MolNFT v1 · #159617 · protein
L-methionine depletion with an engineered human enzyme disrupts prostate cancer metabolism
6OVG · Cystathionine gamma-lyase: “L-methionine depletion with an engineered human enzyme disrupts prostate cancer metabolism”. X-ray diffraction, 1 ligand (SO4), 20 pockets (best druggability 0.81). MolNFT v1 #159617 on GenesisL1: 3D…
- PDB
- 6OVG
- Type
- protein
- Length
- 3,093 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
- SO4
- Pockets
- 20 · best druggability 0.81
Structure
x-ray diffraction · 7 distinct chains · 37% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Cystathionine gamma-lyase (EC 4.4.1.1) | protein | 384 | 38% helix, 17% strand | P32929 |
| B | Cystathionine gamma-lyase (EC 4.4.1.1) | protein | 386 | 38% helix, 17% strand | P32929 |
| C, F | Cystathionine gamma-lyase (EC 4.4.1.1) | protein | 387 | 37% helix, 16% strand | P32929 |
| D | Cystathionine gamma-lyase (EC 4.4.1.1) | protein | 386 | 35% helix, 16% strand | P32929 |
| E | Cystathionine gamma-lyase (EC 4.4.1.1) | protein | 388 | 37% helix, 16% strand | P32929 |
| G | Cystathionine gamma-lyase (EC 4.4.1.1) | protein | 388 | 37% helix, 16% strand | P32929 |
| H | Cystathionine gamma-lyase (EC 4.4.1.1) | protein | 387 | 38% helix, 16% strand | P32929 |
Ligands and binding sites
- SO4 · Sulfate ion · ion · 2 copies · chains A, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 12 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 101 | 0.81 | 0.99 | 21 | empty |
| 2 | 89 | 0.80 | 0.99 | 20 | empty |
| 3 | 212 | 0.61 | 0.82 | 24 | empty |
| 4 | 177 | 0.58 | 0.81 | 26 | SO4 |
| 5 | 185 | 0.56 | 0.80 | 25 | empty |
Interfaces
12 interfaces between chains.
- G–H · 2275 Ų buried · 30 hydrogen bonds · protein-protein
- E–F · 2175 Ų buried · 31 hydrogen bonds · protein-protein
- A–B · 2149 Ų buried · 33 hydrogen bonds · protein-protein
- C–D · 2144 Ų buried · 30 hydrogen bonds · protein-protein
- B–C · 1556 Ų buried · 35 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 8 modified (cofactor).
Compared structures
- 6OVG · L-Methionine Depletion with an Engineered Human Enzyme Disrupts Prostate Cancer Metabolism · 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 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 P32929
- Elsewhere: RCSB PDB 6OVG · PDBe 6OVG · UniProt P32929
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