8ZK8 | pdb_00008zk8

Crystal structure of the Decarboxylase KDC4427 mutant E468L in complex with indole-3-pyruvic acid

PDB DOI: https://doi.org/10.2210/pdb8ZK8/pdb

Classification: LYASE
Organism(s): Enterobacter sp. CGMCC 5087
Expression System: Escherichia coli BL21(DE3)
Mutation(s): Yes

Deposited: 2024-05-15 Released: 2025-05-21
Deposition Author(s): Dong, S., Liu, L., Zhang, H.
Funding Organization(s): National Natural Science Foundation of China (NSFC)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.16 Å
R-Value Free:
0.220 (Depositor), 0.215 (DCC)
R-Value Work:
0.182 (Depositor), 0.179 (DCC)
R-Value Observed:
0.184 (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 the Decarboxylase KDC4427 mutant E468L in complex with indole-3-pyruvic acid

Dong, S., Liu, L., Zhang, H.

To be published.

Macromolecule Content

Total Structure Weight: 125.19 kDa
Atom Count: 8,763
Modeled Residue Count: 1,072
Deposited Residue Count: 1,132
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Indolepyruvate decarboxylase	A, B	566	Enterobacter sp. CGMCC 5087	Mutation(s): 1 Gene Names: ipdC, DEO48_12930
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
TPP (Subject of Investigation/LOI) Query on TPP Download Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain F [auth B] MOL2 format, chain C [auth A] MOL2 format, chain F [auth B] mmCIF format, chain C [auth A] mmCIF format, chain F [auth B]	C [auth A], F [auth B]	THIAMINE DIPHOSPHATE C₁₂ H₁₉ N₄ O₇ P₂ S AYEKOFBPNLCAJY-UHFFFAOYSA-O		Interactions Focus chain C [auth A] Focus chain F [auth B] Interactions & Density Focus chain C [auth A] Focus chain F [auth B]
3IO (Subject of Investigation/LOI) Query on 3IO Download Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain H [auth B] MOL2 format, chain E [auth A] MOL2 format, chain H [auth B] mmCIF format, chain E [auth A] mmCIF format, chain H [auth B]	E [auth A], H [auth B]	3-(1H-INDOL-3-YL)-2-OXOPROPANOIC ACID C₁₁ H₉ N O₃ RSTKLPZEZYGQPY-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Focus chain H [auth B] Interactions & Density Focus chain E [auth A] Focus chain H [auth B]
MG (Subject of Investigation/LOI) Query on MG Download Ideal Coordinates CCD File SDF format, chain D [auth A] SDF format, chain G [auth B] MOL2 format, chain D [auth A] MOL2 format, chain G [auth B] mmCIF format, chain D [auth A] mmCIF format, chain G [auth B]	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]