MolNFT v1 · #175635 · protein
Crystal structure of a tyrosine decarboxylase from enterococcus faecalis K392A mutant in complex with the cofactor plp and L-dopa
7CWZ: “Crystal structure of a tyrosine decarboxylase from enterococcus faecalis K392A mutant in complex with the…”. X-ray diffraction, 3 ligands (PLP, LDP, MG), 19 pockets (best druggability 0.76). MolNFT v1 #175635 on GenesisL1: 3D…
- PDB
- 7CWZ
- Type
- protein
- Length
- 1,794 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Decarboxylase
- EC
- 4.1.1.86
- UniProt
- Q8KXD2
- Ligands
- PLP, LDP, MG
- Pockets
- 19 · best druggability 0.76
Structure
x-ray diffraction · 3 distinct chains · 47% helix, 13% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Decarboxylase (EC 4.1.1.86) | protein | 601 | 47% helix, 12% strand | Q8KXD2 |
| B | Decarboxylase (EC 4.1.1.86) | protein | 601 | 48% helix, 13% strand | Q8KXD2 |
| C | Decarboxylase (EC 4.1.1.86) | protein | 592 | 47% helix, 13% strand | Q8KXD2 |
Ligands and binding sites
- PLP · Pyridoxal-5'-phosphate · ligand · 3 copies · chains A, B, C
- LDP · L-dopamine · ligand · 3 copies · chains A, B, C
- MG · Magnesium ion · metal · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
19 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 83 | 0.76 | 0.98 | 29 | empty |
| 2 | 710 | 0.75 | 0.80 | 64 | MG, PLP, LDP |
| 3 | 595 | 0.73 | 0.80 | 67 | PLP, LDP |
| 4 | 253 | 0.58 | 0.79 | 36 | PLP, LDP |
| 5 | 192 | 0.56 | 0.79 | 33 | empty |
Interfaces
2 interfaces between chains.
- B–C · 7388 Ų buried · 112 hydrogen bonds · protein-protein
- A–B · 65 Ų buried · 1 hydrogen bond · protein-protein
Compared structures
- 7CWZ · Crystal structure of a tyrosine decarboxylase from Enterococcus faecalis K392A mutant in… · 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 Q8KXD2
- Elsewhere: RCSB PDB 7CWZ · PDBe 7CWZ · UniProt Q8KXD2
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