7KG5

Dihydrodipicolinate synthase (DHDPS) from C.jejuni, H56W mutant with pyruvate bound in the active site

PDB DOI: https://doi.org/10.2210/pdb7KG5/pdb

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

Deposited: 2020-10-15 Released: 2021-10-20
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: 1.95 Å
R-Value Free: 0.210
R-Value Work: 0.174
R-Value Observed: 0.176

wwPDB Validation 3D Report Full Report

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., Bhagwa, A., Sanders, D.A.R., Palmer, D.R.J.

To be published.

Macromolecule Content

Total Structure Weight: 210.24 kDa
Atom Count: 15,020
Modelled Residue Count: 1,778
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): 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 7 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
PG4 Query on PG4 Download Ideal Coordinates CCD File SDF format, chain BB [auth D] SDF format, chain R [auth A] MOL2 format, chain BB [auth D] MOL2 format, chain R [auth A]	BB [auth D], R [auth A]	TETRAETHYLENE GLYCOL C₈ H₁₈ O₅ UWHCKJMYHZGTIT-UHFFFAOYSA-N		Interactions Focus chain BB [auth D] Focus chain R [auth A] Interactions & Density Focus chain BB [auth D] Focus chain R [auth A]
PGE Query on PGE Download Ideal Coordinates CCD File SDF format, chain S [auth B] SDF format, chain CB [auth E] SDF format, chain FA [auth C] SDF format, chain T [auth B] MOL2 format, chain S [auth B] MOL2 format, chain CB [auth E] MOL2 format, chain FA [auth C] MOL2 format, chain T [auth B]	CB [auth E], FA [auth C], S [auth B], T [auth B]	TRIETHYLENE GLYCOL C₆ H₁₄ O₄ ZIBGPFATKBEMQZ-UHFFFAOYSA-N		Interactions Focus chain CB [auth E] Focus chain FA [auth C] Focus chain S [auth B] Focus chain T [auth B] Interactions & Density Focus chain CB [auth E] Focus chain FA [auth C] Focus chain S [auth B] Focus chain T [auth B]
PEG Query on PEG Download Ideal Coordinates CCD File SDF format, chain NA [auth C] SDF format, chain O [auth A] SDF format, chain PA [auth C] SDF format, chain RB [auth F] SDF format, chain XA [auth D] SDF format, chain OA [auth C] SDF format, chain P [auth A] SDF format, chain SB [auth F] SDF format, chain YA [auth D] MOL2 format, chain NA [auth C] MOL2 format, chain O [auth A] MOL2 format, chain PA [auth C] MOL2 format, chain RB [auth F] MOL2 format, chain XA [auth D] MOL2 format, chain OA [auth C] MOL2 format, chain P [auth A] MOL2 format, chain SB [auth F] MOL2 format, chain YA [auth D]	NA [auth C] O [auth A] OA [auth C] P [auth A] PA [auth C] NA [auth C], O [auth A], OA [auth C], P [auth A], PA [auth C], RB [auth F], SB [auth F], XA [auth D], YA [auth D]	DI(HYDROXYETHYL)ETHER C₄ H₁₀ O₃ MTHSVFCYNBDYFN-UHFFFAOYSA-N		Interactions Focus chain NA [auth C] Focus chain O [auth A] Focus chain OA [auth C] Focus chain P [auth A] Focus chain PA [auth C] Focus chain RB [auth F] Focus chain SB [auth F] Focus chain XA [auth D] Focus chain YA [auth D] Interactions & Density Focus chain NA [auth C] Focus chain O [auth A] Focus chain OA [auth C] Focus chain P [auth A] Focus chain PA [auth C] Focus chain RB [auth F] Focus chain SB [auth F] Focus chain XA [auth D] Focus chain YA [auth D]
GOL Query on GOL Download Ideal Coordinates CCD File SDF format, chain EA [auth B] SDF format, chain LB [auth E] SDF format, chain MB [auth E] SDF format, chain SA [auth C] MOL2 format, chain EA [auth B] MOL2 format, chain LB [auth E] MOL2 format, chain MB [auth E] MOL2 format, chain SA [auth C]	EA [auth B], LB [auth E], MB [auth E], SA [auth C]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain EA [auth B] Focus chain LB [auth E] Focus chain MB [auth E] Focus chain SA [auth C] Interactions & Density Focus chain EA [auth B] Focus chain LB [auth E] Focus chain MB [auth E] Focus chain SA [auth C]
EDO Query on EDO Download Ideal Coordinates CCD File SDF format, chain JA [auth C] SDF format, chain MA [auth C] SDF format, chain N [auth A] SDF format, chain VA [auth D] SDF format, chain WA [auth D] SDF format, chain AA [auth B] SDF format, chain BA [auth B] SDF format, chain CA [auth B] SDF format, chain DA [auth B] SDF format, chain FB [auth E] SDF format, chain GB [auth E] SDF format, chain HB [auth E] SDF format, chain I [auth A] SDF format, chain IA [auth C] SDF format, chain IB [auth E] SDF format, chain J [auth A] SDF format, chain JB [auth E] SDF format, chain K [auth A] SDF format, chain KA [auth C] SDF format, chain L [auth A] SDF format, chain LA [auth C] SDF format, chain M [auth A] SDF format, chain PB [auth F] SDF format, chain QB [auth F] SDF format, chain X [auth B] SDF format, chain Y [auth B] SDF format, chain Z [auth B] MOL2 format, chain JA [auth C] MOL2 format, chain MA [auth C] MOL2 format, chain N [auth A] MOL2 format, chain VA [auth D] MOL2 format, chain WA [auth D] MOL2 format, chain AA [auth B] MOL2 format, chain BA [auth B] MOL2 format, chain CA [auth B] MOL2 format, chain DA [auth B] MOL2 format, chain FB [auth E] MOL2 format, chain GB [auth E] MOL2 format, chain HB [auth E] MOL2 format, chain I [auth A] MOL2 format, chain IA [auth C] MOL2 format, chain IB [auth E] MOL2 format, chain J [auth A] MOL2 format, chain JB [auth E] MOL2 format, chain K [auth A] MOL2 format, chain KA [auth C] MOL2 format, chain L [auth A] MOL2 format, chain LA [auth C] MOL2 format, chain M [auth A] MOL2 format, chain PB [auth F] MOL2 format, chain QB [auth F] MOL2 format, chain X [auth B] MOL2 format, chain Y [auth B] MOL2 format, chain Z [auth B]	AA [auth B] BA [auth B] CA [auth B] DA [auth B] FB [auth E] AA [auth B], BA [auth B], CA [auth B], DA [auth B], FB [auth E], GB [auth E], HB [auth E], I [auth A], IA [auth C], IB [auth E], J [auth A], JA [auth C], JB [auth E], K [auth A], KA [auth C], L [auth A], LA [auth C], M [auth A], MA [auth C], N [auth A], PB [auth F], QB [auth F], VA [auth D], WA [auth D], X [auth B], Y [auth B], Z [auth B]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain AA [auth B] Focus chain BA [auth B] Focus chain CA [auth B] Focus chain DA [auth B] Focus chain FB [auth E] Focus chain GB [auth E] Focus chain HB [auth E] Focus chain I [auth A] Focus chain IA [auth C] Focus chain IB [auth E] Focus chain J [auth A] Focus chain JA [auth C] Focus chain JB [auth E] Focus chain K [auth A] Focus chain KA [auth C] Focus chain L [auth A] Focus chain LA [auth C] Focus chain M [auth A] Focus chain MA [auth C] Focus chain N [auth A] Focus chain PB [auth F] Focus chain QB [auth F] Focus chain VA [auth D] Focus chain WA [auth D] Focus chain X [auth B] Focus chain Y [auth B] Focus chain Z [auth B] Interactions & Density Focus chain AA [auth B] Focus chain BA [auth B] Focus chain CA [auth B] Focus chain DA [auth B] Focus chain FB [auth E] Focus chain GB [auth E] Focus chain HB [auth E] Focus chain I [auth A] Focus chain IA [auth C] Focus chain IB [auth E] Focus chain J [auth A] Focus chain JA [auth C] Focus chain JB [auth E] Focus chain K [auth A] Focus chain KA [auth C] Focus chain L [auth A] Focus chain LA [auth C] Focus chain M [auth A] Focus chain MA [auth C] Focus chain N [auth A] Focus chain PB [auth F] Focus chain QB [auth F] Focus chain VA [auth D] Focus chain WA [auth D] Focus chain X [auth B] Focus chain Y [auth B] Focus chain Z [auth B]
ACT Query on ACT Download Ideal Coordinates CCD File SDF format, chain AB [auth D] SDF format, chain KB [auth E] SDF format, chain Q [auth A] SDF format, chain QA [auth C] SDF format, chain RA [auth C] SDF format, chain TB [auth F] SDF format, chain UB [auth F] SDF format, chain VB [auth F] SDF format, chain ZA [auth D] MOL2 format, chain AB [auth D] MOL2 format, chain KB [auth E] MOL2 format, chain Q [auth A] MOL2 format, chain QA [auth C] MOL2 format, chain RA [auth C] MOL2 format, chain TB [auth F] MOL2 format, chain UB [auth F] MOL2 format, chain VB [auth F] MOL2 format, chain ZA [auth D]	AB [auth D] KB [auth E] Q [auth A] QA [auth C] RA [auth C] AB [auth D], KB [auth E], Q [auth A], QA [auth C], RA [auth C], TB [auth F], UB [auth F], VB [auth F], ZA [auth D]	ACETATE ION C₂ H₃ O₂ QTBSBXVTEAMEQO-UHFFFAOYSA-M		Interactions Focus chain AB [auth D] Focus chain KB [auth E] Focus chain Q [auth A] Focus chain QA [auth C] Focus chain RA [auth C] Focus chain TB [auth F] Focus chain UB [auth F] Focus chain VB [auth F] Focus chain ZA [auth D] Interactions & Density Focus chain AB [auth D] Focus chain KB [auth E] Focus chain Q [auth A] Focus chain QA [auth C] Focus chain RA [auth C] Focus chain TB [auth F] Focus chain UB [auth F] Focus chain VB [auth F] Focus chain ZA [auth D]
MG Query on MG Download Ideal Coordinates CCD File SDF format, chain GA [auth C] SDF format, chain V [auth B] SDF format, chain DB [auth E] SDF format, chain EB [auth E] SDF format, chain G [auth A] SDF format, chain H [auth A] SDF format, chain HA [auth C] SDF format, chain NB [auth F] SDF format, chain OB [auth F] SDF format, chain TA [auth D] SDF format, chain U [auth B] SDF format, chain UA [auth D] SDF format, chain W [auth B] MOL2 format, chain GA [auth C] MOL2 format, chain V [auth B] MOL2 format, chain DB [auth E] MOL2 format, chain EB [auth E] MOL2 format, chain G [auth A] MOL2 format, chain H [auth A] MOL2 format, chain HA [auth C] MOL2 format, chain NB [auth F] MOL2 format, chain OB [auth F] MOL2 format, chain TA [auth D] MOL2 format, chain U [auth B] MOL2 format, chain UA [auth D] MOL2 format, chain W [auth B]	DB [auth E] EB [auth E] G [auth A] GA [auth C] H [auth A] DB [auth E], EB [auth E], G [auth A], GA [auth C], H [auth A], HA [auth C], NB [auth F], OB [auth F], TA [auth D], U [auth B], UA [auth D], V [auth B], W [auth B]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain DB [auth E] Focus chain EB [auth E] Focus chain G [auth A] Focus chain GA [auth C] Focus chain H [auth A] Focus chain HA [auth C] Focus chain NB [auth F] Focus chain OB [auth F] Focus chain TA [auth D] Focus chain U [auth B] Focus chain UA [auth D] Focus chain V [auth B] Focus chain W [auth B] Interactions & Density Focus chain DB [auth E] Focus chain EB [auth E] Focus chain G [auth A] Focus chain GA [auth C] Focus chain H [auth A] Focus chain HA [auth C] Focus chain NB [auth F] Focus chain OB [auth F] Focus chain TA [auth D] Focus chain U [auth B] Focus chain UA [auth D] Focus chain V [auth B] Focus chain W [auth B]