Research workbench
Crystal structure of a tyrosine decarboxylase from enterococcus faecalis in complex with the cofactor plp and inhibitor methyl- tyrosine
Analyse Crystal structure of a tyrosine decarboxylase from enterococcus faecalis in… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7CX1
- Type
- protein
- Length
- 1,795 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
- GKU
- Pockets
- 14 · best druggability 0.74
Structure
x-ray diffraction · 3 distinct chains · 50% helix, 13% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Decarboxylase (EC 4.1.1.86) | protein | 602 | 51% helix, 13% strand | Q8KXD2 |
| B | Decarboxylase (EC 4.1.1.86) | protein | 603 | 49% helix, 14% strand | Q8KXD2 |
| C | Decarboxylase (EC 4.1.1.86) | protein | 590 | 49% helix, 12% strand | Q8KXD2 |
Ligands and binding sites
- GKU · 4-[(2R)-2-(methylamino)propyl]phenol · ligand · 4 copies · chains A, B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
14 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 66 | 0.74 | 0.99 | 27 | empty |
| 2 | 518 | 0.69 | 0.79 | 49 | GKU |
| 3 | 431 | 0.67 | 0.79 | 42 | GKU |
| 4 | 712 | 0.64 | 0.74 | 61 | empty |
| 5 | 137 | 0.52 | 0.80 | 19 | empty |
Interfaces
2 interfaces between chains.
- B–C · 7251 Ų buried · 120 hydrogen bonds · protein-protein
- A–B · 95 Ų buried · 1 hydrogen bond · protein-protein
Modifications
Observed in the structure: 3 modified (cofactor).
Compared structures
- 7CX1 · Crystal structure of a tyrosine decarboxylase from Enterococcus faecalis in complex with… · the same entry in another collection · chain B against B, 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 7CX1 · PDBe 7CX1 · UniProt Q8KXD2
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