Research workbench
Crystal structure of Oryza sativa TDC with PLP and tryptamine
Analyse Crystal structure of Oryza sativa TDC with PLP and tryptamine in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6KHP
- Type
- protein
- Length
- 966 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 2.299
- Source
- Oryza sativa subsp. japonica
- Molecule
- Tryptophan decarboxylase 1
- EC
- 4.1.1.-
- UniProt
- Q6ZJK7
- Ligands
- PLP, TSS, CA
- Pockets
- 11 · best druggability 0.81
Structure
x-ray diffraction · resolution 2.299 · 2 distinct chains · 49% helix, 13% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Tryptophan decarboxylase 1 (EC 4.1.1.-) | protein | 490 | 50% helix, 12% strand | Q6ZJK7 |
| B | Tryptophan decarboxylase 1 (EC 4.1.1.-) | protein | 476 | 48% helix, 13% strand | Q6ZJK7 |
Ligands and binding sites
- PLP · Pyridoxal-5'-phosphate · ligand · 2 copies · chains A, B
- TSS · 2-(1H-indol-3-yl)ethanamine · ligand · chains A, B
- CA · Calcium ion · metal · 4 copies · chains A, B
- ACT · Acetate ion · additive · 2 copies · chains A, B
- PEG · Di(hydroxyethyl)ether · additive · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
11 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 142 | 0.81 | 0.98 | 36 | TSS, PLP |
| 2 | 74 | 0.72 | 0.97 | 21 | empty |
| 3 | 278 | 0.70 | 0.85 | 43 | PLP |
| 4 | 343 | 0.64 | 0.79 | 47 | CA, PEG |
| 5 | 166 | 0.58 | 0.82 | 26 | empty |
Interfaces
1 interface between chains.
- A–B · 6430 Ų buried · 90 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 cofactor, 1 covalent (pyridoxal phosphate Schiff base, covalent ligand).
Compared structures
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 Q6ZJK7
- Elsewhere: RCSB PDB 6KHP · PDBe 6KHP · UniProt Q6ZJK7
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