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Crystal structure of cystathionine gamma-lyase from lactobacillus plantarum complexed with L-serine
Analyse Crystal structure of cystathionine gamma-lyase from lactobacillus plantarum… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6LDO
- Type
- protein
- Length
- 2,286 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Cystathionine gamma-lyase
- UniProt
- A0A162EFJ4
- Ligands
- KOU, PO4
- Pockets
- 20 · best druggability 0.78
Structure
x-ray diffraction · 1 distinct chain · 38% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D, E, F | Cystathionine gamma-lyase | protein | 381 | 38% helix, 17% strand | A0A162EFJ4 |
Ligands and binding sites
- KOU · (E)-N-({3-hydroxy-2-methyl-5-[(phosphonooxy)methyl]pyridin-4-yl}methylidene)-L-serine · ligand · 6 copies · chains A, B, C, D, E, F
- PO4 · Phosphate ion · ion · 14 copies · chains A, B, C, D, E, F
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 | 119 | 0.78 | 0.97 | 28 | KOU |
| 2 | 106 | 0.78 | 0.98 | 25 | KOU |
| 3 | 116 | 0.78 | 0.97 | 26 | KOU |
| 4 | 115 | 0.77 | 0.96 | 28 | KOU |
| 5 | 108 | 0.77 | 0.97 | 27 | KOU |
Interfaces
10 interfaces between chains.
- E–F · 2626 Ų buried · 34 hydrogen bonds · protein-protein
- C–D · 2563 Ų buried · 29 hydrogen bonds · protein-protein
- A–B · 2551 Ų buried · 33 hydrogen bonds · protein-protein
- A–D · 1506 Ų buried · 20 hydrogen bonds · protein-protein
- B–C · 1412 Ų buried · 20 hydrogen bonds · protein-protein
Compared structures
- 6LDO · Crystal structure of cystathionine gamma-lyase from Lactobacillus plantarum complexed… · the same entry in another collection · chain D against D, 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 A0A162EFJ4
- Elsewhere: RCSB PDB 6LDO · PDBe 6LDO · UniProt A0A162EFJ4
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