MolNFT v1 · #154633 · protein
Crystal structure of oryza sativa tdc with plp and serotonin
6KHN · Tryptophan decarboxylase 1: “Crystal structure of oryza sativa tdc with plp and serotonin”. X-ray diffraction, 3 ligands (PLP, SRO, CA), 11 pockets (best druggability 0.81). MolNFT v1 #154633 on GenesisL1: 3D structure, binding…
- PDB
- 6KHN
- Type
- protein
- Length
- 966 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Tryptophan decarboxylase 1
- EC
- 4.1.1.-
- UniProt
- Q6ZJK7
- Ligands
- PLP, SRO, CA
- Pockets
- 11 · best druggability 0.81
Structure
x-ray diffraction · 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 | 51% 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
- SRO · Serotonin · ligand · chains A, B
- CA · Calcium ion · metal · 4 copies · chains A, B
- PEG · Di(hydroxyethyl)ether · additive · 2 copies · chains A, B
- ACT · Acetate ion · 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, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 157 | 0.81 | 0.97 | 35 | SRO, PLP |
| 2 | 92 | 0.75 | 0.97 | 22 | empty |
| 3 | 299 | 0.71 | 0.84 | 42 | PLP |
| 4 | 246 | 0.62 | 0.81 | 31 | ACT |
| 5 | 201 | 0.60 | 0.82 | 27 | empty |
Interfaces
1 interface between chains.
- A–B · 6560 Ų buried · 89 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 6KHN · PDBe 6KHN · UniProt Q6ZJK7
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