7KKT | pdb_00007kkt

Dihydrodipicolinate synthase (DHDPS) from C.jejuni, N84D mutant with pyruvate bound in the active site and R,R-bislysine bound at the allosteric site

PDB DOI: https://doi.org/10.2210/pdb7KKT/pdb

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

Deposited: 2020-10-28 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: 1.71 Å
R-Value Free:
0.195 (Depositor), 0.195 (DCC)
R-Value Work:
0.164 (Depositor), 0.165 (DCC)
R-Value Observed:
0.165 (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

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

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

To be published.

Macromolecule Content

Total Structure Weight: 209.29 kDa
Atom Count: 15,621
Modeled Residue Count: 1,797
Deposited Residue Count: 1,860
Unique protein chains: 1

Macromolecules

Find similar proteins by:

| 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 Query on 3VN Download:Ideal Coordinates CCD File SDF format, chain G [auth A] SDF format, chain L [auth B] SDF format, chain U [auth C] MOL2 format, chain G [auth A] MOL2 format, chain L [auth B] MOL2 format, chain U [auth C] mmCIF format, chain G [auth A] mmCIF format, chain L [auth B] mmCIF format, chain U [auth C]	G [auth A], L [auth B], U [auth C]	(2R,5R)-2,5-diamino-2,5-bis(4-aminobutyl)hexanedioic acid C₁₄ H₃₀ N₄ O₄ XYUHPPVEDOOPDE-ZIAGYGMSSA-N		Interactions Focus chain G [auth A] Focus chain L [auth B] Focus chain U [auth C] Interactions & Density Focus chain G [auth A] Focus chain L [auth B] Focus chain U [auth C]
PG4 Query on PG4 Download:Ideal Coordinates CCD File SDF format, chain FA [auth D] SDF format, chain M [auth B] MOL2 format, chain FA [auth D] MOL2 format, chain M [auth B] mmCIF format, chain FA [auth D] mmCIF format, chain M [auth B]	FA [auth D], M [auth B]	TETRAETHYLENE GLYCOL C₈ H₁₈ O₅ UWHCKJMYHZGTIT-UHFFFAOYSA-N		Interactions Focus chain FA [auth D] Focus chain M [auth B] Interactions & Density Focus chain FA [auth D] Focus chain M [auth B]
PGE Query on PGE Download:Ideal Coordinates CCD File SDF format, chain EB [auth F] SDF format, chain K [auth A] SDF format, chain X [auth C] MOL2 format, chain EB [auth F] MOL2 format, chain K [auth A] MOL2 format, chain X [auth C] mmCIF format, chain EB [auth F] mmCIF format, chain K [auth A] mmCIF format, chain X [auth C]	EB [auth F], K [auth A], X [auth C]	TRIETHYLENE GLYCOL C₆ H₁₄ O₄ ZIBGPFATKBEMQZ-UHFFFAOYSA-N		Interactions Focus chain EB [auth F] Focus chain K [auth A] Focus chain X [auth C] Interactions & Density Focus chain EB [auth F] Focus chain K [auth A] Focus chain X [auth C]
PEG Query on PEG Download:Ideal Coordinates CCD File SDF format, chain Y [auth C] SDF format, chain WA [auth E] SDF format, chain VA [auth E] MOL2 format, chain Y [auth C] MOL2 format, chain WA [auth E] MOL2 format, chain VA [auth E] mmCIF format, chain Y [auth C] mmCIF format, chain WA [auth E] mmCIF format, chain VA [auth E]	VA [auth E], WA [auth E], Y [auth C]	DI(HYDROXYETHYL)ETHER C₄ H₁₀ O₃ MTHSVFCYNBDYFN-UHFFFAOYSA-N		Interactions Focus chain VA [auth E] Focus chain WA [auth E] Focus chain Y [auth C] Interactions & Density Focus chain VA [auth E] Focus chain WA [auth E] Focus chain Y [auth C]
GOL Query on GOL Download:Ideal Coordinates CCD File SDF format, chain OA [auth D] MOL2 format, chain OA [auth D] mmCIF format, chain OA [auth D]	OA [auth D]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain OA [auth D] Interactions & Density Focus chain OA [auth D]
EDO Query on EDO Download:Ideal Coordinates CCD File SDF format, chain AB [auth E] SDF format, chain BA [auth C] SDF format, chain BB [auth E] SDF format, chain CA [auth C] SDF format, chain DA [auth C] SDF format, chain EA [auth C] SDF format, chain FB [auth F] SDF format, chain GB [auth F] SDF format, chain HB [auth F] SDF format, chain IB [auth F] SDF format, chain JA [auth D] SDF format, chain KA [auth D] SDF format, chain LA [auth D] SDF format, chain MA [auth D] SDF format, chain NA [auth D] SDF format, chain S [auth B] SDF format, chain T [auth B] SDF format, chain YA [auth E] SDF format, chain ZA [auth E] MOL2 format, chain AB [auth E] MOL2 format, chain BA [auth C] MOL2 format, chain BB [auth E] MOL2 format, chain CA [auth C] MOL2 format, chain DA [auth C] MOL2 format, chain EA [auth C] MOL2 format, chain FB [auth F] MOL2 format, chain GB [auth F] MOL2 format, chain HB [auth F] MOL2 format, chain IB [auth F] MOL2 format, chain JA [auth D] MOL2 format, chain KA [auth D] MOL2 format, chain LA [auth D] MOL2 format, chain MA [auth D] MOL2 format, chain NA [auth D] MOL2 format, chain S [auth B] MOL2 format, chain T [auth B] MOL2 format, chain YA [auth E] MOL2 format, chain ZA [auth E] mmCIF format, chain AB [auth E] mmCIF format, chain BA [auth C] mmCIF format, chain BB [auth E] mmCIF format, chain CA [auth C] mmCIF format, chain DA [auth C] mmCIF format, chain EA [auth C] mmCIF format, chain FB [auth F] mmCIF format, chain GB [auth F] mmCIF format, chain HB [auth F] mmCIF format, chain IB [auth F] mmCIF format, chain JA [auth D] mmCIF format, chain KA [auth D] mmCIF format, chain LA [auth D] mmCIF format, chain MA [auth D] mmCIF format, chain NA [auth D] mmCIF format, chain S [auth B] mmCIF format, chain T [auth B] mmCIF format, chain YA [auth E] mmCIF format, chain ZA [auth E]	AB [auth E] BA [auth C] BB [auth E] CA [auth C] DA [auth C] AB [auth E], BA [auth C], BB [auth E], CA [auth C], DA [auth C], EA [auth C], FB [auth F], GB [auth F], HB [auth F], IB [auth F], JA [auth D], KA [auth D], LA [auth D], MA [auth D], NA [auth D], S [auth B], T [auth B], YA [auth E], ZA [auth E]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain AB [auth E] Focus chain BA [auth C] Focus chain BB [auth E] Focus chain CA [auth C] Focus chain DA [auth C] Focus chain EA [auth C] Focus chain FB [auth F] Focus chain GB [auth F] Focus chain HB [auth F] Focus chain IB [auth F] Focus chain JA [auth D] Focus chain KA [auth D] Focus chain LA [auth D] Focus chain MA [auth D] Focus chain NA [auth D] Focus chain S [auth B] Focus chain T [auth B] Focus chain YA [auth E] Focus chain ZA [auth E] Interactions & Density Focus chain AB [auth E] Focus chain BA [auth C] Focus chain BB [auth E] Focus chain CA [auth C] Focus chain DA [auth C] Focus chain EA [auth C] Focus chain FB [auth F] Focus chain GB [auth F] Focus chain HB [auth F] Focus chain IB [auth F] Focus chain JA [auth D] Focus chain KA [auth D] Focus chain LA [auth D] Focus chain MA [auth D] Focus chain NA [auth D] Focus chain S [auth B] Focus chain T [auth B] Focus chain YA [auth E] Focus chain ZA [auth E]
ACT Query on ACT Download:Ideal Coordinates CCD File SDF format, chain AA [auth C] SDF format, chain IA [auth D] SDF format, chain R [auth B] SDF format, chain XA [auth E] SDF format, chain Z [auth C] SDF format, chain Q [auth B] MOL2 format, chain AA [auth C] MOL2 format, chain IA [auth D] MOL2 format, chain R [auth B] MOL2 format, chain XA [auth E] MOL2 format, chain Z [auth C] MOL2 format, chain Q [auth B] mmCIF format, chain AA [auth C] mmCIF format, chain IA [auth D] mmCIF format, chain R [auth B] mmCIF format, chain XA [auth E] mmCIF format, chain Z [auth C] mmCIF format, chain Q [auth B]	AA [auth C] IA [auth D] Q [auth B] R [auth B] XA [auth E] AA [auth C], IA [auth D], Q [auth B], R [auth B], XA [auth E], Z [auth C]	ACETATE ION C₂ H₃ O₂ QTBSBXVTEAMEQO-UHFFFAOYSA-M		Interactions Focus chain AA [auth C] Focus chain IA [auth D] Focus chain Q [auth B] Focus chain R [auth B] Focus chain XA [auth E] Focus chain Z [auth C] Interactions & Density Focus chain AA [auth C] Focus chain IA [auth D] Focus chain Q [auth B] Focus chain R [auth B] Focus chain XA [auth E] Focus chain Z [auth C]
MG Query on MG Download:Ideal Coordinates CCD File SDF format, chain CB [auth F] SDF format, chain DB [auth F] SDF format, chain GA [auth D] SDF format, chain H [auth A] SDF format, chain HA [auth D] SDF format, chain J [auth A] SDF format, chain N [auth B] SDF format, chain O [auth B] SDF format, chain P [auth B] SDF format, chain PA [auth E] SDF format, chain QA [auth E] SDF format, chain RA [auth E] SDF format, chain TA [auth E] SDF format, chain UA [auth E] SDF format, chain V [auth C] SDF format, chain W [auth C] SDF format, chain SA [auth E] SDF format, chain I [auth A] MOL2 format, chain CB [auth F] MOL2 format, chain DB [auth F] MOL2 format, chain GA [auth D] MOL2 format, chain H [auth A] MOL2 format, chain HA [auth D] MOL2 format, chain J [auth A] MOL2 format, chain N [auth B] MOL2 format, chain O [auth B] MOL2 format, chain P [auth B] MOL2 format, chain PA [auth E] MOL2 format, chain QA [auth E] MOL2 format, chain RA [auth E] MOL2 format, chain TA [auth E] MOL2 format, chain UA [auth E] MOL2 format, chain V [auth C] MOL2 format, chain W [auth C] MOL2 format, chain SA [auth E] MOL2 format, chain I [auth A] mmCIF format, chain CB [auth F] mmCIF format, chain DB [auth F] mmCIF format, chain GA [auth D] mmCIF format, chain H [auth A] mmCIF format, chain HA [auth D] mmCIF format, chain J [auth A] mmCIF format, chain N [auth B] mmCIF format, chain O [auth B] mmCIF format, chain P [auth B] mmCIF format, chain PA [auth E] mmCIF format, chain QA [auth E] mmCIF format, chain RA [auth E] mmCIF format, chain TA [auth E] mmCIF format, chain UA [auth E] mmCIF format, chain V [auth C] mmCIF format, chain W [auth C] mmCIF format, chain SA [auth E] mmCIF format, chain I [auth A]	CB [auth F] DB [auth F] GA [auth D] H [auth A] HA [auth D] CB [auth F], DB [auth F], GA [auth D], H [auth A], HA [auth D], I [auth A], J [auth A], N [auth B], O [auth B], P [auth B], PA [auth E], QA [auth E], RA [auth E], SA [auth E], TA [auth E], UA [auth E], V [auth C], W [auth C]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain CB [auth F] Focus chain DB [auth F] Focus chain GA [auth D] Focus chain H [auth A] Focus chain HA [auth D] Focus chain I [auth A] Focus chain J [auth A] Focus chain N [auth B] Focus chain O [auth B] Focus chain P [auth B] Focus chain PA [auth E] Focus chain QA [auth E] Focus chain RA [auth E] Focus chain SA [auth E] Focus chain TA [auth E] Focus chain UA [auth E] Focus chain V [auth C] Focus chain W [auth C] Interactions & Density Focus chain CB [auth F] Focus chain DB [auth F] Focus chain GA [auth D] Focus chain H [auth A] Focus chain HA [auth D] Focus chain I [auth A] Focus chain J [auth A] Focus chain N [auth B] Focus chain O [auth B] Focus chain P [auth B] Focus chain PA [auth E] Focus chain QA [auth E] Focus chain RA [auth E] Focus chain SA [auth E] Focus chain TA [auth E] Focus chain UA [auth E] Focus chain V [auth C] Focus chain W [auth C]