MolNFT v1 · #139119 · protein
Crystal structure of metb from corynebacterium glutamicum
5X5H · Cystathionine beta-LYASES/CYSTATHIONINE gamma-synthases: “Crystal structure of metb from corynebacterium glutamicum”. X-ray diffraction, 2 ligands (PLP, MG), 4 pockets (best druggability 0.58). MolNFT v1 #139119 on GenesisL1: 3D…
- PDB
- 5X5H
- Type
- protein
- Length
- 385 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Cystathionine beta-LYASES/CYSTATHIONINE gamma-synthases
- EC
- 2.5.1.48
- UniProt
- Q79VD9
- Ligands
- PLP, MG
- Pockets
- 4 · best druggability 0.58
Structure
x-ray diffraction · 1 distinct chain · 39% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Cystathionine beta-LYASES/CYSTATHIONINE gamma-synthases (EC 2.5.1.48) | protein | 385 | 39% helix, 17% strand | Q79VD9 |
Ligands and binding sites
- PLP · Pyridoxal-5'-phosphate · ligand · chains A
- MG · Magnesium ion · metal · 2 copies · chains A
- GOL · Glycerol · additive · 3 copies · chains A
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 | 57 | 0.58 | 0.90 | 21 | GOL |
| 2 | 103 | 0.54 | 0.83 | 26 | PLP |
| 3 | 135 | 0.40 | 0.74 | 19 | empty |
| 4 | 93 | 0.36 | 0.75 | 24 | empty |
Modifications
Observed in the structure: 1 cofactor (pyridoxal phosphate Schiff base).
Compared structures
- 5X5H · Crystal structure of metB from Corynebacterium glutamicum · 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 Q79VD9
- Elsewhere: RCSB PDB 5X5H · PDBe 5X5H · UniProt Q79VD9
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