7KR7 | pdb_00007kr7

Dihydrodipicolinate synthase (DHDPS) from C.jejuni, H56A mutant with pyruvate bound in the active site and L-lysine at the allosteric site

PDB DOI: https://doi.org/10.2210/pdb7KR7/pdb

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

Deposited: 2020-11-18 Released: 2021-11-24
Deposition Author(s): Saran, S., Sanders, D.A.R.
Funding Organization(s): Natural Sciences and Engineering Research Council (NSERC, Canada)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.22 Å
R-Value Free:
0.189 (Depositor), 0.189 (DCC)
R-Value Work:
0.149 (Depositor), 0.153 (DCC)
R-Value Observed:
0.151 (Depositor)

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

ALLOSTERIC SITE RESIDUE 'H56' CAPS THE INHIBITOR AT THE TIGHT DIMER INTERFACE FOR TRANSMITTING THE ALLOSTERIC INHIBITION SIGNALS IN Cj.DHDPS

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

To be published.

Macromolecule Content

Total Structure Weight: 208.34 kDa
Atom Count: 14,969
Modeled Residue Count: 1,777
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 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 DA [auth D] SDF format, chain EA [auth D] SDF format, chain HA [auth E] SDF format, chain I [auth A] SDF format, chain N [auth B] SDF format, chain X [auth C] MOL2 format, chain DA [auth D] MOL2 format, chain EA [auth D] MOL2 format, chain HA [auth E] MOL2 format, chain I [auth A] MOL2 format, chain N [auth B] MOL2 format, chain X [auth C] mmCIF format, chain DA [auth D] mmCIF format, chain EA [auth D] mmCIF format, chain HA [auth E] mmCIF format, chain I [auth A] mmCIF format, chain N [auth B] mmCIF format, chain X [auth C]	DA [auth D] EA [auth D] HA [auth E] I [auth A] N [auth B] DA [auth D], EA [auth D], HA [auth E], I [auth A], N [auth B], X [auth C]	TRIETHYLENE GLYCOL C₆ H₁₄ O₄ ZIBGPFATKBEMQZ-UHFFFAOYSA-N		Interactions Focus chain DA [auth D] Focus chain EA [auth D] Focus chain HA [auth E] Focus chain I [auth A] Focus chain N [auth B] Focus chain X [auth C] Interactions & Density Focus chain DA [auth D] Focus chain EA [auth D] Focus chain HA [auth E] Focus chain I [auth A] Focus chain N [auth B] Focus chain X [auth C]
LYS (Subject of Investigation/LOI) Query on LYS Download:Ideal Coordinates CCD File SDF format, chain CA [auth D] SDF format, chain G [auth A] SDF format, chain GA [auth E] SDF format, chain M [auth B] SDF format, chain MA [auth F] SDF format, chain V [auth C] MOL2 format, chain CA [auth D] MOL2 format, chain G [auth A] MOL2 format, chain GA [auth E] MOL2 format, chain M [auth B] MOL2 format, chain MA [auth F] MOL2 format, chain V [auth C] mmCIF format, chain CA [auth D] mmCIF format, chain G [auth A] mmCIF format, chain GA [auth E] mmCIF format, chain M [auth B] mmCIF format, chain MA [auth F] mmCIF format, chain V [auth C]	CA [auth D] G [auth A] GA [auth E] M [auth B] MA [auth F] CA [auth D], G [auth A], GA [auth E], M [auth B], MA [auth F], V [auth C]	LYSINE C₆ H₁₅ N₂ O₂ KDXKERNSBIXSRK-YFKPBYRVSA-O		Interactions Focus chain CA [auth D] Focus chain G [auth A] Focus chain GA [auth E] Focus chain M [auth B] Focus chain MA [auth F] Focus chain V [auth C] Interactions & Density Focus chain CA [auth D] Focus chain G [auth A] Focus chain GA [auth E] Focus chain M [auth B] Focus chain MA [auth F] Focus chain V [auth C]
PEG (Subject of Investigation/LOI) Query on PEG Download:Ideal Coordinates CCD File SDF format, chain RA [auth F] SDF format, chain T [auth B] SDF format, chain TA [auth F] SDF format, chain SA [auth F] SDF format, chain LA [auth E] MOL2 format, chain RA [auth F] MOL2 format, chain T [auth B] MOL2 format, chain TA [auth F] MOL2 format, chain SA [auth F] MOL2 format, chain LA [auth E] mmCIF format, chain RA [auth F] mmCIF format, chain T [auth B] mmCIF format, chain TA [auth F] mmCIF format, chain SA [auth F] mmCIF format, chain LA [auth E]	LA [auth E], RA [auth F], SA [auth F], T [auth B], TA [auth F]	DI(HYDROXYETHYL)ETHER C₄ H₁₀ O₃ MTHSVFCYNBDYFN-UHFFFAOYSA-N		Interactions Focus chain LA [auth E] Focus chain RA [auth F] Focus chain SA [auth F] Focus chain T [auth B] Focus chain TA [auth F] Interactions & Density Focus chain LA [auth E] Focus chain RA [auth F] Focus chain SA [auth F] Focus chain T [auth B] Focus chain TA [auth F]
GOL (Subject of Investigation/LOI) Query on GOL Download:Ideal Coordinates CCD File SDF format, chain U [auth B] MOL2 format, chain U [auth B] mmCIF format, chain U [auth B]	U [auth B]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain U [auth B] Interactions & Density Focus chain U [auth B]
EDO (Subject of Investigation/LOI) Query on EDO Download:Ideal Coordinates CCD File SDF format, chain IA [auth E] SDF format, chain J [auth A] SDF format, chain K [auth A] SDF format, chain O [auth B] SDF format, chain OA [auth F] SDF format, chain P [auth B] SDF format, chain R [auth B] SDF format, chain Y [auth C] SDF format, chain Z [auth C] SDF format, chain Q [auth B] MOL2 format, chain IA [auth E] MOL2 format, chain J [auth A] MOL2 format, chain K [auth A] MOL2 format, chain O [auth B] MOL2 format, chain OA [auth F] MOL2 format, chain P [auth B] MOL2 format, chain R [auth B] MOL2 format, chain Y [auth C] MOL2 format, chain Z [auth C] MOL2 format, chain Q [auth B] mmCIF format, chain IA [auth E] mmCIF format, chain J [auth A] mmCIF format, chain K [auth A] mmCIF format, chain O [auth B] mmCIF format, chain OA [auth F] mmCIF format, chain P [auth B] mmCIF format, chain R [auth B] mmCIF format, chain Y [auth C] mmCIF format, chain Z [auth C] mmCIF format, chain Q [auth B]	IA [auth E] J [auth A] K [auth A] O [auth B] OA [auth F] IA [auth E], J [auth A], K [auth A], O [auth B], OA [auth F], P [auth B], Q [auth B], R [auth B], Y [auth C], Z [auth C]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain IA [auth E] Focus chain J [auth A] Focus chain K [auth A] Focus chain O [auth B] Focus chain OA [auth F] Focus chain P [auth B] Focus chain Q [auth B] Focus chain R [auth B] Focus chain Y [auth C] Focus chain Z [auth C] Interactions & Density Focus chain IA [auth E] Focus chain J [auth A] Focus chain K [auth A] Focus chain O [auth B] Focus chain OA [auth F] Focus chain P [auth B] Focus chain Q [auth B] Focus chain R [auth B] Focus chain Y [auth C] Focus chain Z [auth C]
ACT (Subject of Investigation/LOI) Query on ACT Download:Ideal Coordinates CCD File SDF format, chain AA [auth C] SDF format, chain BA [auth C] SDF format, chain FA [auth D] SDF format, chain JA [auth E] SDF format, chain KA [auth E] SDF format, chain L [auth A] SDF format, chain PA [auth F] SDF format, chain QA [auth F] SDF format, chain S [auth B] MOL2 format, chain AA [auth C] MOL2 format, chain BA [auth C] MOL2 format, chain FA [auth D] MOL2 format, chain JA [auth E] MOL2 format, chain KA [auth E] MOL2 format, chain L [auth A] MOL2 format, chain PA [auth F] MOL2 format, chain QA [auth F] MOL2 format, chain S [auth B] mmCIF format, chain AA [auth C] mmCIF format, chain BA [auth C] mmCIF format, chain FA [auth D] mmCIF format, chain JA [auth E] mmCIF format, chain KA [auth E] mmCIF format, chain L [auth A] mmCIF format, chain PA [auth F] mmCIF format, chain QA [auth F] mmCIF format, chain S [auth B]	AA [auth C] BA [auth C] FA [auth D] JA [auth E] KA [auth E] AA [auth C], BA [auth C], FA [auth D], JA [auth E], KA [auth E], L [auth A], PA [auth F], QA [auth F], S [auth B]	ACETATE ION C₂ H₃ O₂ QTBSBXVTEAMEQO-UHFFFAOYSA-M		Interactions Focus chain AA [auth C] Focus chain BA [auth C] Focus chain FA [auth D] Focus chain JA [auth E] Focus chain KA [auth E] Focus chain L [auth A] Focus chain PA [auth F] Focus chain QA [auth F] Focus chain S [auth B] Interactions & Density Focus chain AA [auth C] Focus chain BA [auth C] Focus chain FA [auth D] Focus chain JA [auth E] Focus chain KA [auth E] Focus chain L [auth A] Focus chain PA [auth F] Focus chain QA [auth F] Focus chain S [auth B]
MG (Subject of Investigation/LOI) Query on MG Download:Ideal Coordinates CCD File SDF format, chain H [auth A] SDF format, chain NA [auth F] SDF format, chain W [auth C] MOL2 format, chain H [auth A] MOL2 format, chain NA [auth F] MOL2 format, chain W [auth C] mmCIF format, chain H [auth A] mmCIF format, chain NA [auth F] mmCIF format, chain W [auth C]	H [auth A], NA [auth F], W [auth C]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain H [auth A] Focus chain NA [auth F] Focus chain W [auth C] Interactions & Density Focus chain H [auth A] Focus chain NA [auth F] Focus chain W [auth C]