7E4S | pdb_00007e4s

Crystal structure of Lactobacillus rhamnosus 4-deoxy-L-threo-5-hexosulose-uronate ketol-isomerase KduI complexed with HEPES

PDB DOI: https://doi.org/10.2210/pdb7E4S/pdb

Classification: ISOMERASE
Organism(s): Lacticaseibacillus rhamnosus
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2021-02-15 Released: 2022-02-23
Deposition Author(s): Yamamoto, Y., Takase, R., Mikami, B., Hashimoto, W.
Funding Organization(s): Japan Society for the Promotion of Science (JSPS)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.79 Å
R-Value Free:
0.238 (Depositor), 0.236 (DCC)
R-Value Work:
0.165 (Depositor), 0.169 (DCC)
R-Value Observed:
0.168 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.2 of the entry. See complete history.

Literature

Crystal structures of Lacticaseibacillus 4-deoxy-L-threo-5-hexosulose-uronate ketol-isomerase KduI in complex with substrate analogs

Iwase, H., Yamamoto, Y., Yamada, A., Kawai, K., Oiki, S., Watanabe, D., Mikami, B., Takase, R., Hashimoto, W.

(2023) J Appl Glycosci (1999)

DOI: https://doi.org/10.5458/jag.jag.JAG-2023_0003

Macromolecule Content

Total Structure Weight: 201.81 kDa
Atom Count: 13,356
Modeled Residue Count: 1,646
Deposited Residue Count: 1,734
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
5-dehydro-4-deoxy-D-glucuronate isomerase	A, B, C, D, E A, B, C, D, E, F	289	Lacticaseibacillus rhamnosus	Mutation(s): 0 Gene Names: kduI1, kduI, GKD15_03440, LRHP344_00167 EC: 5.3.1.17

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
EPE (Subject of Investigation/LOI) Query on EPE Download:Ideal Coordinates CCD File SDF format, chain Q [auth F] SDF format, chain O [auth E] SDF format, chain M [auth D] SDF format, chain K [auth C] SDF format, chain I [auth B] SDF format, chain G [auth A] MOL2 format, chain Q [auth F] MOL2 format, chain O [auth E] MOL2 format, chain M [auth D] MOL2 format, chain K [auth C] MOL2 format, chain I [auth B] MOL2 format, chain G [auth A] mmCIF format, chain Q [auth F] mmCIF format, chain O [auth E] mmCIF format, chain M [auth D] mmCIF format, chain K [auth C] mmCIF format, chain I [auth B] mmCIF format, chain G [auth A]	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]	4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID C₈ H₁₈ N₂ O₄ S JKMHFZQWWAIEOD-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]
ZN Query on ZN Download:Ideal Coordinates CCD File SDF format, chain R [auth F] SDF format, chain P [auth E] SDF format, chain N [auth D] SDF format, chain L [auth C] SDF format, chain J [auth B] SDF format, chain H [auth A] MOL2 format, chain R [auth F] MOL2 format, chain P [auth E] MOL2 format, chain N [auth D] MOL2 format, chain L [auth C] MOL2 format, chain J [auth B] MOL2 format, chain H [auth A] mmCIF format, chain R [auth F] mmCIF format, chain P [auth E] mmCIF format, chain N [auth D] mmCIF format, chain L [auth C] mmCIF format, chain J [auth B] mmCIF format, chain H [auth A]	H [auth A] J [auth B] L [auth C] N [auth D] P [auth E] H [auth A], J [auth B], L [auth C], N [auth D], P [auth E], R [auth F]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-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 E] 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 E] Focus chain R [auth F]