MolNFT v1 · #117778 · protein
Engineered human cystathionine gamma lyase (E59T, E339V) to deplet cysteine
5EIG · Cystathionine gamma-lyase: “Engineered human cystathionine gamma lyase (E59T, E339V) to deplet cysteine”. X-ray diffraction, 2 ligands (CYS, SO4), 20 pockets (best druggability 0.80). MolNFT v1 #117778 on GenesisL1: 3D structure…
- PDB
- 5EIG
- Type
- protein
- Length
- 3,087 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, SO4
- Pockets
- 20 · best druggability 0.80
Structure
x-ray diffraction · 8 distinct chains · 38% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Cystathionine gamma-lyase (EC 4.4.1.1) | protein | 384 | 39% helix, 16% strand | P32929 |
| B | Cystathionine gamma-lyase (EC 4.4.1.1) | protein | 386 | 38% helix, 16% strand | P32929 |
| C | Cystathionine gamma-lyase (EC 4.4.1.1) | protein | 388 | 38% helix, 16% strand | P32929 |
| D | Cystathionine gamma-lyase (EC 4.4.1.1) | protein | 387 | 39% helix, 16% strand | P32929 |
| E | Cystathionine gamma-lyase (EC 4.4.1.1) | protein | 385 | 39% helix, 16% strand | P32929 |
| F | Cystathionine gamma-lyase (EC 4.4.1.1) | protein | 382 | 38% helix, 16% strand | P32929 |
| G | Cystathionine gamma-lyase (EC 4.4.1.1) | protein | 388 | 38% helix, 16% strand | P32929 |
| H | Cystathionine gamma-lyase (EC 4.4.1.1) | protein | 387 | 38% helix, 16% strand | P32929 |
Ligands and binding sites
- CYS · Cysteine · ligand · 3 copies · chains C, D, E, F, G, H
- SO4 · Sulfate ion · ion · 5 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, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 92 | 0.80 | 0.99 | 20 | empty |
| 2 | 92 | 0.80 | 0.99 | 20 | empty |
| 3 | 68 | 0.56 | 0.88 | 19 | empty |
| 4 | 72 | 0.54 | 0.86 | 21 | empty |
| 5 | 94 | 0.54 | 0.84 | 25 | empty |
Interfaces
12 interfaces between chains.
- G–H · 2440 Ų buried · 31 hydrogen bonds · protein-protein
- C–D · 2253 Ų buried · 36 hydrogen bonds · protein-protein
- E–F · 2209 Ų buried · 32 hydrogen bonds · protein-protein
- A–B · 2187 Ų buried · 33 hydrogen bonds · protein-protein
- B–C · 1500 Ų buried · 35 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 8 modified (nonstandard, cofactor).
Compared structures
- 5EIG · Engineered human cystathionine gamma lyase (E59T, E339V) to deplet cysteine · the same entry in another collection · chain H against H, TM-score 1.00
- P32929 · AlphaFold monomer V2.0 prediction for cystathionine gamma-lyase (P32929) · a predicted model of the same protein · chain E 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 5EIG · PDBe 5EIG · UniProt P32929
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