MolNFT v1 · #60329 · protein
Crystal structure of human cystathionase (cystathionine gamma lyase) in complex with dl-propargylglycine
3COG · Cystathionine gamma-lyase: “Crystal structure of human cystathionase (cystathionine gamma lyase) in complex with dl-propargylglycine”. X-ray diffraction, 3 ligands (PLP, 2AG, NO3), 15 pockets (best druggability 0.75). MolNFT v1…
- PDB
- 3COG
- Type
- protein
- Length
- 1,531 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Cystathionine gamma-lyase
- EC
- 4.4.1.1
- UniProt
- P32929
- Ligands
- PLP, 2AG, NO3
- Pockets
- 15 · best druggability 0.75
Structure
x-ray diffraction · 4 distinct chains · 39% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Cystathionine gamma-lyase (EC 4.4.1.1) | protein | 376 | 39% helix, 16% strand | P32929 |
| B | Cystathionine gamma-lyase (EC 4.4.1.1) | protein | 373 | 38% helix, 17% strand | P32929 |
| C | Cystathionine gamma-lyase (EC 4.4.1.1) | protein | 390 | 39% helix, 16% strand | P32929 |
| D | Cystathionine gamma-lyase (EC 4.4.1.1) | protein | 392 | 39% helix, 16% strand | P32929 |
Ligands and binding sites
- PLP · Pyridoxal-5'-phosphate · ligand · 3 copies · chains A, B, C, D
- 2AG · (2S)-2-aminopent-4-enoic acid · ligand · 3 copies · chains A, B, C, D
- NO3 · Nitrate ion · ion · 3 copies · chains A, C, D
- GOL · Glycerol · additive · 5 copies · chains A, B, C, D
- PEG · Di(hydroxyethyl)ether · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
15 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 63 | 0.75 | 0.98 | 20 | empty |
| 2 | 480 | 0.69 | 0.80 | 58 | empty |
| 3 | 63 | 0.50 | 0.85 | 22 | empty |
| 4 | 106 | 0.47 | 0.80 | 24 | empty |
| 5 | 167 | 0.46 | 0.76 | 34 | empty |
Interfaces
6 interfaces between chains.
- C–D · 2506 Ų buried · 26 hydrogen bonds · protein-protein
- A–B · 2172 Ų buried · 22 hydrogen bonds · protein-protein
- A–D · 1502 Ų buried · 35 hydrogen bonds · protein-protein
- B–C · 1461 Ų buried · 34 hydrogen bonds · protein-protein
- B–D · 878 Ų buried · 14 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 3 cofactor, 3 covalent (pyridoxal phosphate Schiff base, covalent ligand).
Compared structures
- 3COG · Crystal structure of human cystathionase (Cystathionine gamma lyase) in complex with… · the same entry in another collection · chain D against D, 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 0.99
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 3COG · PDBe 3COG · UniProt P32929
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