Research workbench
Crystal structure of cystathionine gamma-lyase from toxoplasma gondii
Analyse Crystal structure of cystathionine gamma-lyase from toxoplasma gondii in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7NL1
- Type
- protein
- Length
- 3,166 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Cystathione gamma lyase, putative
- EC
- 4.4.1.1
- UniProt
- A0A125YN40
- Ligands
- PLP
- Pockets
- 20 · best druggability 0.81
Structure
x-ray diffraction · 6 distinct chains · 38% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, G | Cystathione gamma lyase, putative (EC 4.4.1.1) | protein | 397 | 38% helix, 16% strand | A0A125YN40 |
| C, H | Cystathione gamma lyase, putative (EC 4.4.1.1) | protein | 399 | 39% helix, 16% strand | A0A125YN40 |
| D | Cystathione gamma lyase, putative (EC 4.4.1.1) | protein | 400 | 38% helix, 16% strand | A0A125YN40 |
| E | Cystathione gamma lyase, putative (EC 4.4.1.1) | protein | 389 | 38% helix, 16% strand | A0A125YN40 |
| F | Cystathione gamma lyase, putative (EC 4.4.1.1) | protein | 394 | 37% helix, 16% strand | A0A125YN40 |
| B | Cystathione gamma lyase, putative (EC 4.4.1.1) | protein | 391 | 39% helix, 16% strand | A0A125YN40 |
Ligands and binding sites
- PLP · Pyridoxal-5'-phosphate · ligand · 8 copies · chains A, B, C, D, E, F, G, H
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 15 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 136 | 0.81 | 0.98 | 43 | empty |
| 2 | 137 | 0.81 | 0.98 | 39 | empty |
| 3 | 130 | 0.81 | 0.99 | 39 | empty |
| 4 | 128 | 0.80 | 0.98 | 39 | empty |
| 5 | 991 | 0.79 | 0.81 | 91 | empty |
Interfaces
17 interfaces between chains.
- G–H · 2683 Ų buried · 35 hydrogen bonds · protein-protein
- C–D · 2655 Ų buried · 30 hydrogen bonds · protein-protein
- A–B · 2597 Ų buried · 34 hydrogen bonds · protein-protein
- E–F · 2596 Ų buried · 33 hydrogen bonds · protein-protein
- A–C · 2426 Ų buried · 38 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 8 cofactor (pyridoxal phosphate Schiff base).
Compared structures
- 7NL1 · Crystal structure of cystathionine gamma-lyase from Toxoplasma gondii · 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 A0A125YN40
- Elsewhere: RCSB PDB 7NL1 · PDBe 7NL1 · UniProt A0A125YN40
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