7KWN

Dihydrodipicolinate synthase from C. jejuni with pyruvate bound to the active site in C2221 space group

PDB DOI: https://doi.org/10.2210/pdb7KWN/pdb

Classification: LYASE
Organism(s): Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2020-12-01 Released: 2021-12-08
Deposition Author(s): Saran, S., Sanders, D.A.R.
Funding Organization(s): Natural Sciences and Engineering Research Council (NSERC, Canada)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.24 Å
R-Value Free: 0.216
R-Value Work: 0.177
R-Value Observed: 0.179

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

B-FACTOR ANALYSIS SUGGEST THAT L-LYSINE AND R, R-BISLYSINE ALLOSTERICALLY INHIBIT Cj.DHDPS ENZYME BY DECREASING PROTEIN DYNAMICS.

Saran, S., Sanders, D.A.R.

To be published.

Macromolecule Content

Total Structure Weight: 207.72 kDa
Atom Count: 14,484
Modelled Residue Count: 1,778
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
4-hydroxy-tetrahydrodipicolinate synthase	A, B, C, D, E A, B, C, D, E, F	310	Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819	Mutation(s): 0 Gene Names: dapA, Cj0806 EC: 4.3.3.7
UniProt
Find proteins for Q9PPB4 (Campylobacter jejuni subsp. jejuni serotype O:2 (strain ATCC 700819 / NCTC 11168)) Explore Q9PPB4 Go to UniProtKB: Q9PPB4
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q9PPB4
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 6 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
PGE (Subject of Investigation/LOI) Query on PGE Download Ideal Coordinates CCD File SDF format, chain CA [auth E] SDF format, chain FA [auth F] SDF format, chain G [auth A] SDF format, chain N [auth B] SDF format, chain W [auth C] SDF format, chain Z [auth D] MOL2 format, chain CA [auth E] MOL2 format, chain FA [auth F] MOL2 format, chain G [auth A] MOL2 format, chain N [auth B] MOL2 format, chain W [auth C] MOL2 format, chain Z [auth D] mmCIF format, chain CA [auth E] mmCIF format, chain FA [auth F] mmCIF format, chain G [auth A] mmCIF format, chain N [auth B] mmCIF format, chain W [auth C] mmCIF format, chain Z [auth D]	CA [auth E] FA [auth F] G [auth A] N [auth B] W [auth C] CA [auth E], FA [auth F], G [auth A], N [auth B], W [auth C], Z [auth D]	TRIETHYLENE GLYCOL C₆ H₁₄ O₄ ZIBGPFATKBEMQZ-UHFFFAOYSA-N		Interactions Focus chain CA [auth E] Focus chain FA [auth F] Focus chain G [auth A] Focus chain N [auth B] Focus chain W [auth C] Focus chain Z [auth D] Interactions & Density Focus chain CA [auth E] Focus chain FA [auth F] Focus chain G [auth A] Focus chain N [auth B] Focus chain W [auth C] Focus chain Z [auth D]
PEG (Subject of Investigation/LOI) Query on PEG Download Ideal Coordinates CCD File SDF format, chain BA [auth D] SDF format, chain EA [auth E] SDF format, chain GA [auth F] SDF format, chain Q [auth B] SDF format, chain R [auth B] MOL2 format, chain BA [auth D] MOL2 format, chain EA [auth E] MOL2 format, chain GA [auth F] MOL2 format, chain Q [auth B] MOL2 format, chain R [auth B] mmCIF format, chain BA [auth D] mmCIF format, chain EA [auth E] mmCIF format, chain GA [auth F] mmCIF format, chain Q [auth B] mmCIF format, chain R [auth B]	BA [auth D], EA [auth E], GA [auth F], Q [auth B], R [auth B]	DI(HYDROXYETHYL)ETHER C₄ H₁₀ O₃ MTHSVFCYNBDYFN-UHFFFAOYSA-N		Interactions Focus chain BA [auth D] Focus chain EA [auth E] Focus chain GA [auth F] Focus chain Q [auth B] Focus chain R [auth B] Interactions & Density Focus chain BA [auth D] Focus chain EA [auth E] Focus chain GA [auth F] Focus chain Q [auth B] Focus chain R [auth B]
GOL (Subject of Investigation/LOI) Query on GOL Download Ideal Coordinates CCD File SDF format, chain AA [auth D] SDF format, chain H [auth A] SDF format, chain I [auth A] MOL2 format, chain AA [auth D] MOL2 format, chain H [auth A] MOL2 format, chain I [auth A] mmCIF format, chain AA [auth D] mmCIF format, chain H [auth A] mmCIF format, chain I [auth A]	AA [auth D], H [auth A], I [auth A]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain AA [auth D] Focus chain H [auth A] Focus chain I [auth A] Interactions & Density Focus chain AA [auth D] Focus chain H [auth A] Focus chain I [auth A]
EDO (Subject of Investigation/LOI) Query on EDO Download Ideal Coordinates CCD File SDF format, chain HA [auth F] SDF format, chain IA [auth F] SDF format, chain JA [auth F] SDF format, chain M [auth A] SDF format, chain U [auth B] SDF format, chain V [auth B] SDF format, chain Y [auth C] MOL2 format, chain HA [auth F] MOL2 format, chain IA [auth F] MOL2 format, chain JA [auth F] MOL2 format, chain M [auth A] MOL2 format, chain U [auth B] MOL2 format, chain V [auth B] MOL2 format, chain Y [auth C] mmCIF format, chain HA [auth F] mmCIF format, chain IA [auth F] mmCIF format, chain JA [auth F] mmCIF format, chain M [auth A] mmCIF format, chain U [auth B] mmCIF format, chain V [auth B] mmCIF format, chain Y [auth C]	HA [auth F] IA [auth F] JA [auth F] M [auth A] U [auth B] HA [auth F], IA [auth F], JA [auth F], M [auth A], U [auth B], V [auth B], Y [auth C]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain HA [auth F] Focus chain IA [auth F] Focus chain JA [auth F] Focus chain M [auth A] Focus chain U [auth B] Focus chain V [auth B] Focus chain Y [auth C] Interactions & Density Focus chain HA [auth F] Focus chain IA [auth F] Focus chain JA [auth F] Focus chain M [auth A] Focus chain U [auth B] Focus chain V [auth B] Focus chain Y [auth C]
ACT (Subject of Investigation/LOI) Query on ACT Download Ideal Coordinates CCD File SDF format, chain DA [auth E] SDF format, chain J [auth A] SDF format, chain K [auth A] SDF format, chain L [auth A] SDF format, chain O [auth B] SDF format, chain P [auth B] SDF format, chain X [auth C] MOL2 format, chain DA [auth E] MOL2 format, chain J [auth A] MOL2 format, chain K [auth A] MOL2 format, chain L [auth A] MOL2 format, chain O [auth B] MOL2 format, chain P [auth B] MOL2 format, chain X [auth C] mmCIF format, chain DA [auth E] mmCIF format, chain J [auth A] mmCIF format, chain K [auth A] mmCIF format, chain L [auth A] mmCIF format, chain O [auth B] mmCIF format, chain P [auth B] mmCIF format, chain X [auth C]	DA [auth E] J [auth A] K [auth A] L [auth A] O [auth B] DA [auth E], J [auth A], K [auth A], L [auth A], O [auth B], P [auth B], X [auth C]	ACETATE ION C₂ H₃ O₂ QTBSBXVTEAMEQO-UHFFFAOYSA-M		Interactions Focus chain DA [auth E] Focus chain J [auth A] Focus chain K [auth A] Focus chain L [auth A] Focus chain O [auth B] Focus chain P [auth B] Focus chain X [auth C] Interactions & Density Focus chain DA [auth E] Focus chain J [auth A] Focus chain K [auth A] Focus chain L [auth A] Focus chain O [auth B] Focus chain P [auth B] Focus chain X [auth C]
MG (Subject of Investigation/LOI) Query on MG Download Ideal Coordinates CCD File SDF format, chain S [auth B] SDF format, chain T [auth B] MOL2 format, chain S [auth B] MOL2 format, chain T [auth B] mmCIF format, chain S [auth B] mmCIF format, chain T [auth B]	S [auth B], T [auth B]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain S [auth B] Focus chain T [auth B] Interactions & Density Focus chain S [auth B] Focus chain T [auth B]