Research workbench
Crystal structure of cystathionine beta-lyase from legionella pneumophila philadelphia 1 in complex with alanyl-plp and serine
Analyse Crystal structure of cystathionine beta-lyase from legionella pneumophila… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6CJA
- 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
- Ligands
- F0G, SER
- Pockets
- 16 · best druggability 0.79
Structure
x-ray diffraction · 1 distinct chain · 38% 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 | 38% helix, 17% strand | Q5ZX43 |
Ligands and binding sites
- F0G · (E)-N-({3-hydroxy-2-methyl-5-[(phosphonooxy)methyl]pyridin-4-yl}methylidene)-L-alanine · ligand · 4 copies · chains A, B, C, D
- SER · Serine · ligand · 4 copies · chains A, B, C, D
- GOL · Glycerol · additive · 3 copies · chains A, D, B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
16 pockets found on a 1 Å grid, 9 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 85 | 0.79 | 0.98 | 17 | empty |
| 2 | 84 | 0.76 | 0.98 | 25 | F0G |
| 3 | 81 | 0.75 | 0.98 | 26 | F0G |
| 4 | 84 | 0.75 | 0.97 | 26 | F0G |
| 5 | 68 | 0.74 | 0.99 | 37 | empty |
Interfaces
6 interfaces between chains.
- A–B · 2498 Ų buried · 35 hydrogen bonds · protein-protein
- C–D · 2489 Ų buried · 37 hydrogen bonds · protein-protein
- B–D · 1577 Ų buried · 18 hydrogen bonds · protein-protein
- A–C · 1570 Ų buried · 18 hydrogen bonds · protein-protein
- A–D · 956 Ų buried · 11 hydrogen bonds · protein-protein
Compared structures
- 6CJA · Crystal structure of Cystathionine beta-lyase from Legionella pneumophila Philadelphia 1… · the same entry in another collection · chain B against B, 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 6CJA · PDBe 6CJA · UniProt Q5ZX43
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