MolNFT v1 · #175636 · protein
Crystal structure of a tyrosine decarboxylase from enterococcus faecalis in complex with the cofactor plp and inhibitor carbidopa
7CX0: “Crystal structure of a tyrosine decarboxylase from enterococcus faecalis in complex with the cofactor plp and…”. X-ray diffraction, 2 ligands (PLP, 142), 19 pockets (best druggability 0.76). MolNFT v1 #175636 on GenesisL1: 3D…
- PDB
- 7CX0
- Type
- protein
- Length
- 1,793 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, 142
- Pockets
- 19 · best druggability 0.76
Structure
x-ray diffraction · 3 distinct chains · 49% helix, 12% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Decarboxylase (EC 4.1.1.86) | protein | 602 | 49% helix, 13% strand | Q8KXD2 |
| B | Decarboxylase (EC 4.1.1.86) | protein | 603 | 48% helix, 13% strand | Q8KXD2 |
| C | Decarboxylase (EC 4.1.1.86) | protein | 588 | 48% helix, 10% strand | Q8KXD2 |
Ligands and binding sites
- PLP · Pyridoxal-5'-phosphate · ligand · 3 copies · chains A, B, C
- 142 · Carbidopa · ligand · 3 copies · chains A, B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
19 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 586 | 0.76 | 0.83 | 75 | PLP, 142 |
| 2 | 589 | 0.75 | 0.82 | 54 | PLP, 142 |
| 3 | 58 | 0.72 | 0.99 | 24 | empty |
| 4 | 483 | 0.58 | 0.74 | 53 | empty |
| 5 | 160 | 0.56 | 0.81 | 21 | empty |
Interfaces
2 interfaces between chains.
- B–C · 7286 Ų buried · 106 hydrogen bonds · protein-protein
- A–B · 137 Ų buried · 2 hydrogen bonds · protein-protein
Compared structures
- 7CX0 · Crystal structure of a tyrosine decarboxylase from Enterococcus faecalis in complex with… · 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 7CX0 · PDBe 7CX0 · UniProt Q8KXD2
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