Research workbench
Carbon Sulfoxide lyase
Analyse Carbon Sulfoxide lyase in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 8IRK
- Type
- protein
- Length
- 1,500 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 2.35
- Source
- Mycolicibacterium smegmatis MC2 155
- Molecule
- Probable hercynylcysteine sulfoxide lyase
- EC
- 4.4.-.-
- UniProt
- A0R5M7
- Ligands
- PLP, PYR
- Pockets
- 12 · best druggability 0.84
Structure
x-ray diffraction · resolution 2.35 · 4 distinct chains · 43% helix, 15% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Probable hercynylcysteine sulfoxide lyase (EC 4.4.-.-) | protein | 379 | 43% helix, 15% strand | A0R5M7 |
| B | Probable hercynylcysteine sulfoxide lyase (EC 4.4.-.-) | protein | 373 | 43% helix, 15% strand | A0R5M7 |
| C | Probable hercynylcysteine sulfoxide lyase (EC 4.4.-.-) | protein | 376 | 43% helix, 14% strand | A0R5M7 |
| D | Probable hercynylcysteine sulfoxide lyase (EC 4.4.-.-) | protein | 372 | 43% helix, 15% strand | A0R5M7 |
Ligands and binding sites
- PLP · Pyridoxal-5'-phosphate · ligand · 4 copies · chains A, C, B, D
- PYR · Pyruvic acid · ligand · chains A, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
12 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 887 | 0.84 | 0.86 | 105 | PLP |
| 2 | 1140 | 0.83 | 0.84 | 136 | PLP, PYR |
| 3 | 466 | 0.68 | 0.80 | 60 | empty |
| 4 | 51 | 0.68 | 0.97 | 25 | empty |
| 5 | 73 | 0.51 | 0.85 | 18 | empty |
Interfaces
4 interfaces between chains.
- A–C · 2209 Ų buried · 27 hydrogen bonds · protein-protein
- B–D · 2134 Ų buried · 26 hydrogen bonds · protein-protein
- A–B · 659 Ų buried · 6 hydrogen bonds · protein-protein
- B–C · 78 Ų buried · 3 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 cofactor (pyridoxal phosphate Schiff base).
Compared structures
- A0R5M7 · AlphaFold monomer V2.0 prediction for probable hercynylcysteine sulfoxide lyase (A0R5M7) · a predicted model of the same protein · chain D 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 A0R5M7
- Elsewhere: RCSB PDB 8IRK · PDBe 8IRK · UniProt A0R5M7
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