8X0P

Crystal structure of Tyrosine decarboxylase in complex with the cofactor PLP and inhibitor carbidopa

PDB DOI: https://doi.org/10.2210/pdb8X0P/pdb

Classification: LYASE
Organism(s): Papaver somniferum
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2023-11-05 Released: 2025-02-12
Deposition Author(s): Wang, H., Yu, J., Yao, M.
Funding Organization(s): Japan Society for the Promotion of Science (JSPS)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 3.35 Å
R-Value Free:
0.251 (Depositor), 0.254 (DCC)
R-Value Work:
0.214 (Depositor), 0.217 (DCC)
R-Value Observed:
0.216 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.0 of the entry. See complete history.

Literature

Crystal structure of Tyrosine decarboxylase in complex with the cofactor PLP and inhibitor carbidopa

Wang, H., Yu, J., Yao, M.

To be published.

Macromolecule Content

Total Structure Weight: 359.38 kDa
Atom Count: 22,985
Modelled Residue Count: 2,889
Deposited Residue Count: 3,186
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Tyrosine/DOPA decarboxylase 2	A, B, C, D, E A, B, C, D, E, F	531	Papaver somniferum	Mutation(s): 0 Gene Names: TYDC2 EC: 4.1.1.28 (PDB Primary Data), 4.1.1.25 (PDB Primary Data)
UniProt
Find proteins for P54769 (Papaver somniferum) Explore P54769 Go to UniProtKB: P54769
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P54769
Sequence Annotations Expand
Reference Sequence LOADING

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
PLP (Subject of Investigation/LOI) Query on PLP Download Ideal Coordinates CCD File SDF format, chain G [auth A] SDF format, chain I [auth B] SDF format, chain K [auth C] SDF format, chain M [auth D] SDF format, chain O [auth E] SDF format, chain Q [auth F] MOL2 format, chain G [auth A] MOL2 format, chain I [auth B] MOL2 format, chain K [auth C] MOL2 format, chain M [auth D] MOL2 format, chain O [auth E] MOL2 format, chain Q [auth F] mmCIF format, chain G [auth A] mmCIF format, chain I [auth B] mmCIF format, chain K [auth C] mmCIF format, chain M [auth D] mmCIF format, chain O [auth E] mmCIF format, chain Q [auth F]	G [auth A] I [auth B] K [auth C] M [auth D] O [auth E] G [auth A], I [auth B], K [auth C], M [auth D], O [auth E], Q [auth F]	PYRIDOXAL-5'-PHOSPHATE C₈ H₁₀ N O₆ P NGVDGCNFYWLIFO-UHFFFAOYSA-N		Interactions Focus chain G [auth A] Focus chain I [auth B] Focus chain K [auth C] Focus chain M [auth D] Focus chain O [auth E] Focus chain Q [auth F] Interactions & Density Focus chain G [auth A] Focus chain I [auth B] Focus chain K [auth C] Focus chain M [auth D] Focus chain O [auth E] Focus chain Q [auth F]
142 (Subject of Investigation/LOI) Query on 142 Download Ideal Coordinates CCD File SDF format, chain H [auth A] SDF format, chain J [auth B] SDF format, chain L [auth C] SDF format, chain N [auth D] SDF format, chain P [auth F] SDF format, chain R [auth F] MOL2 format, chain H [auth A] MOL2 format, chain J [auth B] MOL2 format, chain L [auth C] MOL2 format, chain N [auth D] MOL2 format, chain P [auth F] MOL2 format, chain R [auth F] mmCIF format, chain H [auth A] mmCIF format, chain J [auth B] mmCIF format, chain L [auth C] mmCIF format, chain N [auth D] mmCIF format, chain P [auth F] mmCIF format, chain R [auth F]	H [auth A] J [auth B] L [auth C] N [auth D] P [auth F] H [auth A], J [auth B], L [auth C], N [auth D], P [auth F], R [auth F]	CARBIDOPA C₁₀ H₁₄ N₂ O₄ TZFNLOMSOLWIDK-JTQLQIEISA-N		Interactions Focus chain H [auth A] Focus chain J [auth B] Focus chain L [auth C] Focus chain N [auth D] Focus chain P [auth F] Focus chain R [auth F] Interactions & Density Focus chain H [auth A] Focus chain J [auth B] Focus chain L [auth C] Focus chain N [auth D] Focus chain P [auth F] Focus chain R [auth F]