7KM1

Dihydrodipicolinate synthase (DHDPS) from C.jejuni, H59N mutant with pyruvate bound in the active site and R,R-bislysine bound at the allosteric site

PDB DOI: https://doi.org/10.2210/pdb7KM1/pdb

Classification: LYASE
Organism(s): Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819
Expression System: Escherichia coli
Mutation(s): Yes

Deposited: 2020-11-02 Released: 2021-11-17
Deposition Author(s): Saran, S., Majdi Yazdi, M., Sanders, D.A.R.
Funding Organization(s): Natural Sciences and Engineering Research Council (NSERC, Canada)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.84 Å
R-Value Free: 0.211
R-Value Work: 0.181
R-Value Observed: 0.183

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

H59 PLAYS THE MOST VITAL ROLE IN THE TRANSMISSION OF THE ALLOSTERIC INHIBITION SIGNALS IN Cj.DHDPS ENZYME

Saran, S., Skovpen, Y., Majdi Yazdi, M., Palmer, D.R.J., Sanders, D.A.R.

To be published.

Macromolecule Content

Total Structure Weight: 210.28 kDa
Atom Count: 14,728
Modelled Residue Count: 1,777
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): 1 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 8 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 DA [auth C] SDF format, chain DB [auth F] SDF format, chain I [auth A] MOL2 format, chain DA [auth C] MOL2 format, chain DB [auth F] MOL2 format, chain I [auth A] mmCIF format, chain DA [auth C] mmCIF format, chain DB [auth F] mmCIF format, chain I [auth A]	DA [auth C], DB [auth F], I [auth A]	(2R,5R)-2,5-diamino-2,5-bis(4-aminobutyl)hexanedioic acid C₁₄ H₃₀ N₄ O₄ XYUHPPVEDOOPDE-ZIAGYGMSSA-N		Interactions Focus chain DA [auth C] Focus chain DB [auth F] Focus chain I [auth A] Interactions & Density Focus chain DA [auth C] Focus chain DB [auth F] Focus chain I [auth A]
PG4 (Subject of Investigation/LOI) Query on PG4 Download Ideal Coordinates CCD File SDF format, chain CA [auth C] SDF format, chain CB [auth F] SDF format, chain G [auth A] SDF format, chain H [auth A] SDF format, chain TA [auth E] MOL2 format, chain CA [auth C] MOL2 format, chain CB [auth F] MOL2 format, chain G [auth A] MOL2 format, chain H [auth A] MOL2 format, chain TA [auth E] mmCIF format, chain CA [auth C] mmCIF format, chain CB [auth F] mmCIF format, chain G [auth A] mmCIF format, chain H [auth A] mmCIF format, chain TA [auth E]	CA [auth C], CB [auth F], G [auth A], H [auth A], TA [auth E]	TETRAETHYLENE GLYCOL C₈ H₁₈ O₅ UWHCKJMYHZGTIT-UHFFFAOYSA-N		Interactions Focus chain CA [auth C] Focus chain CB [auth F] Focus chain G [auth A] Focus chain H [auth A] Focus chain TA [auth E] Interactions & Density Focus chain CA [auth C] Focus chain CB [auth F] Focus chain G [auth A] Focus chain H [auth A] Focus chain TA [auth E]
PGE (Subject of Investigation/LOI) Query on PGE Download Ideal Coordinates CCD File SDF format, chain EA [auth C] SDF format, chain FA [auth C] SDF format, chain MA [auth D] SDF format, chain S [auth B] SDF format, chain UA [auth E] MOL2 format, chain EA [auth C] MOL2 format, chain FA [auth C] MOL2 format, chain MA [auth D] MOL2 format, chain S [auth B] MOL2 format, chain UA [auth E] mmCIF format, chain EA [auth C] mmCIF format, chain FA [auth C] mmCIF format, chain MA [auth D] mmCIF format, chain S [auth B] mmCIF format, chain UA [auth E]	EA [auth C], FA [auth C], MA [auth D], S [auth B], UA [auth E]	TRIETHYLENE GLYCOL C₆ H₁₄ O₄ ZIBGPFATKBEMQZ-UHFFFAOYSA-N		Interactions Focus chain EA [auth C] Focus chain FA [auth C] Focus chain MA [auth D] Focus chain S [auth B] Focus chain UA [auth E] Interactions & Density Focus chain EA [auth C] Focus chain FA [auth C] Focus chain MA [auth D] Focus chain S [auth B] Focus chain UA [auth E]
PEG (Subject of Investigation/LOI) Query on PEG Download Ideal Coordinates CCD File SDF format, chain JA [auth C] SDF format, chain L [auth A] SDF format, chain M [auth A] SDF format, chain N [auth A] SDF format, chain PA [auth D] SDF format, chain YA [auth E] MOL2 format, chain JA [auth C] MOL2 format, chain L [auth A] MOL2 format, chain M [auth A] MOL2 format, chain N [auth A] MOL2 format, chain PA [auth D] MOL2 format, chain YA [auth E] mmCIF format, chain JA [auth C] mmCIF format, chain L [auth A] mmCIF format, chain M [auth A] mmCIF format, chain N [auth A] mmCIF format, chain PA [auth D] mmCIF format, chain YA [auth E]	JA [auth C] L [auth A] M [auth A] N [auth A] PA [auth D] JA [auth C], L [auth A], M [auth A], N [auth A], PA [auth D], YA [auth E]	DI(HYDROXYETHYL)ETHER C₄ H₁₀ O₃ MTHSVFCYNBDYFN-UHFFFAOYSA-N		Interactions Focus chain JA [auth C] Focus chain L [auth A] Focus chain M [auth A] Focus chain N [auth A] Focus chain PA [auth D] Focus chain YA [auth E] Interactions & Density Focus chain JA [auth C] Focus chain L [auth A] Focus chain M [auth A] Focus chain N [auth A] Focus chain PA [auth D] Focus chain YA [auth E]
GOL (Subject of Investigation/LOI) Query on GOL Download Ideal Coordinates CCD File SDF format, chain BB [auth E] SDF format, chain IB [auth F] MOL2 format, chain BB [auth E] MOL2 format, chain IB [auth F] mmCIF format, chain BB [auth E] mmCIF format, chain IB [auth F]	BB [auth E], IB [auth F]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain BB [auth E] Focus chain IB [auth F] Interactions & Density Focus chain BB [auth E] Focus chain IB [auth F]
EDO (Subject of Investigation/LOI) Query on EDO Download Ideal Coordinates CCD File SDF format, chain EB [auth F] SDF format, chain FB [auth F] SDF format, chain GA [auth C] SDF format, chain HA [auth C] SDF format, chain IA [auth C] SDF format, chain J [auth A] SDF format, chain K [auth A] SDF format, chain NA [auth D] SDF format, chain OA [auth D] SDF format, chain T [auth B] SDF format, chain U [auth B] SDF format, chain V [auth B] SDF format, chain VA [auth E] SDF format, chain W [auth B] SDF format, chain WA [auth E] SDF format, chain X [auth B] SDF format, chain XA [auth E] SDF format, chain Y [auth B] MOL2 format, chain EB [auth F] MOL2 format, chain FB [auth F] MOL2 format, chain GA [auth C] MOL2 format, chain HA [auth C] MOL2 format, chain IA [auth C] MOL2 format, chain J [auth A] MOL2 format, chain K [auth A] MOL2 format, chain NA [auth D] MOL2 format, chain OA [auth D] MOL2 format, chain T [auth B] MOL2 format, chain U [auth B] MOL2 format, chain V [auth B] MOL2 format, chain VA [auth E] MOL2 format, chain W [auth B] MOL2 format, chain WA [auth E] MOL2 format, chain X [auth B] MOL2 format, chain XA [auth E] MOL2 format, chain Y [auth B] mmCIF format, chain EB [auth F] mmCIF format, chain FB [auth F] mmCIF format, chain GA [auth C] mmCIF format, chain HA [auth C] mmCIF format, chain IA [auth C] mmCIF format, chain J [auth A] mmCIF format, chain K [auth A] mmCIF format, chain NA [auth D] mmCIF format, chain OA [auth D] mmCIF format, chain T [auth B] mmCIF format, chain U [auth B] mmCIF format, chain V [auth B] mmCIF format, chain VA [auth E] mmCIF format, chain W [auth B] mmCIF format, chain WA [auth E] mmCIF format, chain X [auth B] mmCIF format, chain XA [auth E] mmCIF format, chain Y [auth B]	EB [auth F] FB [auth F] GA [auth C] HA [auth C] IA [auth C] EB [auth F], FB [auth F], GA [auth C], HA [auth C], IA [auth C], J [auth A], K [auth A], NA [auth D], OA [auth D], T [auth B], U [auth B], V [auth B], VA [auth E], W [auth B], WA [auth E], X [auth B], XA [auth E], Y [auth B]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain EB [auth F] Focus chain FB [auth F] Focus chain GA [auth C] Focus chain HA [auth C] Focus chain IA [auth C] Focus chain J [auth A] Focus chain K [auth A] Focus chain NA [auth D] Focus chain OA [auth D] Focus chain T [auth B] Focus chain U [auth B] Focus chain V [auth B] Focus chain VA [auth E] Focus chain W [auth B] Focus chain WA [auth E] Focus chain X [auth B] Focus chain XA [auth E] Focus chain Y [auth B] Interactions & Density Focus chain EB [auth F] Focus chain FB [auth F] Focus chain GA [auth C] Focus chain HA [auth C] Focus chain IA [auth C] Focus chain J [auth A] Focus chain K [auth A] Focus chain NA [auth D] Focus chain OA [auth D] Focus chain T [auth B] Focus chain U [auth B] Focus chain V [auth B] Focus chain VA [auth E] Focus chain W [auth B] Focus chain WA [auth E] Focus chain X [auth B] Focus chain XA [auth E] Focus chain Y [auth B]
ACT (Subject of Investigation/LOI) Query on ACT Download Ideal Coordinates CCD File SDF format, chain AB [auth E] SDF format, chain BA [auth B] SDF format, chain GB [auth F] SDF format, chain HB [auth F] SDF format, chain LA [auth C] SDF format, chain Q [auth A] SDF format, chain R [auth A] SDF format, chain SA [auth D] SDF format, chain ZA [auth E] MOL2 format, chain AB [auth E] MOL2 format, chain BA [auth B] MOL2 format, chain GB [auth F] MOL2 format, chain HB [auth F] MOL2 format, chain LA [auth C] MOL2 format, chain Q [auth A] MOL2 format, chain R [auth A] MOL2 format, chain SA [auth D] MOL2 format, chain ZA [auth E] mmCIF format, chain AB [auth E] mmCIF format, chain BA [auth B] mmCIF format, chain GB [auth F] mmCIF format, chain HB [auth F] mmCIF format, chain LA [auth C] mmCIF format, chain Q [auth A] mmCIF format, chain R [auth A] mmCIF format, chain SA [auth D] mmCIF format, chain ZA [auth E]	AB [auth E] BA [auth B] GB [auth F] HB [auth F] LA [auth C] AB [auth E], BA [auth B], GB [auth F], HB [auth F], LA [auth C], Q [auth A], R [auth A], SA [auth D], ZA [auth E]	ACETATE ION C₂ H₃ O₂ QTBSBXVTEAMEQO-UHFFFAOYSA-M		Interactions Focus chain AB [auth E] Focus chain BA [auth B] Focus chain GB [auth F] Focus chain HB [auth F] Focus chain LA [auth C] Focus chain Q [auth A] Focus chain R [auth A] Focus chain SA [auth D] Focus chain ZA [auth E] Interactions & Density Focus chain AB [auth E] Focus chain BA [auth B] Focus chain GB [auth F] Focus chain HB [auth F] Focus chain LA [auth C] Focus chain Q [auth A] Focus chain R [auth A] Focus chain SA [auth D] Focus chain ZA [auth E]
MG (Subject of Investigation/LOI) Query on MG Download Ideal Coordinates CCD File SDF format, chain AA [auth B] SDF format, chain KA [auth C] SDF format, chain O [auth A] SDF format, chain P [auth A] SDF format, chain QA [auth D] SDF format, chain RA [auth D] SDF format, chain Z [auth B] MOL2 format, chain AA [auth B] MOL2 format, chain KA [auth C] MOL2 format, chain O [auth A] MOL2 format, chain P [auth A] MOL2 format, chain QA [auth D] MOL2 format, chain RA [auth D] MOL2 format, chain Z [auth B] mmCIF format, chain AA [auth B] mmCIF format, chain KA [auth C] mmCIF format, chain O [auth A] mmCIF format, chain P [auth A] mmCIF format, chain QA [auth D] mmCIF format, chain RA [auth D] mmCIF format, chain Z [auth B]	AA [auth B] KA [auth C] O [auth A] P [auth A] QA [auth D] AA [auth B], KA [auth C], O [auth A], P [auth A], QA [auth D], RA [auth D], Z [auth B]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain AA [auth B] Focus chain KA [auth C] Focus chain O [auth A] Focus chain P [auth A] Focus chain QA [auth D] Focus chain RA [auth D] Focus chain Z [auth B] Interactions & Density Focus chain AA [auth B] Focus chain KA [auth C] Focus chain O [auth A] Focus chain P [auth A] Focus chain QA [auth D] Focus chain RA [auth D] Focus chain Z [auth B]