8JG7

Serine decarboxylase

PDB DOI: https://doi.org/10.2210/pdb8JG7/pdb

Classification: BIOSYNTHETIC PROTEIN
Organism(s): Arabidopsis thaliana
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2023-05-19 Released: 2024-05-22
Deposition Author(s): Wang, H., Gong, W.
Funding Organization(s): Other government

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.85 Å
R-Value Free: 0.262
R-Value Work: 0.214
R-Value Observed: 0.216

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 aserine decarboxylase from Arabidopsis thaliana

Wang, H.

To be published.

Macromolecule Content

Total Structure Weight: 191.36 kDa
Atom Count: 13,088
Modelled Residue Count: 1,632
Deposited Residue Count: 1,672
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Serine decarboxylase	A, B [auth C], C [auth D], D [auth E]	418	Arabidopsis thaliana	Mutation(s): 0 Gene Names: SDC, EMB1075, SDC1, At1g43710, F2J6.7 EC: 4.1.1
UniProt
Find proteins for Q9MA74 (Arabidopsis thaliana) Explore Q9MA74 Go to UniProtKB: Q9MA74
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q9MA74
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 E [auth A] SDF format, chain H [auth C] SDF format, chain K [auth D] SDF format, chain N [auth E] MOL2 format, chain E [auth A] MOL2 format, chain H [auth C] MOL2 format, chain K [auth D] MOL2 format, chain N [auth E] mmCIF format, chain E [auth A] mmCIF format, chain H [auth C] mmCIF format, chain K [auth D] mmCIF format, chain N [auth E]	E [auth A], H [auth C], K [auth D], N [auth E]	PYRIDOXAL-5'-PHOSPHATE C₈ H₁₀ N O₆ P NGVDGCNFYWLIFO-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Focus chain H [auth C] Focus chain K [auth D] Focus chain N [auth E] Interactions & Density Focus chain E [auth A] Focus chain H [auth C] Focus chain K [auth D] Focus chain N [auth E]
GOL Query on GOL Download Ideal Coordinates CCD File SDF format, chain G [auth A] SDF format, chain J [auth C] SDF format, chain M [auth D] SDF format, chain P [auth E] MOL2 format, chain G [auth A] MOL2 format, chain J [auth C] MOL2 format, chain M [auth D] MOL2 format, chain P [auth E] mmCIF format, chain G [auth A] mmCIF format, chain J [auth C] mmCIF format, chain M [auth D] mmCIF format, chain P [auth E]	G [auth A], J [auth C], M [auth D], P [auth E]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain G [auth A] Focus chain J [auth C] Focus chain M [auth D] Focus chain P [auth E] Interactions & Density Focus chain G [auth A] Focus chain J [auth C] Focus chain M [auth D] Focus chain P [auth E]
ZN Query on ZN Download Ideal Coordinates CCD File SDF format, chain F [auth A] SDF format, chain I [auth C] SDF format, chain L [auth D] SDF format, chain O [auth E] MOL2 format, chain F [auth A] MOL2 format, chain I [auth C] MOL2 format, chain L [auth D] MOL2 format, chain O [auth E] mmCIF format, chain F [auth A] mmCIF format, chain I [auth C] mmCIF format, chain L [auth D] mmCIF format, chain O [auth E]	F [auth A], I [auth C], L [auth D], O [auth E]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N		Interactions Focus chain F [auth A] Focus chain I [auth C] Focus chain L [auth D] Focus chain O [auth E] Interactions & Density Focus chain F [auth A] Focus chain I [auth C] Focus chain L [auth D] Focus chain O [auth E]