MolNFT v1 · #145280 · protein
Crystal structure of cystathionine beta-lyase from legionella pneumophila philadelphia 1 covalently bound to pyridoxal phosphate
6CJB: “Crystal structure of cystathionine beta-lyase from legionella pneumophila philadelphia 1 covalently bound to…”. X-ray diffraction, 15 pockets (best druggability 0.80). MolNFT v1 #145280 on GenesisL1: 3D structure, binding sites and…
- PDB
- 6CJB
- Type
- protein
- Length
- 1,524 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Cystathionine beta-lyase
- EC
- 4.4.1.8
- UniProt
- Q5ZX43
- Pockets
- 15 · best druggability 0.80
Structure
x-ray diffraction · 1 distinct chain · 37% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | Cystathionine beta-lyase (EC 4.4.1.8) | protein | 381 | 37% helix, 17% strand | Q5ZX43 |
Ligands and binding sites
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
15 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 96 | 0.80 | 0.98 | 16 | empty |
| 2 | 80 | 0.51 | 0.84 | 22 | empty |
| 3 | 130 | 0.50 | 0.80 | 20 | empty |
| 4 | 118 | 0.49 | 0.80 | 18 | empty |
| 5 | 132 | 0.48 | 0.79 | 19 | empty |
Interfaces
6 interfaces between chains.
- A–B · 2476 Ų buried · 43 hydrogen bonds · protein-protein
- C–D · 2458 Ų buried · 43 hydrogen bonds · protein-protein
- B–D · 1578 Ų buried · 18 hydrogen bonds · protein-protein
- A–C · 1578 Ų buried · 18 hydrogen bonds · protein-protein
- B–C · 970 Ų buried · 9 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 modified (cofactor).
Compared structures
- 6CJB · Crystal structure of Cystathionine beta-lyase from Legionella pneumophila Philadelphia 1… · 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
- Every structure of UniProt Q5ZX43
- Elsewhere: RCSB PDB 6CJB · PDBe 6CJB · UniProt Q5ZX43
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