxidase
- UniProt
- P76342
- Ligands
- URE, MTE, MO, O
- Pockets
- 14 · best druggability 0.78
Structure
x-ray diffraction · 3 distinct chains · 25% helix, 27% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, D, E | Bacterial sulfite oxidase | protein | 262 | 24% helix, 27% strand | P76342 |
| B | Bacterial sulfite oxidase | protein | 263 | 25% helix, 27% strand | P76342 |
| C | Bacterial sulfite oxidase | protein | 264 | 25% helix, 27% strand | P76342 |
Ligands and binding sites
- URE · Urea · ligand · 5 copies · chains A, B, C, D, E
- 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 · 5 copies · chains A, B, C, D, E
- MO · Molybdenum atom · metal · 5 copies · chains A, B, C, D, E
- O · Oxygen atom · ion · 5 copies · chains A, B, C, D, E
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
14 pockets found on a 1 Å grid, 10 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 164 | 0.78 | 0.94 | 27 | URE, MO, O, MTE |
| 2 | 165 | 0.77 | 0.93 | 28 | URE, MO, O, MTE |
| 3 | 172 | 0.77 | 0.93 | 28 | URE, MO, O, MTE |
| 4 | 165 | 0.77 | 0.93 | 31 | URE, MO, O, MTE |
| 5 | 153 | 0.76 | 0.93 | 29 | URE, MO, O, MTE |
Interfaces
5 interfaces between chains.
- A–C · 595 Ų buried · 6 hydrogen bonds · protein-protein
- C–E · 588 Ų buried · 6 hydrogen bonds · protein-protein
- B–E · 580 Ų buried · 5 hydrogen bonds · protein-protein
- B–D · 578 Ų buried · 7 hydrogen bonds · protein-protein
- A–D · 565 Ų buried · 6 hydrogen bonds · protein-protein
Compared structures
- 1XDQ · Structural and Biochemical Identification of a Novel Bacterial Oxidoreductase · the same entry in another collection · chain E against E, 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 1XDQ · PDBe 1XDQ · UniProt P76342
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