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Crystal structure of oryza sativa tdc with plp

Analyse Crystal structure of oryza sativa tdc with plp in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 6KHO
Type: protein
Length: 965 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, CA
Pockets: 11 · best druggability 0.85

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	50% helix, 13% strand	Q6ZJK7
B	Tryptophan decarboxylase 1 (EC 4.1.1.-)	protein	475	48% helix, 13% strand	Q6ZJK7

Ligands and binding sites

PLP · Pyridoxal-5'-phosphate · ligand · 2 copies · chains A, B
CA · Calcium ion · metal · 4 copies · chains A, B
ACT · Acetate ion · additive · 4 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, 4 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	236	0.85	0.97	54	ACT, PLP
2	260	0.69	0.85	42	PLP, ACT
3	210	0.58	0.80	33	PEG
4	220	0.57	0.79	25	empty
5	96	0.47	0.80	19	CA

Interfaces

1 interface between chains.

A–B · 6522 Å² buried · 87 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 2 cofactor (pyridoxal phosphate Schiff base).

Compared structures

6KHO · Crystal structure of Oryza sativa TDC with PLP · the same entry in another collection · chain A against A, TM-score 1.00
Q6ZJK7 · AlphaFold monomer V2.0 prediction for tryptophan decarboxylase 1 (Q6ZJK7) · a predicted model of the same protein · chain A against A, TM-score 0.99

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 6KHO · PDBe 6KHO · UniProt Q6ZJK7

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