Research workbench
Crystal structure of the plp-bound C-S lyase from staphylococcus hominis
Analyse Crystal structure of the plp-bound C-S lyase from staphylococcus hominis in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6QP2
- Type
- protein
- Length
- 780 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Aminotransferase; Polyhistidine tag
- Ligands
- PLP
- Pockets
- 11 · best druggability 0.79
Structure
x-ray diffraction · 3 distinct chains · 43% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Aminotransferase | protein | 383 | 43% helix, 16% strand | — |
| B | Aminotransferase | protein | 391 | 43% helix, 17% strand | — |
| C | Polyhistidine tag | protein | 6 | 0% helix, 0% strand | — |
Ligands and binding sites
- PLP · Pyridoxal-5'-phosphate · ligand · 2 copies · chains A, B, 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, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1038 | 0.79 | 0.81 | 109 | PLP |
| 2 | 525 | 0.70 | 0.79 | 61 | PLP |
| 3 | 65 | 0.48 | 0.84 | 16 | empty |
| 4 | 87 | 0.45 | 0.80 | 16 | empty |
| 5 | 138 | 0.43 | 0.75 | 24 | empty |
Interfaces
3 interfaces between chains.
- A–B · 2536 Ų buried · 36 hydrogen bonds · protein-protein
- A–C · 432 Ų buried · 4 hydrogen bonds · protein-protein
- B–C · 168 Ų buried · 1 hydrogen bond · protein-protein
Modifications
Observed in the structure: 2 cofactor (pyridoxal phosphate Schiff base).
Compared structures
- 6QP2 · Crystal structure of the PLP-bound C-S lyase from Staphylococcus hominis · 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
- Elsewhere: RCSB PDB 6QP2 · PDBe 6QP2
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