Research workbench
Crystal structure of catharanthus roseus tryptophan decarboxylase in complex with L-tryptophan
Analyse Crystal structure of catharanthus roseus tryptophan decarboxylase in complex… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6EEW
- Type
- protein
- Length
- 1,878 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Aromatic-L-amino-acid decarboxylase
- EC
- 4.1.1.28
- UniProt
- P17770
- Ligands
- TRP, CA
- Pockets
- 20 · best druggability 0.76
Structure
x-ray diffraction · 4 distinct chains · 51% helix, 13% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Aromatic-L-amino-acid decarboxylase (EC 4.1.1.28) | protein | 479 | 51% helix, 13% strand | P17770 |
| B | Aromatic-L-amino-acid decarboxylase (EC 4.1.1.28) | protein | 468 | 50% helix, 13% strand | P17770 |
| C | Aromatic-L-amino-acid decarboxylase (EC 4.1.1.28) | protein | 467 | 51% helix, 13% strand | P17770 |
| D | Aromatic-L-amino-acid decarboxylase (EC 4.1.1.28) | protein | 464 | 52% helix, 13% strand | P17770 |
Ligands and binding sites
- TRP · Tryptophan · ligand · 4 copies · chains A, B, C, D
- CA · Calcium ion · metal · 4 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 9 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 100 | 0.76 | 0.97 | 28 | empty |
| 2 | 101 | 0.75 | 0.97 | 26 | empty |
| 3 | 943 | 0.75 | 0.78 | 102 | TRP |
| 4 | 382 | 0.69 | 0.82 | 52 | TRP |
| 5 | 379 | 0.69 | 0.82 | 45 | TRP |
Interfaces
6 interfaces between chains.
- A–B · 6662 Ų buried · 91 hydrogen bonds · protein-protein
- C–D · 6474 Ų buried · 90 hydrogen bonds · protein-protein
- B–C · 150 Ų buried · 1 hydrogen bond · protein-protein
- A–C · 134 Ų buried · 2 hydrogen bonds · protein-protein
- B–D · 102 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 modified (cofactor).
Compared structures
- 6EEW · Crystal structure of Catharanthus roseus tryptophan decarboxylase in complex with… · the same entry in another collection · chain D against D, TM-score 1.00
- P17770 · AlphaFold monomer V2.0 prediction for aromatic-L-amino-acid decarboxylase (P17770) · a predicted model of the same protein · chain D 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 P17770
- Elsewhere: RCSB PDB 6EEW · PDBe 6EEW · UniProt P17770
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