7CWZ | pdb_00007cwz

Crystal structure of a tyrosine decarboxylase from Enterococcus faecalis K392A mutant in complex with the cofactor PLP and L-dopa

PDB DOI: https://doi.org/10.2210/pdb7CWZ/pdb

Classification: LYASE
Organism(s): Enterococcus faecalis
Expression System: Escherichia coli BL21
Mutation(s): Yes

Deposited: 2020-09-01 Released: 2021-09-01
Deposition Author(s): Yu, X., Gong, M., Huang, J., Liu, W., Chen, C., Guo, R.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.97 Å
R-Value Free:
0.293 (Depositor), 0.330 (DCC)
R-Value Work:
0.243 (Depositor), 0.250 (DCC)
R-Value Observed:
0.245 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.1 of the entry. See complete history.

Literature

Crystal structure of a tyrosine decarboxylase from Enterococcus faecalis K392A mutant in complex with the cofactor PLP and L-dopa

Yu, X., Gong, M., Huang, J., Liu, W., Chen, C., Guo, R.

To be published.

Macromolecule Content

Total Structure Weight: 211.48 kDa
Atom Count: 14,223
Modeled Residue Count: 1,794
Deposited Residue Count: 1,860
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Decarboxylase	A, B, C	620	Enterococcus faecalis	Mutation(s): 1 Gene Names: tyrDC, ddc, ELS84_1624, KUB3007_C03520, NCTC8729_00604 EC: 4.1.1.86 (PDB Primary Data), 4.1.1.25 (UniProt), 4.1.1 (UniProt)
UniProt
Find proteins for Q838D6 (Enterococcus faecalis (strain ATCC 700802 / V583)) Explore Q838D6 Go to UniProtKB: Q838D6
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q838D6
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 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 J [auth C] SDF format, chain H [auth B] SDF format, chain E [auth A] MOL2 format, chain J [auth C] MOL2 format, chain H [auth B] MOL2 format, chain E [auth A] mmCIF format, chain J [auth C] mmCIF format, chain H [auth B] mmCIF format, chain E [auth A]	E [auth A], H [auth B], J [auth C]	PYRIDOXAL-5'-PHOSPHATE C₈ H₁₀ N O₆ P NGVDGCNFYWLIFO-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Focus chain H [auth B] Focus chain J [auth C] Interactions & Density Focus chain E [auth A] Focus chain H [auth B] Focus chain J [auth C]
LDP (Subject of Investigation/LOI) Query on LDP Download Ideal Coordinates CCD File SDF format, chain K [auth C] SDF format, chain I [auth B] SDF format, chain F [auth A] MOL2 format, chain K [auth C] MOL2 format, chain I [auth B] MOL2 format, chain F [auth A] mmCIF format, chain K [auth C] mmCIF format, chain I [auth B] mmCIF format, chain F [auth A]	F [auth A], I [auth B], K [auth C]	L-DOPAMINE C₈ H₁₁ N O₂ VYFYYTLLBUKUHU-UHFFFAOYSA-N		Interactions Focus chain F [auth A] Focus chain I [auth B] Focus chain K [auth C] Interactions & Density Focus chain F [auth A] Focus chain I [auth B] Focus chain K [auth C]
MG (Subject of Investigation/LOI) Query on MG Download Ideal Coordinates CCD File SDF format, chain G [auth B] SDF format, chain D [auth A] MOL2 format, chain G [auth B] MOL2 format, chain D [auth A] mmCIF format, chain G [auth B] mmCIF format, chain D [auth A]	D [auth A], G [auth B]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain D [auth A] Focus chain G [auth B] Interactions & Density Focus chain D [auth A] Focus chain G [auth B]