7KH4 | pdb_00007kh4

Dihydrodipicolinate synthase (DHDPS) from C.jejuni, H56W mutant with pyruvate bound in the active site and R,R-bislysine bound at the allosteric site

PDB DOI: https://doi.org/10.2210/pdb7KH4/pdb

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

Deposited: 2020-10-19 Released: 2021-10-27
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: 1.75 Å
R-Value Free:
0.185 (Depositor), 0.192 (DCC)
R-Value Work:
0.157 (Depositor), 0.165 (DCC)
R-Value Observed:
0.158 (Depositor)

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

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

Literature

Fluorescence-based Assay Development for Screening Novel Inhibitors of Dihydrodipicolinate Synthase from Campylobacter jejuni

Majdi Yazd, M., Reddy Annadi, K., Saran, S., Bhagwat, A., Sanders, D.A.R., Palmer, D.R.J.

To be published.

Macromolecule Content

Total Structure Weight: 212.55 kDa
Atom Count: 15,441
Modeled Residue Count: 1,793
Deposited Residue Count: 1,860
Unique protein chains: 1

Macromolecules

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| 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% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% 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 G [auth A] SDF format, chain BB [auth D] SDF format, chain AA [auth B] MOL2 format, chain G [auth A] MOL2 format, chain BB [auth D] MOL2 format, chain AA [auth B] mmCIF format, chain G [auth A] mmCIF format, chain BB [auth D] mmCIF format, chain AA [auth B]	AA [auth B], BB [auth D], G [auth A]	(2R,5R)-2,5-diamino-2,5-bis(4-aminobutyl)hexanedioic acid C₁₄ H₃₀ N₄ O₄ XYUHPPVEDOOPDE-ZIAGYGMSSA-N		Interactions Focus chain AA [auth B] Focus chain BB [auth D] Focus chain G [auth A] Interactions & Density Focus chain AA [auth B] Focus chain BB [auth D] Focus chain G [auth A]
PG4 (Subject of Investigation/LOI) Query on PG4 Download:Ideal Coordinates CCD File SDF format, chain UB [auth E] SDF format, chain SA [auth C] SDF format, chain L [auth A] SDF format, chain IC [auth F] SDF format, chain EA [auth B] SDF format, chain DB [auth D] MOL2 format, chain UB [auth E] MOL2 format, chain SA [auth C] MOL2 format, chain L [auth A] MOL2 format, chain IC [auth F] MOL2 format, chain EA [auth B] MOL2 format, chain DB [auth D] mmCIF format, chain UB [auth E] mmCIF format, chain SA [auth C] mmCIF format, chain L [auth A] mmCIF format, chain IC [auth F] mmCIF format, chain EA [auth B] mmCIF format, chain DB [auth D]	DB [auth D] EA [auth B] IC [auth F] L [auth A] SA [auth C] DB [auth D], EA [auth B], IC [auth F], L [auth A], SA [auth C], UB [auth E]	TETRAETHYLENE GLYCOL C₈ H₁₈ O₅ UWHCKJMYHZGTIT-UHFFFAOYSA-N		Interactions Focus chain DB [auth D] Focus chain EA [auth B] Focus chain IC [auth F] Focus chain L [auth A] Focus chain SA [auth C] Focus chain UB [auth E] Interactions & Density Focus chain DB [auth D] Focus chain EA [auth B] Focus chain IC [auth F] Focus chain L [auth A] Focus chain SA [auth C] Focus chain UB [auth E]
PGE (Subject of Investigation/LOI) Query on PGE Download:Ideal Coordinates CCD File SDF format, chain PA [auth B] SDF format, chain OB [auth D] SDF format, chain NB [auth D] SDF format, chain DC [auth E] MOL2 format, chain PA [auth B] MOL2 format, chain OB [auth D] MOL2 format, chain NB [auth D] MOL2 format, chain DC [auth E] mmCIF format, chain PA [auth B] mmCIF format, chain OB [auth D] mmCIF format, chain NB [auth D] mmCIF format, chain DC [auth E]	DC [auth E], NB [auth D], OB [auth D], PA [auth B]	TRIETHYLENE GLYCOL C₆ H₁₄ O₄ ZIBGPFATKBEMQZ-UHFFFAOYSA-N		Interactions Focus chain DC [auth E] Focus chain NB [auth D] Focus chain OB [auth D] Focus chain PA [auth B] Interactions & Density Focus chain DC [auth E] Focus chain NB [auth D] Focus chain OB [auth D] Focus chain PA [auth B]
PEG (Subject of Investigation/LOI) Query on PEG Download:Ideal Coordinates CCD File SDF format, chain ZA [auth C] SDF format, chain X [auth A] SDF format, chain W [auth A] SDF format, chain MC [auth F] SDF format, chain MA [auth B] SDF format, chain LC [auth F] SDF format, chain LA [auth B] SDF format, chain KA [auth B] SDF format, chain IB [auth D] SDF format, chain BC [auth E] MOL2 format, chain ZA [auth C] MOL2 format, chain X [auth A] MOL2 format, chain W [auth A] MOL2 format, chain MC [auth F] MOL2 format, chain MA [auth B] MOL2 format, chain LC [auth F] MOL2 format, chain LA [auth B] MOL2 format, chain KA [auth B] MOL2 format, chain IB [auth D] MOL2 format, chain BC [auth E] mmCIF format, chain ZA [auth C] mmCIF format, chain X [auth A] mmCIF format, chain W [auth A] mmCIF format, chain MC [auth F] mmCIF format, chain MA [auth B] mmCIF format, chain LC [auth F] mmCIF format, chain LA [auth B] mmCIF format, chain KA [auth B] mmCIF format, chain IB [auth D] mmCIF format, chain BC [auth E]	BC [auth E] IB [auth D] KA [auth B] LA [auth B] LC [auth F] BC [auth E], IB [auth D], KA [auth B], LA [auth B], LC [auth F], MA [auth B], MC [auth F], W [auth A], X [auth A], ZA [auth C]	DI(HYDROXYETHYL)ETHER C₄ H₁₀ O₃ MTHSVFCYNBDYFN-UHFFFAOYSA-N		Interactions Focus chain BC [auth E] Focus chain IB [auth D] Focus chain KA [auth B] Focus chain LA [auth B] Focus chain LC [auth F] Focus chain MA [auth B] Focus chain MC [auth F] Focus chain W [auth A] Focus chain X [auth A] Focus chain ZA [auth C] Interactions & Density Focus chain BC [auth E] Focus chain IB [auth D] Focus chain KA [auth B] Focus chain LA [auth B] Focus chain LC [auth F] Focus chain MA [auth B] Focus chain MC [auth F] Focus chain W [auth A] Focus chain X [auth A] Focus chain ZA [auth C]
GOL (Subject of Investigation/LOI) Query on GOL Download:Ideal Coordinates CCD File SDF format, chain AB [auth C] MOL2 format, chain AB [auth C] mmCIF format, chain AB [auth C]	AB [auth C]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain AB [auth C] Interactions & Density Focus chain AB [auth C]
EDO (Subject of Investigation/LOI) Query on EDO Download:Ideal Coordinates CCD File SDF format, chain ZB [auth E] SDF format, chain YB [auth E] SDF format, chain YA [auth C] SDF format, chain XB [auth E] SDF format, chain XA [auth C] SDF format, chain WB [auth E] SDF format, chain WA [auth C] SDF format, chain VB [auth E] SDF format, chain VA [auth C] SDF format, chain V [auth A] SDF format, chain UA [auth C] SDF format, chain U [auth A] SDF format, chain TA [auth C] SDF format, chain T [auth A] SDF format, chain S [auth A] SDF format, chain R [auth A] SDF format, chain Q [auth A] SDF format, chain P [auth A] SDF format, chain O [auth A] SDF format, chain N [auth A] SDF format, chain M [auth A] SDF format, chain KC [auth F] SDF format, chain JC [auth F] SDF format, chain JA [auth B] SDF format, chain IA [auth B] SDF format, chain HB [auth D] SDF format, chain HA [auth B] SDF format, chain GB [auth D] SDF format, chain GA [auth B] SDF format, chain FB [auth D] SDF format, chain FA [auth B] SDF format, chain EB [auth D] SDF format, chain AC [auth E] MOL2 format, chain ZB [auth E] MOL2 format, chain YB [auth E] MOL2 format, chain YA [auth C] MOL2 format, chain XB [auth E] MOL2 format, chain XA [auth C] MOL2 format, chain WB [auth E] MOL2 format, chain WA [auth C] MOL2 format, chain VB [auth E] MOL2 format, chain VA [auth C] MOL2 format, chain V [auth A] MOL2 format, chain UA [auth C] MOL2 format, chain U [auth A] MOL2 format, chain TA [auth C] MOL2 format, chain T [auth A] MOL2 format, chain S [auth A] MOL2 format, chain R [auth A] MOL2 format, chain Q [auth A] MOL2 format, chain P [auth A] MOL2 format, chain O [auth A] MOL2 format, chain N [auth A] MOL2 format, chain M [auth A] MOL2 format, chain KC [auth F] MOL2 format, chain JC [auth F] MOL2 format, chain JA [auth B] MOL2 format, chain IA [auth B] MOL2 format, chain HB [auth D] MOL2 format, chain HA [auth B] MOL2 format, chain GB [auth D] MOL2 format, chain GA [auth B] MOL2 format, chain FB [auth D] MOL2 format, chain FA [auth B] MOL2 format, chain EB [auth D] MOL2 format, chain AC [auth E] mmCIF format, chain ZB [auth E] mmCIF format, chain YB [auth E] mmCIF format, chain YA [auth C] mmCIF format, chain XB [auth E] mmCIF format, chain XA [auth C] mmCIF format, chain WB [auth E] mmCIF format, chain WA [auth C] mmCIF format, chain VB [auth E] mmCIF format, chain VA [auth C] mmCIF format, chain V [auth A] mmCIF format, chain UA [auth C] mmCIF format, chain U [auth A] mmCIF format, chain TA [auth C] mmCIF format, chain T [auth A] mmCIF format, chain S [auth A] mmCIF format, chain R [auth A] mmCIF format, chain Q [auth A] mmCIF format, chain P [auth A] mmCIF format, chain O [auth A] mmCIF format, chain N [auth A] mmCIF format, chain M [auth A] mmCIF format, chain KC [auth F] mmCIF format, chain JC [auth F] mmCIF format, chain JA [auth B] mmCIF format, chain IA [auth B] mmCIF format, chain HB [auth D] mmCIF format, chain HA [auth B] mmCIF format, chain GB [auth D] mmCIF format, chain GA [auth B] mmCIF format, chain FB [auth D] mmCIF format, chain FA [auth B] mmCIF format, chain EB [auth D] mmCIF format, chain AC [auth E]	AC [auth E] EB [auth D] FA [auth B] FB [auth D] GA [auth B] AC [auth E], EB [auth D], FA [auth B], FB [auth D], GA [auth B], GB [auth D], HA [auth B], HB [auth D], IA [auth B], JA [auth B], JC [auth F], KC [auth F], M [auth A], N [auth A], O [auth A], P [auth A], Q [auth A], R [auth A], S [auth A], T [auth A], TA [auth C], U [auth A], UA [auth C], V [auth A], VA [auth C], VB [auth E], WA [auth C], WB [auth E], XA [auth C], XB [auth E], YA [auth C], YB [auth E], ZB [auth E]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain AC [auth E] Focus chain EB [auth D] Focus chain FA [auth B] Focus chain FB [auth D] Focus chain GA [auth B] Focus chain GB [auth D] Focus chain HA [auth B] Focus chain HB [auth D] Focus chain IA [auth B] Focus chain JA [auth B] Focus chain JC [auth F] Focus chain KC [auth F] Focus chain M [auth A] Focus chain N [auth A] Focus chain O [auth A] Focus chain P [auth A] Focus chain Q [auth A] Focus chain R [auth A] Focus chain S [auth A] Focus chain T [auth A] Focus chain TA [auth C] Focus chain U [auth A] Focus chain UA [auth C] Focus chain V [auth A] Focus chain VA [auth C] Focus chain VB [auth E] Focus chain WA [auth C] Focus chain WB [auth E] Focus chain XA [auth C] Focus chain XB [auth E] Focus chain YA [auth C] Focus chain YB [auth E] Focus chain ZB [auth E] Interactions & Density Focus chain AC [auth E] Focus chain EB [auth D] Focus chain FA [auth B] Focus chain FB [auth D] Focus chain GA [auth B] Focus chain GB [auth D] Focus chain HA [auth B] Focus chain HB [auth D] Focus chain IA [auth B] Focus chain JA [auth B] Focus chain JC [auth F] Focus chain KC [auth F] Focus chain M [auth A] Focus chain N [auth A] Focus chain O [auth A] Focus chain P [auth A] Focus chain Q [auth A] Focus chain R [auth A] Focus chain S [auth A] Focus chain T [auth A] Focus chain TA [auth C] Focus chain U [auth A] Focus chain UA [auth C] Focus chain V [auth A] Focus chain VA [auth C] Focus chain VB [auth E] Focus chain WA [auth C] Focus chain WB [auth E] Focus chain XA [auth C] Focus chain XB [auth E] Focus chain YA [auth C] Focus chain YB [auth E] Focus chain ZB [auth E]
ACT (Subject of Investigation/LOI) Query on ACT Download:Ideal Coordinates CCD File SDF format, chain Z [auth A] SDF format, chain Y [auth A] SDF format, chain QC [auth F] SDF format, chain PC [auth F] SDF format, chain OC [auth F] SDF format, chain OA [auth B] SDF format, chain NC [auth F] SDF format, chain NA [auth B] SDF format, chain MB [auth D] SDF format, chain LB [auth D] SDF format, chain KB [auth D] SDF format, chain JB [auth D] SDF format, chain CC [auth E] MOL2 format, chain Z [auth A] MOL2 format, chain Y [auth A] MOL2 format, chain QC [auth F] MOL2 format, chain PC [auth F] MOL2 format, chain OC [auth F] MOL2 format, chain OA [auth B] MOL2 format, chain NC [auth F] MOL2 format, chain NA [auth B] MOL2 format, chain MB [auth D] MOL2 format, chain LB [auth D] MOL2 format, chain KB [auth D] MOL2 format, chain JB [auth D] MOL2 format, chain CC [auth E] mmCIF format, chain Z [auth A] mmCIF format, chain Y [auth A] mmCIF format, chain QC [auth F] mmCIF format, chain PC [auth F] mmCIF format, chain OC [auth F] mmCIF format, chain OA [auth B] mmCIF format, chain NC [auth F] mmCIF format, chain NA [auth B] mmCIF format, chain MB [auth D] mmCIF format, chain LB [auth D] mmCIF format, chain KB [auth D] mmCIF format, chain JB [auth D] mmCIF format, chain CC [auth E]	CC [auth E] JB [auth D] KB [auth D] LB [auth D] MB [auth D] CC [auth E], JB [auth D], KB [auth D], LB [auth D], MB [auth D], NA [auth B], NC [auth F], OA [auth B], OC [auth F], PC [auth F], QC [auth F], Y [auth A], Z [auth A]	ACETATE ION C₂ H₃ O₂ QTBSBXVTEAMEQO-UHFFFAOYSA-M		Interactions Focus chain CC [auth E] Focus chain JB [auth D] Focus chain KB [auth D] Focus chain LB [auth D] Focus chain MB [auth D] Focus chain NA [auth B] Focus chain NC [auth F] Focus chain OA [auth B] Focus chain OC [auth F] Focus chain PC [auth F] Focus chain QC [auth F] Focus chain Y [auth A] Focus chain Z [auth A] Interactions & Density Focus chain CC [auth E] Focus chain JB [auth D] Focus chain KB [auth D] Focus chain LB [auth D] Focus chain MB [auth D] Focus chain NA [auth B] Focus chain NC [auth F] Focus chain OA [auth B] Focus chain OC [auth F] Focus chain PC [auth F] Focus chain QC [auth F] Focus chain Y [auth A] Focus chain Z [auth A]
MG (Subject of Investigation/LOI) Query on MG Download:Ideal Coordinates CCD File SDF format, chain TB [auth E] SDF format, chain SB [auth E] SDF format, chain RB [auth E] SDF format, chain RA [auth C] SDF format, chain QB [auth E] SDF format, chain QA [auth C] SDF format, chain PB [auth E] SDF format, chain K [auth A] SDF format, chain J [auth A] SDF format, chain I [auth A] SDF format, chain HC [auth F] SDF format, chain H [auth A] SDF format, chain GC [auth F] SDF format, chain FC [auth F] SDF format, chain EC [auth F] SDF format, chain DA [auth B] SDF format, chain CB [auth D] SDF format, chain CA [auth B] SDF format, chain BA [auth B] MOL2 format, chain TB [auth E] MOL2 format, chain SB [auth E] MOL2 format, chain RB [auth E] MOL2 format, chain RA [auth C] MOL2 format, chain QB [auth E] MOL2 format, chain QA [auth C] MOL2 format, chain PB [auth E] MOL2 format, chain K [auth A] MOL2 format, chain J [auth A] MOL2 format, chain I [auth A] MOL2 format, chain HC [auth F] MOL2 format, chain H [auth A] MOL2 format, chain GC [auth F] MOL2 format, chain FC [auth F] MOL2 format, chain EC [auth F] MOL2 format, chain DA [auth B] MOL2 format, chain CB [auth D] MOL2 format, chain CA [auth B] MOL2 format, chain BA [auth B] mmCIF format, chain TB [auth E] mmCIF format, chain SB [auth E] mmCIF format, chain RB [auth E] mmCIF format, chain RA [auth C] mmCIF format, chain QB [auth E] mmCIF format, chain QA [auth C] mmCIF format, chain PB [auth E] mmCIF format, chain K [auth A] mmCIF format, chain J [auth A] mmCIF format, chain I [auth A] mmCIF format, chain HC [auth F] mmCIF format, chain H [auth A] mmCIF format, chain GC [auth F] mmCIF format, chain FC [auth F] mmCIF format, chain EC [auth F] mmCIF format, chain DA [auth B] mmCIF format, chain CB [auth D] mmCIF format, chain CA [auth B] mmCIF format, chain BA [auth B]	BA [auth B] CA [auth B] CB [auth D] DA [auth B] EC [auth F] BA [auth B], CA [auth B], CB [auth D], DA [auth B], EC [auth F], FC [auth F], GC [auth F], H [auth A], HC [auth F], I [auth A], J [auth A], K [auth A], PB [auth E], QA [auth C], QB [auth E], RA [auth C], RB [auth E], SB [auth E], TB [auth E]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain BA [auth B] Focus chain CA [auth B] Focus chain CB [auth D] Focus chain DA [auth B] Focus chain EC [auth F] Focus chain FC [auth F] Focus chain GC [auth F] Focus chain H [auth A] Focus chain HC [auth F] Focus chain I [auth A] Focus chain J [auth A] Focus chain K [auth A] Focus chain PB [auth E] Focus chain QA [auth C] Focus chain QB [auth E] Focus chain RA [auth C] Focus chain RB [auth E] Focus chain SB [auth E] Focus chain TB [auth E] Interactions & Density Focus chain BA [auth B] Focus chain CA [auth B] Focus chain CB [auth D] Focus chain DA [auth B] Focus chain EC [auth F] Focus chain FC [auth F] Focus chain GC [auth F] Focus chain H [auth A] Focus chain HC [auth F] Focus chain I [auth A] Focus chain J [auth A] Focus chain K [auth A] Focus chain PB [auth E] Focus chain QA [auth C] Focus chain QB [auth E] Focus chain RA [auth C] Focus chain RB [auth E] Focus chain SB [auth E] Focus chain TB [auth E]