7KKD

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

PDB DOI: https://doi.org/10.2210/pdb7KKD/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: 1.60 Å
R-Value Free: 0.182
R-Value Work: 0.153
R-Value Observed: 0.154

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: 208.2 kDa
Atom Count: 15,889
Modelled Residue Count: 1,796
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 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 AA [auth C] SDF format, chain G [auth A] SDF format, chain O [auth B] MOL2 format, chain AA [auth C] MOL2 format, chain G [auth A] MOL2 format, chain O [auth B] mmCIF format, chain AA [auth C] mmCIF format, chain G [auth A] mmCIF format, chain O [auth B]	AA [auth C], G [auth A], O [auth B]	(2R,5R)-2,5-diamino-2,5-bis(4-aminobutyl)hexanedioic acid C₁₄ H₃₀ N₄ O₄ XYUHPPVEDOOPDE-ZIAGYGMSSA-N		Interactions Focus chain AA [auth C] Focus chain G [auth A] Focus chain O [auth B] Interactions & Density Focus chain AA [auth C] Focus chain G [auth A] Focus chain O [auth B]
PGE (Subject of Investigation/LOI) Query on PGE Download Ideal Coordinates CCD File SDF format, chain IA [auth D] SDF format, chain M [auth A] SDF format, chain MA [auth E] SDF format, chain SA [auth F] SDF format, chain Z [auth B] MOL2 format, chain IA [auth D] MOL2 format, chain M [auth A] MOL2 format, chain MA [auth E] MOL2 format, chain SA [auth F] MOL2 format, chain Z [auth B] mmCIF format, chain IA [auth D] mmCIF format, chain M [auth A] mmCIF format, chain MA [auth E] mmCIF format, chain SA [auth F] mmCIF format, chain Z [auth B]	IA [auth D], M [auth A], MA [auth E], SA [auth F], Z [auth B]	TRIETHYLENE GLYCOL C₆ H₁₄ O₄ ZIBGPFATKBEMQZ-UHFFFAOYSA-N		Interactions Focus chain IA [auth D] Focus chain M [auth A] Focus chain MA [auth E] Focus chain SA [auth F] Focus chain Z [auth B] Interactions & Density Focus chain IA [auth D] Focus chain M [auth A] Focus chain MA [auth E] Focus chain SA [auth F] Focus chain Z [auth B]
PEG (Subject of Investigation/LOI) Query on PEG Download Ideal Coordinates CCD File SDF format, chain NA [auth E] SDF format, chain N [auth A] MOL2 format, chain NA [auth E] MOL2 format, chain N [auth A] mmCIF format, chain NA [auth E] mmCIF format, chain N [auth A]	N [auth A], NA [auth E]	DI(HYDROXYETHYL)ETHER C₄ H₁₀ O₃ MTHSVFCYNBDYFN-UHFFFAOYSA-N		Interactions Focus chain N [auth A] Focus chain NA [auth E] Interactions & Density Focus chain N [auth A] Focus chain NA [auth E]
EDO (Subject of Investigation/LOI) Query on EDO Download Ideal Coordinates CCD File SDF format, chain EA [auth C] SDF format, chain K [auth A] SDF format, chain KA [auth E] SDF format, chain L [auth A] SDF format, chain LA [auth E] SDF format, chain RA [auth F] SDF format, chain V [auth B] SDF format, chain W [auth B] SDF format, chain X [auth B] SDF format, chain Y [auth B] MOL2 format, chain EA [auth C] MOL2 format, chain K [auth A] MOL2 format, chain KA [auth E] MOL2 format, chain L [auth A] MOL2 format, chain LA [auth E] MOL2 format, chain RA [auth F] MOL2 format, chain V [auth B] MOL2 format, chain W [auth B] MOL2 format, chain X [auth B] MOL2 format, chain Y [auth B] mmCIF format, chain EA [auth C] mmCIF format, chain K [auth A] mmCIF format, chain KA [auth E] mmCIF format, chain L [auth A] mmCIF format, chain LA [auth E] mmCIF format, chain RA [auth F] mmCIF format, chain V [auth B] mmCIF format, chain W [auth B] mmCIF format, chain X [auth B] mmCIF format, chain Y [auth B]	EA [auth C] K [auth A] KA [auth E] L [auth A] LA [auth E] EA [auth C], K [auth A], KA [auth E], L [auth A], LA [auth E], RA [auth F], V [auth B], W [auth B], X [auth B], Y [auth B]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain EA [auth C] Focus chain K [auth A] Focus chain KA [auth E] Focus chain L [auth A] Focus chain LA [auth E] Focus chain RA [auth F] Focus chain V [auth B] Focus chain W [auth B] Focus chain X [auth B] Focus chain Y [auth B] Interactions & Density Focus chain EA [auth C] Focus chain K [auth A] Focus chain KA [auth E] Focus chain L [auth A] Focus chain LA [auth E] Focus chain RA [auth F] Focus chain V [auth B] Focus chain W [auth B] Focus chain X [auth B] Focus chain Y [auth B]
ACT (Subject of Investigation/LOI) Query on ACT Download Ideal Coordinates CCD File SDF format, chain CA [auth C] SDF format, chain DA [auth C] SDF format, chain HA [auth D] SDF format, chain I [auth A] SDF format, chain J [auth A] SDF format, chain JA [auth E] SDF format, chain PA [auth F] SDF format, chain QA [auth F] SDF format, chain T [auth B] SDF format, chain U [auth B] MOL2 format, chain CA [auth C] MOL2 format, chain DA [auth C] MOL2 format, chain HA [auth D] MOL2 format, chain I [auth A] MOL2 format, chain J [auth A] MOL2 format, chain JA [auth E] MOL2 format, chain PA [auth F] MOL2 format, chain QA [auth F] MOL2 format, chain T [auth B] MOL2 format, chain U [auth B] mmCIF format, chain CA [auth C] mmCIF format, chain DA [auth C] mmCIF format, chain HA [auth D] mmCIF format, chain I [auth A] mmCIF format, chain J [auth A] mmCIF format, chain JA [auth E] mmCIF format, chain PA [auth F] mmCIF format, chain QA [auth F] mmCIF format, chain T [auth B] mmCIF format, chain U [auth B]	CA [auth C] DA [auth C] HA [auth D] I [auth A] J [auth A] CA [auth C], DA [auth C], HA [auth D], I [auth A], J [auth A], JA [auth E], PA [auth F], QA [auth F], T [auth B], U [auth B]	ACETATE ION C₂ H₃ O₂ QTBSBXVTEAMEQO-UHFFFAOYSA-M		Interactions Focus chain CA [auth C] Focus chain DA [auth C] Focus chain HA [auth D] Focus chain I [auth A] Focus chain J [auth A] Focus chain JA [auth E] Focus chain PA [auth F] Focus chain QA [auth F] Focus chain T [auth B] Focus chain U [auth B] Interactions & Density Focus chain CA [auth C] Focus chain DA [auth C] Focus chain HA [auth D] Focus chain I [auth A] Focus chain J [auth A] Focus chain JA [auth E] Focus chain PA [auth F] Focus chain QA [auth F] Focus chain T [auth B] Focus chain U [auth B]
MG (Subject of Investigation/LOI) Query on MG Download Ideal Coordinates CCD File SDF format, chain BA [auth C] SDF format, chain FA [auth D] SDF format, chain GA [auth D] SDF format, chain H [auth A] SDF format, chain OA [auth F] SDF format, chain P [auth B] SDF format, chain Q [auth B] SDF format, chain R [auth B] SDF format, chain S [auth B] MOL2 format, chain BA [auth C] MOL2 format, chain FA [auth D] MOL2 format, chain GA [auth D] MOL2 format, chain H [auth A] MOL2 format, chain OA [auth F] MOL2 format, chain P [auth B] MOL2 format, chain Q [auth B] MOL2 format, chain R [auth B] MOL2 format, chain S [auth B] mmCIF format, chain BA [auth C] mmCIF format, chain FA [auth D] mmCIF format, chain GA [auth D] mmCIF format, chain H [auth A] mmCIF format, chain OA [auth F] mmCIF format, chain P [auth B] mmCIF format, chain Q [auth B] mmCIF format, chain R [auth B] mmCIF format, chain S [auth B]	BA [auth C] FA [auth D] GA [auth D] H [auth A] OA [auth F] BA [auth C], FA [auth D], GA [auth D], H [auth A], OA [auth F], P [auth B], Q [auth B], R [auth B], S [auth B]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain BA [auth C] Focus chain FA [auth D] Focus chain GA [auth D] Focus chain H [auth A] Focus chain OA [auth F] Focus chain P [auth B] Focus chain Q [auth B] Focus chain R [auth B] Focus chain S [auth B] Interactions & Density Focus chain BA [auth C] Focus chain FA [auth D] Focus chain GA [auth D] Focus chain H [auth A] Focus chain OA [auth F] Focus chain P [auth B] Focus chain Q [auth B] Focus chain R [auth B] Focus chain S [auth B]