Research workbench
Inactive conformation of engineered human cystathionine gamma lyase (E59N, R119L, E339V) to depleting methionine
Analyse Inactive conformation of engineered human cystathionine gamma lyase (E59N… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5TT2
- Type
- protein
- Length
- 686 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Cystathionine gamma-lyase
- EC
- 4.4.1.1
- UniProt
- P32929
- Ligands
- SO4
- Pockets
- 6 · best druggability 0.77
Structure
x-ray diffraction · 1 distinct chain · 40% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| C, D | Cystathionine gamma-lyase (EC 4.4.1.1) | protein | 343 | 40% helix, 17% strand | P32929 |
Ligands and binding sites
- SO4 · Sulfate ion · ion · 4 copies · chains C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 630 | 0.77 | 0.82 | 67 | SO4 |
| 2 | 562 | 0.77 | 0.83 | 67 | SO4 |
| 3 | 168 | 0.58 | 0.82 | 22 | empty |
| 4 | 269 | 0.52 | 0.75 | 34 | empty |
| 5 | 63 | 0.31 | 0.75 | 18 | empty |
Interfaces
1 interface between chains.
- C–D · 1061 Ų buried · 28 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 modified (cofactor).
Compared structures
- 5TT2 · Inactive conformation of engineered human cystathionine gamma lyase (E59N, R119L, E339V)… · the same entry in another collection · chain C against C, TM-score 1.00
- P32929 · AlphaFold monomer V2.0 prediction for cystathionine gamma-lyase (P32929) · a predicted model of the same protein · chain D against A, TM-score 0.95
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 P32929
- Elsewhere: RCSB PDB 5TT2 · PDBe 5TT2 · UniProt P32929
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