Research workbench
Active conformation for engineered human cystathionine gamma lyase (E59N, R119L, E339V) to depleting methionine
Analyse Active conformation for 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
- 5TSU
- Type
- protein
- Length
- 3,077 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Cystathionine gamma-lyase
- EC
- 4.4.1.1
- UniProt
- P32929
- Ligands
- CYS, LPI, MET, SO4
- Pockets
- 20 · best druggability 0.81
Structure
x-ray diffraction · 8 distinct chains · 39% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Cystathionine gamma-lyase (EC 4.4.1.1) | protein | 384 | 40% helix, 16% strand | P32929 |
| B | Cystathionine gamma-lyase (EC 4.4.1.1) | protein | 385 | 38% helix, 16% strand | P32929 |
| C | Cystathionine gamma-lyase (EC 4.4.1.1) | protein | 386 | 39% helix, 16% strand | P32929 |
| D | Cystathionine gamma-lyase (EC 4.4.1.1) | protein | 384 | 40% helix, 16% strand | P32929 |
| E | Cystathionine gamma-lyase (EC 4.4.1.1) | protein | 385 | 40% helix, 16% strand | P32929 |
| F | Cystathionine gamma-lyase (EC 4.4.1.1) | protein | 381 | 39% helix, 17% strand | P32929 |
| G | Cystathionine gamma-lyase (EC 4.4.1.1) | protein | 386 | 38% helix, 16% strand | P32929 |
| H | Cystathionine gamma-lyase (EC 4.4.1.1) | protein | 386 | 39% helix, 16% strand | P32929 |
Ligands and binding sites
- CYS · Cysteine · ligand · 3 copies · chains E, F, G, H
- LPI · N-({3-hydroxy-2-methyl-5-[(phosphonooxy)methyl]pyridin-4-yl}methyl)-L-methionine · ligand · 2 copies · chains C, D, E, F
- MET · Methionine · ligand · chains A, B
- SO4 · Sulfate ion · ion · 3 copies · chains A, B, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 18 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 97 | 0.81 | 0.99 | 20 | empty |
| 2 | 99 | 0.80 | 0.98 | 20 | empty |
| 3 | 686 | 0.79 | 0.84 | 73 | empty |
| 4 | 668 | 0.79 | 0.83 | 80 | empty |
| 5 | 53 | 0.70 | 0.98 | 21 | LPI |
Interfaces
19 interfaces between chains.
- E–F · 2206 Ų buried · 30 hydrogen bonds · protein-protein
- G–H · 2202 Ų buried · 33 hydrogen bonds · protein-protein
- C–D · 2193 Ų buried · 30 hydrogen bonds · protein-protein
- A–B · 2177 Ų buried · 29 hydrogen bonds · protein-protein
- B–C · 1485 Ų buried · 36 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 6 modified, 1 covalent (cofactor, covalent ligand).
Compared structures
- 5TSU · Active conformation for Engineered human cystathionine gamma lyase (E59N, R119L, E339V)… · the same entry in another collection · chain G against G, TM-score 1.00
- P32929 · AlphaFold monomer V2.0 prediction for cystathionine gamma-lyase (P32929) · a predicted model of the same protein · chain F 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 P32929
- Elsewhere: RCSB PDB 5TSU · PDBe 5TSU · UniProt P32929
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.