7KXH

Dihydrodipicolinate synthase (DHDPS) from C.jejuni with pyruvate bound in the active site and R,R-bislysine bound at the allosteric site in C2221 space group

PDB DOI: https://doi.org/10.2210/pdb7KXH/pdb

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

Deposited: 2020-12-03 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: 1.94 Å
R-Value Free: 0.192
R-Value Work: 0.164
R-Value Observed: 0.166

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: 209.02 kDa
Atom Count: 14,766
Modelled Residue Count: 1,777
Deposited Residue Count: 1,860
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(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
3VN (Subject of Investigation/LOI) Query on 3VN Download Ideal Coordinates CCD File SDF format, chain G [auth A] SDF format, chain LA [auth E] SDF format, chain U [auth C] MOL2 format, chain G [auth A] MOL2 format, chain LA [auth E] MOL2 format, chain U [auth C]	G [auth A], LA [auth E], U [auth C]	(2R,5R)-2,5-diamino-2,5-bis(4-aminobutyl)hexanedioic acid C₁₄ H₃₀ N₄ O₄ XYUHPPVEDOOPDE-ZIAGYGMSSA-N		Interactions Focus chain G [auth A] Focus chain LA [auth E] Focus chain U [auth C] Interactions & Density Focus chain G [auth A] Focus chain LA [auth E] Focus chain U [auth C]
PGE (Subject of Investigation/LOI) Query on PGE Download Ideal Coordinates CCD File SDF format, chain FA [auth D] SDF format, chain J [auth A] SDF format, chain MA [auth E] SDF format, chain N [auth B] SDF format, chain SA [auth F] SDF format, chain X [auth C] MOL2 format, chain FA [auth D] MOL2 format, chain J [auth A] MOL2 format, chain MA [auth E] MOL2 format, chain N [auth B] MOL2 format, chain SA [auth F] MOL2 format, chain X [auth C]	FA [auth D] J [auth A] MA [auth E] N [auth B] SA [auth F] FA [auth D], J [auth A], MA [auth E], N [auth B], SA [auth F], X [auth C]	TRIETHYLENE GLYCOL C₆ H₁₄ O₄ ZIBGPFATKBEMQZ-UHFFFAOYSA-N		Interactions Focus chain FA [auth D] Focus chain J [auth A] Focus chain MA [auth E] Focus chain N [auth B] Focus chain SA [auth F] Focus chain X [auth C] Interactions & Density Focus chain FA [auth D] Focus chain J [auth A] Focus chain MA [auth E] Focus chain N [auth B] Focus chain SA [auth F] Focus chain X [auth C]
PEG (Subject of Investigation/LOI) Query on PEG Download Ideal Coordinates CCD File SDF format, chain JA [auth D] SDF format, chain KA [auth D] SDF format, chain L [auth A] SDF format, chain PA [auth E] SDF format, chain YA [auth F] MOL2 format, chain JA [auth D] MOL2 format, chain KA [auth D] MOL2 format, chain L [auth A] MOL2 format, chain PA [auth E] MOL2 format, chain YA [auth F]	JA [auth D], KA [auth D], L [auth A], PA [auth E], YA [auth F]	DI(HYDROXYETHYL)ETHER C₄ H₁₀ O₃ MTHSVFCYNBDYFN-UHFFFAOYSA-N		Interactions Focus chain JA [auth D] Focus chain KA [auth D] Focus chain L [auth A] Focus chain PA [auth E] Focus chain YA [auth F] Interactions & Density Focus chain JA [auth D] Focus chain KA [auth D] Focus chain L [auth A] Focus chain PA [auth E] Focus chain YA [auth F]
EDO (Subject of Investigation/LOI) Query on EDO Download Ideal Coordinates CCD File SDF format, chain AA [auth C] SDF format, chain BA [auth C] SDF format, chain HA [auth D] SDF format, chain IA [auth D] SDF format, chain OA [auth E] SDF format, chain Q [auth B] SDF format, chain R [auth B] SDF format, chain S [auth B] SDF format, chain T [auth B] SDF format, chain VA [auth F] SDF format, chain WA [auth F] SDF format, chain XA [auth F] MOL2 format, chain AA [auth C] MOL2 format, chain BA [auth C] MOL2 format, chain HA [auth D] MOL2 format, chain IA [auth D] MOL2 format, chain OA [auth E] MOL2 format, chain Q [auth B] MOL2 format, chain R [auth B] MOL2 format, chain S [auth B] MOL2 format, chain T [auth B] MOL2 format, chain VA [auth F] MOL2 format, chain WA [auth F] MOL2 format, chain XA [auth F]	AA [auth C] BA [auth C] HA [auth D] IA [auth D] OA [auth E] AA [auth C], BA [auth C], HA [auth D], IA [auth D], OA [auth E], Q [auth B], R [auth B], S [auth B], T [auth B], VA [auth F], WA [auth F], XA [auth F]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain AA [auth C] Focus chain BA [auth C] Focus chain HA [auth D] Focus chain IA [auth D] Focus chain OA [auth E] Focus chain Q [auth B] Focus chain R [auth B] Focus chain S [auth B] Focus chain T [auth B] Focus chain VA [auth F] Focus chain WA [auth F] Focus chain XA [auth F] Interactions & Density Focus chain AA [auth C] Focus chain BA [auth C] Focus chain HA [auth D] Focus chain IA [auth D] Focus chain OA [auth E] Focus chain Q [auth B] Focus chain R [auth B] Focus chain S [auth B] Focus chain T [auth B] Focus chain VA [auth F] Focus chain WA [auth F] Focus chain XA [auth F]
ACT (Subject of Investigation/LOI) Query on ACT Download Ideal Coordinates CCD File SDF format, chain GA [auth D] SDF format, chain K [auth A] SDF format, chain NA [auth E] SDF format, chain O [auth B] SDF format, chain P [auth B] SDF format, chain TA [auth F] SDF format, chain UA [auth F] SDF format, chain Y [auth C] SDF format, chain Z [auth C] MOL2 format, chain GA [auth D] MOL2 format, chain K [auth A] MOL2 format, chain NA [auth E] MOL2 format, chain O [auth B] MOL2 format, chain P [auth B] MOL2 format, chain TA [auth F] MOL2 format, chain UA [auth F] MOL2 format, chain Y [auth C] MOL2 format, chain Z [auth C]	GA [auth D] K [auth A] NA [auth E] O [auth B] P [auth B] GA [auth D], K [auth A], NA [auth E], O [auth B], P [auth B], TA [auth F], UA [auth F], Y [auth C], Z [auth C]	ACETATE ION C₂ H₃ O₂ QTBSBXVTEAMEQO-UHFFFAOYSA-M		Interactions Focus chain GA [auth D] Focus chain K [auth A] Focus chain NA [auth E] Focus chain O [auth B] Focus chain P [auth B] Focus chain TA [auth F] Focus chain UA [auth F] Focus chain Y [auth C] Focus chain Z [auth C] Interactions & Density Focus chain GA [auth D] Focus chain K [auth A] Focus chain NA [auth E] Focus chain O [auth B] Focus chain P [auth B] Focus chain TA [auth F] Focus chain UA [auth F] Focus chain Y [auth C] Focus chain Z [auth C]
MG (Subject of Investigation/LOI) Query on MG Download Ideal Coordinates CCD File SDF format, chain CA [auth D] SDF format, chain DA [auth D] SDF format, chain EA [auth D] SDF format, chain H [auth A] SDF format, chain I [auth A] SDF format, chain M [auth B] SDF format, chain QA [auth F] SDF format, chain RA [auth F] SDF format, chain V [auth C] SDF format, chain W [auth C] MOL2 format, chain CA [auth D] MOL2 format, chain DA [auth D] MOL2 format, chain EA [auth D] MOL2 format, chain H [auth A] MOL2 format, chain I [auth A] MOL2 format, chain M [auth B] MOL2 format, chain QA [auth F] MOL2 format, chain RA [auth F] MOL2 format, chain V [auth C] MOL2 format, chain W [auth C]	CA [auth D] DA [auth D] EA [auth D] H [auth A] I [auth A] CA [auth D], DA [auth D], EA [auth D], H [auth A], I [auth A], M [auth B], QA [auth F], RA [auth F], V [auth C], W [auth C]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain CA [auth D] Focus chain DA [auth D] Focus chain EA [auth D] Focus chain H [auth A] Focus chain I [auth A] Focus chain M [auth B] Focus chain QA [auth F] Focus chain RA [auth F] Focus chain V [auth C] Focus chain W [auth C] Interactions & Density Focus chain CA [auth D] Focus chain DA [auth D] Focus chain EA [auth D] Focus chain H [auth A] Focus chain I [auth A] Focus chain M [auth B] Focus chain QA [auth F] Focus chain RA [auth F] Focus chain V [auth C] Focus chain W [auth C]