MolNFT v1 · #117064 · protein
Crystal structure of methionine gamma-lyase from clostridium sporogenes
5DX5: “Crystal structure of methionine gamma-lyase from clostridium sporogenes”. X-ray diffraction, 3 ligands (PLP, NA, CL), 4 pockets (best druggability 0.77). MolNFT v1 #117064 on GenesisL1: 3D structure, binding sites and pockets in…
- PDB
- 5DX5
- Type
- protein
- Length
- 797 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Methionine gamma-lyase
- EC
- 4.4.1.11
- UniProt
- J7TA22
- Ligands
- PLP, NA, CL
- Pockets
- 4 · best druggability 0.77
Structure
x-ray diffraction · 2 distinct chains · 41% helix, 15% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Methionine gamma-lyase (EC 4.4.1.11) | protein | 399 | 41% helix, 15% strand | J7TA22 |
| B | Methionine gamma-lyase (EC 4.4.1.11) | protein | 398 | 42% helix, 15% strand | J7TA22 |
Ligands and binding sites
- PLP · Pyridoxal-5'-phosphate · ligand · 2 copies · chains A, B
- NA · Sodium ion · metal · chains B
- CL · Chloride ion · ion · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 509 | 0.77 | 0.84 | 80 | PLP, CL |
| 2 | 722 | 0.77 | 0.81 | 90 | PLP, CL |
| 3 | 67 | 0.36 | 0.77 | 16 | empty |
| 4 | 53 | 0.33 | 0.78 | 14 | empty |
Interfaces
1 interface between chains.
- A–B · 2839 Ų buried · 47 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 cofactor (pyridoxal phosphate Schiff base).
Compared structures
- 5DX5 · Crystal structure of methionine gamma-lyase from Clostridium sporogenes · the same entry in another collection · 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 J7TA22
- Elsewhere: RCSB PDB 5DX5 · PDBe 5DX5 · UniProt J7TA22
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