7KK1

Dihydrodipicolinate synthase (DHDPS) from C.jejuni, N84A mutant with pyruvate bound in the active site and L-lysine bound at the allosteric site

PDB DOI: https://doi.org/10.2210/pdb7KK1/pdb

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

Deposited: 2020-10-27 Released: 2021-11-03
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: 1.77 Å
R-Value Free: 0.199
R-Value Work: 0.168
R-Value Observed: 0.170

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

A TIGHT DIMER INTERFACE N84 RESIDUE, PLAYS A CRITICAL ROLE IN THE TRANSMISSION OF THE ALLOSTERIC INHIBITION SIGNALS IN Cj.DHDPS

Saran, S., Majdi Yazd, M., Palmer, D.R.J., Sanders, D.A.R.

To be published.

Macromolecule Content

Total Structure Weight: 209.62 kDa
Atom Count: 15,136
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 7 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 BB [auth D] SDF format, chain HA [auth B] SDF format, chain IB [auth E] SDF format, chain P [auth A] SDF format, chain RA [auth C] SDF format, chain UB [auth F] MOL2 format, chain BB [auth D] MOL2 format, chain HA [auth B] MOL2 format, chain IB [auth E] MOL2 format, chain P [auth A] MOL2 format, chain RA [auth C] MOL2 format, chain UB [auth F] mmCIF format, chain BB [auth D] mmCIF format, chain HA [auth B] mmCIF format, chain IB [auth E] mmCIF format, chain P [auth A] mmCIF format, chain RA [auth C] mmCIF format, chain UB [auth F]	BB [auth D] HA [auth B] IB [auth E] P [auth A] RA [auth C] BB [auth D], HA [auth B], IB [auth E], P [auth A], RA [auth C], UB [auth F]	TRIETHYLENE GLYCOL C₆ H₁₄ O₄ ZIBGPFATKBEMQZ-UHFFFAOYSA-N		Interactions Focus chain BB [auth D] Focus chain HA [auth B] Focus chain IB [auth E] Focus chain P [auth A] Focus chain RA [auth C] Focus chain UB [auth F] Interactions & Density Focus chain BB [auth D] Focus chain HA [auth B] Focus chain IB [auth E] Focus chain P [auth A] Focus chain RA [auth C] Focus chain UB [auth F]
LYS (Subject of Investigation/LOI) Query on LYS Download Ideal Coordinates CCD File SDF format, chain CB [auth E] SDF format, chain G [auth A] SDF format, chain IA [auth C] SDF format, chain LB [auth F] SDF format, chain R [auth B] SDF format, chain TA [auth D] MOL2 format, chain CB [auth E] MOL2 format, chain G [auth A] MOL2 format, chain IA [auth C] MOL2 format, chain LB [auth F] MOL2 format, chain R [auth B] MOL2 format, chain TA [auth D] mmCIF format, chain CB [auth E] mmCIF format, chain G [auth A] mmCIF format, chain IA [auth C] mmCIF format, chain LB [auth F] mmCIF format, chain R [auth B] mmCIF format, chain TA [auth D]	CB [auth E] G [auth A] IA [auth C] LB [auth F] R [auth B] CB [auth E], G [auth A], IA [auth C], LB [auth F], R [auth B], TA [auth D]	LYSINE C₆ H₁₅ N₂ O₂ KDXKERNSBIXSRK-YFKPBYRVSA-O		Interactions Focus chain CB [auth E] Focus chain G [auth A] Focus chain IA [auth C] Focus chain LB [auth F] Focus chain R [auth B] Focus chain TA [auth D] Interactions & Density Focus chain CB [auth E] Focus chain G [auth A] Focus chain IA [auth C] Focus chain LB [auth F] Focus chain R [auth B] Focus chain TA [auth D]
PEG (Subject of Investigation/LOI) Query on PEG Download Ideal Coordinates CCD File SDF format, chain JB [auth E] SDF format, chain Q [auth A] SDF format, chain SA [auth C] MOL2 format, chain JB [auth E] MOL2 format, chain Q [auth A] MOL2 format, chain SA [auth C] mmCIF format, chain JB [auth E] mmCIF format, chain Q [auth A] mmCIF format, chain SA [auth C]	JB [auth E], Q [auth A], SA [auth C]	DI(HYDROXYETHYL)ETHER C₄ H₁₀ O₃ MTHSVFCYNBDYFN-UHFFFAOYSA-N		Interactions Focus chain JB [auth E] Focus chain Q [auth A] Focus chain SA [auth C] Interactions & Density Focus chain JB [auth E] Focus chain Q [auth A] Focus chain SA [auth C]
GOL (Subject of Investigation/LOI) Query on GOL Download Ideal Coordinates CCD File SDF format, chain KB [auth E] MOL2 format, chain KB [auth E] mmCIF format, chain KB [auth E]	KB [auth E]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain KB [auth E] Interactions & Density Focus chain KB [auth E]
EDO (Subject of Investigation/LOI) Query on EDO Download Ideal Coordinates CCD File 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 J [auth A] SDF format, chain K [auth A] SDF format, chain L [auth A] SDF format, chain LA [auth C] SDF format, chain M [auth A] SDF format, chain N [auth A] SDF format, chain NA [auth C] SDF format, chain O [auth A] SDF format, chain OB [auth F] SDF format, chain PB [auth F] SDF format, chain QB [auth F] SDF format, chain RB [auth F] SDF format, chain SB [auth F] SDF format, chain WA [auth D] SDF format, chain X [auth B] SDF format, chain Y [auth B] SDF format, chain YA [auth D] SDF format, chain Z [auth B] SDF format, chain GB [auth E] SDF format, chain MA [auth C] SDF format, chain XA [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 J [auth A] MOL2 format, chain K [auth A] MOL2 format, chain L [auth A] MOL2 format, chain LA [auth C] MOL2 format, chain M [auth A] MOL2 format, chain N [auth A] MOL2 format, chain NA [auth C] MOL2 format, chain O [auth A] MOL2 format, chain OB [auth F] MOL2 format, chain PB [auth F] MOL2 format, chain QB [auth F] MOL2 format, chain RB [auth F] MOL2 format, chain SB [auth F] MOL2 format, chain WA [auth D] MOL2 format, chain X [auth B] MOL2 format, chain Y [auth B] MOL2 format, chain YA [auth D] MOL2 format, chain Z [auth B] MOL2 format, chain GB [auth E] MOL2 format, chain MA [auth C] MOL2 format, chain XA [auth D] mmCIF format, chain AA [auth B] mmCIF format, chain BA [auth B] mmCIF format, chain CA [auth B] mmCIF format, chain DA [auth B] mmCIF format, chain FB [auth E] mmCIF format, chain J [auth A] mmCIF format, chain K [auth A] mmCIF format, chain L [auth A] mmCIF format, chain LA [auth C] mmCIF format, chain M [auth A] mmCIF format, chain N [auth A] mmCIF format, chain NA [auth C] mmCIF format, chain O [auth A] mmCIF format, chain OB [auth F] mmCIF format, chain PB [auth F] mmCIF format, chain QB [auth F] mmCIF format, chain RB [auth F] mmCIF format, chain SB [auth F] mmCIF format, chain WA [auth D] mmCIF format, chain X [auth B] mmCIF format, chain Y [auth B] mmCIF format, chain YA [auth D] mmCIF format, chain Z [auth B] mmCIF format, chain GB [auth E] mmCIF format, chain MA [auth C] mmCIF format, chain XA [auth D]	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], J [auth A], K [auth A], L [auth A], LA [auth C], M [auth A], MA [auth C], N [auth A], NA [auth C], O [auth A], OB [auth F], PB [auth F], QB [auth F], RB [auth F], SB [auth F], WA [auth D], X [auth B], XA [auth D], Y [auth B], YA [auth D], 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 J [auth A] Focus chain K [auth A] 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 NA [auth C] Focus chain O [auth A] Focus chain OB [auth F] Focus chain PB [auth F] Focus chain QB [auth F] Focus chain RB [auth F] Focus chain SB [auth F] Focus chain WA [auth D] Focus chain X [auth B] Focus chain XA [auth D] Focus chain Y [auth B] Focus chain YA [auth D] 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 J [auth A] Focus chain K [auth A] 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 NA [auth C] Focus chain O [auth A] Focus chain OB [auth F] Focus chain PB [auth F] Focus chain QB [auth F] Focus chain RB [auth F] Focus chain SB [auth F] Focus chain WA [auth D] Focus chain X [auth B] Focus chain XA [auth D] Focus chain Y [auth B] Focus chain YA [auth D] Focus chain Z [auth B]
ACT (Subject of Investigation/LOI) Query on ACT Download Ideal Coordinates CCD File SDF format, chain AB [auth D] SDF format, chain EA [auth B] SDF format, chain FA [auth B] SDF format, chain GA [auth B] SDF format, chain HB [auth E] SDF format, chain OA [auth C] SDF format, chain PA [auth C] SDF format, chain QA [auth C] SDF format, chain TB [auth F] SDF format, chain ZA [auth D] MOL2 format, chain AB [auth D] MOL2 format, chain EA [auth B] MOL2 format, chain FA [auth B] MOL2 format, chain GA [auth B] MOL2 format, chain HB [auth E] MOL2 format, chain OA [auth C] MOL2 format, chain PA [auth C] MOL2 format, chain QA [auth C] MOL2 format, chain TB [auth F] MOL2 format, chain ZA [auth D] mmCIF format, chain AB [auth D] mmCIF format, chain EA [auth B] mmCIF format, chain FA [auth B] mmCIF format, chain GA [auth B] mmCIF format, chain HB [auth E] mmCIF format, chain OA [auth C] mmCIF format, chain PA [auth C] mmCIF format, chain QA [auth C] mmCIF format, chain TB [auth F] mmCIF format, chain ZA [auth D]	AB [auth D] EA [auth B] FA [auth B] GA [auth B] HB [auth E] AB [auth D], EA [auth B], FA [auth B], GA [auth B], HB [auth E], OA [auth C], PA [auth C], QA [auth C], TB [auth F], ZA [auth D]	ACETATE ION C₂ H₃ O₂ QTBSBXVTEAMEQO-UHFFFAOYSA-M		Interactions Focus chain AB [auth D] Focus chain EA [auth B] Focus chain FA [auth B] Focus chain GA [auth B] Focus chain HB [auth E] Focus chain OA [auth C] Focus chain PA [auth C] Focus chain QA [auth C] Focus chain TB [auth F] Focus chain ZA [auth D] Interactions & Density Focus chain AB [auth D] Focus chain EA [auth B] Focus chain FA [auth B] Focus chain GA [auth B] Focus chain HB [auth E] Focus chain OA [auth C] Focus chain PA [auth C] Focus chain QA [auth C] Focus chain TB [auth F] Focus chain ZA [auth D]
MG (Subject of Investigation/LOI) Query on MG Download Ideal Coordinates CCD File SDF format, chain DB [auth E] SDF format, chain H [auth A] SDF format, chain I [auth A] SDF format, chain JA [auth C] SDF format, chain KA [auth C] SDF format, chain MB [auth F] SDF format, chain NB [auth F] SDF format, chain S [auth B] SDF format, chain T [auth B] SDF format, chain U [auth B] SDF format, chain V [auth B] SDF format, chain VA [auth D] SDF format, chain W [auth B] SDF format, chain EB [auth E] SDF format, chain UA [auth D] MOL2 format, chain DB [auth E] MOL2 format, chain H [auth A] MOL2 format, chain I [auth A] MOL2 format, chain JA [auth C] MOL2 format, chain KA [auth C] MOL2 format, chain MB [auth F] MOL2 format, chain NB [auth F] MOL2 format, chain S [auth B] MOL2 format, chain T [auth B] MOL2 format, chain U [auth B] MOL2 format, chain V [auth B] MOL2 format, chain VA [auth D] MOL2 format, chain W [auth B] MOL2 format, chain EB [auth E] MOL2 format, chain UA [auth D] mmCIF format, chain DB [auth E] mmCIF format, chain H [auth A] mmCIF format, chain I [auth A] mmCIF format, chain JA [auth C] mmCIF format, chain KA [auth C] mmCIF format, chain MB [auth F] mmCIF format, chain NB [auth F] mmCIF format, chain S [auth B] mmCIF format, chain T [auth B] mmCIF format, chain U [auth B] mmCIF format, chain V [auth B] mmCIF format, chain VA [auth D] mmCIF format, chain W [auth B] mmCIF format, chain EB [auth E] mmCIF format, chain UA [auth D]	DB [auth E] EB [auth E] H [auth A] I [auth A] JA [auth C] DB [auth E], EB [auth E], H [auth A], I [auth A], JA [auth C], KA [auth C], MB [auth F], NB [auth F], S [auth B], T [auth B], U [auth B], UA [auth D], V [auth B], VA [auth D], W [auth B]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain DB [auth E] Focus chain EB [auth E] Focus chain H [auth A] Focus chain I [auth A] Focus chain JA [auth C] Focus chain KA [auth C] Focus chain MB [auth F] Focus chain NB [auth F] Focus chain S [auth B] Focus chain T [auth B] Focus chain U [auth B] Focus chain UA [auth D] Focus chain V [auth B] Focus chain VA [auth D] Focus chain W [auth B] Interactions & Density Focus chain DB [auth E] Focus chain EB [auth E] Focus chain H [auth A] Focus chain I [auth A] Focus chain JA [auth C] Focus chain KA [auth C] Focus chain MB [auth F] Focus chain NB [auth F] Focus chain S [auth B] Focus chain T [auth B] Focus chain U [auth B] Focus chain UA [auth D] Focus chain V [auth B] Focus chain VA [auth D] Focus chain W [auth B]