Research workbench
Crystal structure of cystathionine beta-lyase from klebsiella pneumoniae
Analyse Crystal structure of cystathionine beta-lyase from klebsiella pneumoniae in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 8DUY
- Type
- protein
- Length
- 1,566 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
- Q0ZBA0
- Ligands
- CL
- Pockets
- 20 · best druggability 0.86
Structure
x-ray diffraction · 2 distinct chains · 40% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C | Cystathionine beta-lyase (EC 4.4.1.8) | protein | 391 | 40% helix, 17% strand | Q0ZBA0 |
| B, D | Cystathionine beta-lyase (EC 4.4.1.8) | protein | 392 | 41% helix, 17% strand | Q0ZBA0 |
Ligands and binding sites
- CL · Chloride ion · ion · 8 copies · chains A, B, C, D
- MPD · (4S)-2-methyl-2,4-pentanediol · additive · 3 copies · chains A, D, B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 9 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 352 | 0.86 | 0.95 | 79 | empty |
| 2 | 455 | 0.71 | 0.81 | 43 | CL, MPD |
| 3 | 427 | 0.70 | 0.81 | 42 | CL, MPD |
| 4 | 448 | 0.70 | 0.80 | 50 | CL |
| 5 | 450 | 0.70 | 0.80 | 43 | CL, MPD |
Interfaces
6 interfaces between chains.
- A–D · 2616 Ų buried · 33 hydrogen bonds · protein-protein
- B–C · 2572 Ų buried · 32 hydrogen bonds · protein-protein
- B–D · 1400 Ų buried · 25 hydrogen bonds · protein-protein
- A–C · 1393 Ų buried · 20 hydrogen bonds · protein-protein
- A–B · 823 Ų buried · 13 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 modified (cofactor).
Compared structures
- 8DUY · Crystal structure of Cystathionine beta-lyase from Klebsiella pneumoniae · 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 Q0ZBA0
- Elsewhere: RCSB PDB 8DUY · PDBe 8DUY · UniProt Q0ZBA0
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.