MolNFT v1 · #161784 · protein
Crystal structure of the plp-bound C-S lyase from bacillus subtilis (strain 168)
6QP3 · Cystathionine beta-lyase patb: “Crystal structure of the plp-bound C-S lyase from bacillus subtilis (strain 168)”. X-ray diffraction, 1 ligand (PLP), 16 pockets (best druggability 0.79). MolNFT v1 #161784 on GenesisL1: 3D structure…
- PDB
- 6QP3
- Type
- protein
- Length
- 1,545 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Cystathionine beta-lyase patb
- EC
- 4.4.1.13
- UniProt
- Q08432
- Ligands
- PLP
- Pockets
- 16 · best druggability 0.79
Structure
x-ray diffraction · 3 distinct chains · 47% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Cystathionine beta-lyase patb (EC 4.4.1.13) | protein | 387 | 47% helix, 15% strand | Q08432 |
| B, D | Cystathionine beta-lyase patb (EC 4.4.1.13) | protein | 386 | 48% helix, 17% strand | Q08432 |
| C | Cystathionine beta-lyase patb (EC 4.4.1.13) | protein | 386 | 46% helix, 17% strand | Q08432 |
Ligands and binding sites
- PLP · Pyridoxal-5'-phosphate · ligand · 4 copies · chains A, D, B, C
- ACT · Acetate ion · additive · 4 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
16 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1103 | 0.79 | 0.81 | 106 | ACT, PLP |
| 2 | 513 | 0.73 | 0.82 | 68 | empty |
| 3 | 688 | 0.73 | 0.79 | 58 | ACT, PLP |
| 4 | 679 | 0.73 | 0.79 | 60 | ACT, PLP |
| 5 | 228 | 0.50 | 0.76 | 32 | empty |
Interfaces
3 interfaces between chains.
- B–C · 2523 Ų buried · 44 hydrogen bonds · protein-protein
- A–D · 2483 Ų buried · 43 hydrogen bonds · protein-protein
- A–B · 662 Ų buried · 12 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 cofactor (pyridoxal phosphate Schiff base).
Compared structures
- 6QP3 · Crystal structure of the PLP-bound C-S lyase from Bacillus subtilis (strain 168) · the same entry in another collection · chain D against D, TM-score 1.00
- Q08432 · AlphaFold monomer V2.0 prediction for cystathionine beta-lyase patb (Q08432) · a predicted model of the same protein · chain C 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 Q08432
- Elsewhere: RCSB PDB 6QP3 · PDBe 6QP3 · UniProt Q08432
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