7KTO

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

PDB DOI: https://doi.org/10.2210/pdb7KTO/pdb

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

Deposited: 2020-11-24 Released: 2021-12-01
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: 2.13 Å
R-Value Free: 0.247
R-Value Work: 0.202
R-Value Observed: 0.204

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: 208.94 kDa
Atom Count: 15,154
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 7 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 G [auth A] SDF format, chain PA [auth F] SDF format, chain Z [auth D] MOL2 format, chain G [auth A] MOL2 format, chain PA [auth F] MOL2 format, chain Z [auth D] mmCIF format, chain G [auth A] mmCIF format, chain PA [auth F] mmCIF format, chain Z [auth D]	G [auth A], PA [auth F], Z [auth D]	(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 PA [auth F] Focus chain Z [auth D] Interactions & Density Focus chain G [auth A] Focus chain PA [auth F] Focus chain Z [auth D]
PGE (Subject of Investigation/LOI) Query on PGE Download Ideal Coordinates CCD File SDF format, chain CA [auth D] SDF format, chain I [auth A] SDF format, chain S [auth B] SDF format, chain T [auth B] SDF format, chain UA [auth F] SDF format, chain X [auth C] MOL2 format, chain CA [auth D] MOL2 format, chain I [auth A] MOL2 format, chain S [auth B] MOL2 format, chain T [auth B] MOL2 format, chain UA [auth F] MOL2 format, chain X [auth C] mmCIF format, chain CA [auth D] mmCIF format, chain I [auth A] mmCIF format, chain S [auth B] mmCIF format, chain T [auth B] mmCIF format, chain UA [auth F] mmCIF format, chain X [auth C]	CA [auth D] I [auth A] S [auth B] T [auth B] UA [auth F] CA [auth D], I [auth A], S [auth B], T [auth B], UA [auth F], X [auth C]	TRIETHYLENE GLYCOL C₆ H₁₄ O₄ ZIBGPFATKBEMQZ-UHFFFAOYSA-N		Interactions Focus chain CA [auth D] Focus chain I [auth A] Focus chain S [auth B] Focus chain T [auth B] Focus chain UA [auth F] Focus chain X [auth C] Interactions & Density Focus chain CA [auth D] Focus chain I [auth A] Focus chain S [auth B] Focus chain T [auth B] Focus chain UA [auth F] Focus chain X [auth C]
PEG (Subject of Investigation/LOI) Query on PEG Download Ideal Coordinates CCD File SDF format, chain DA [auth D] SDF format, chain EA [auth D] SDF format, chain K [auth A] SDF format, chain L [auth A] SDF format, chain MA [auth E] SDF format, chain VA [auth F] MOL2 format, chain DA [auth D] MOL2 format, chain EA [auth D] MOL2 format, chain K [auth A] MOL2 format, chain L [auth A] MOL2 format, chain MA [auth E] MOL2 format, chain VA [auth F] mmCIF format, chain DA [auth D] mmCIF format, chain EA [auth D] mmCIF format, chain K [auth A] mmCIF format, chain L [auth A] mmCIF format, chain MA [auth E] mmCIF format, chain VA [auth F]	DA [auth D] EA [auth D] K [auth A] L [auth A] MA [auth E] DA [auth D], EA [auth D], K [auth A], L [auth A], MA [auth E], VA [auth F]	DI(HYDROXYETHYL)ETHER C₄ H₁₀ O₃ MTHSVFCYNBDYFN-UHFFFAOYSA-N		Interactions Focus chain DA [auth D] Focus chain EA [auth D] Focus chain K [auth A] Focus chain L [auth A] Focus chain MA [auth E] Focus chain VA [auth F] Interactions & Density Focus chain DA [auth D] Focus chain EA [auth D] Focus chain K [auth A] Focus chain L [auth A] Focus chain MA [auth E] Focus chain VA [auth F]
GOL (Subject of Investigation/LOI) Query on GOL Download Ideal Coordinates CCD File SDF format, chain J [auth A] SDF format, chain Y [auth C] MOL2 format, chain J [auth A] MOL2 format, chain Y [auth C] mmCIF format, chain J [auth A] mmCIF format, chain Y [auth C]	J [auth A], Y [auth C]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain J [auth A] Focus chain Y [auth C] Interactions & Density Focus chain J [auth A] Focus chain Y [auth C]
EDO (Subject of Investigation/LOI) Query on EDO Download Ideal Coordinates CCD File SDF format, chain AA [auth D] SDF format, chain BA [auth D] SDF format, chain H [auth A] SDF format, chain JA [auth E] SDF format, chain KA [auth E] SDF format, chain LA [auth E] SDF format, chain O [auth B] SDF format, chain P [auth B] SDF format, chain Q [auth B] SDF format, chain QA [auth F] SDF format, chain R [auth B] SDF format, chain RA [auth F] SDF format, chain SA [auth F] SDF format, chain TA [auth F] SDF format, chain V [auth C] SDF format, chain W [auth C] MOL2 format, chain AA [auth D] MOL2 format, chain BA [auth D] MOL2 format, chain H [auth A] MOL2 format, chain JA [auth E] MOL2 format, chain KA [auth E] MOL2 format, chain LA [auth E] MOL2 format, chain O [auth B] MOL2 format, chain P [auth B] MOL2 format, chain Q [auth B] MOL2 format, chain QA [auth F] MOL2 format, chain R [auth B] MOL2 format, chain RA [auth F] MOL2 format, chain SA [auth F] MOL2 format, chain TA [auth F] MOL2 format, chain V [auth C] MOL2 format, chain W [auth C] mmCIF format, chain AA [auth D] mmCIF format, chain BA [auth D] mmCIF format, chain H [auth A] mmCIF format, chain JA [auth E] mmCIF format, chain KA [auth E] mmCIF format, chain LA [auth E] mmCIF format, chain O [auth B] mmCIF format, chain P [auth B] mmCIF format, chain Q [auth B] mmCIF format, chain QA [auth F] mmCIF format, chain R [auth B] mmCIF format, chain RA [auth F] mmCIF format, chain SA [auth F] mmCIF format, chain TA [auth F] mmCIF format, chain V [auth C] mmCIF format, chain W [auth C]	AA [auth D] BA [auth D] H [auth A] JA [auth E] KA [auth E] AA [auth D], BA [auth D], H [auth A], JA [auth E], KA [auth E], LA [auth E], O [auth B], P [auth B], Q [auth B], QA [auth F], R [auth B], RA [auth F], SA [auth F], TA [auth F], V [auth C], W [auth C]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain AA [auth D] Focus chain BA [auth D] Focus chain H [auth A] Focus chain JA [auth E] Focus chain KA [auth E] Focus chain LA [auth E] Focus chain O [auth B] Focus chain P [auth B] Focus chain Q [auth B] Focus chain QA [auth F] Focus chain R [auth B] Focus chain RA [auth F] Focus chain SA [auth F] Focus chain TA [auth F] Focus chain V [auth C] Focus chain W [auth C] Interactions & Density Focus chain AA [auth D] Focus chain BA [auth D] Focus chain H [auth A] Focus chain JA [auth E] Focus chain KA [auth E] Focus chain LA [auth E] Focus chain O [auth B] Focus chain P [auth B] Focus chain Q [auth B] Focus chain QA [auth F] Focus chain R [auth B] Focus chain RA [auth F] Focus chain SA [auth F] Focus chain TA [auth F] Focus chain V [auth C] Focus chain W [auth C]
ACT (Subject of Investigation/LOI) Query on ACT Download Ideal Coordinates CCD File SDF format, chain FA [auth D] SDF format, chain GA [auth D] SDF format, chain HA [auth D] SDF format, chain IA [auth D] SDF format, chain M [auth A] SDF format, chain N [auth A] SDF format, chain NA [auth E] SDF format, chain U [auth B] SDF format, chain WA [auth F] MOL2 format, chain FA [auth D] MOL2 format, chain GA [auth D] MOL2 format, chain HA [auth D] MOL2 format, chain IA [auth D] MOL2 format, chain M [auth A] MOL2 format, chain N [auth A] MOL2 format, chain NA [auth E] MOL2 format, chain U [auth B] MOL2 format, chain WA [auth F] mmCIF format, chain FA [auth D] mmCIF format, chain GA [auth D] mmCIF format, chain HA [auth D] mmCIF format, chain IA [auth D] mmCIF format, chain M [auth A] mmCIF format, chain N [auth A] mmCIF format, chain NA [auth E] mmCIF format, chain U [auth B] mmCIF format, chain WA [auth F]	FA [auth D] GA [auth D] HA [auth D] IA [auth D] M [auth A] FA [auth D], GA [auth D], HA [auth D], IA [auth D], M [auth A], N [auth A], NA [auth E], U [auth B], WA [auth F]	ACETATE ION C₂ H₃ O₂ QTBSBXVTEAMEQO-UHFFFAOYSA-M		Interactions Focus chain FA [auth D] Focus chain GA [auth D] Focus chain HA [auth D] Focus chain IA [auth D] Focus chain M [auth A] Focus chain N [auth A] Focus chain NA [auth E] Focus chain U [auth B] Focus chain WA [auth F] Interactions & Density Focus chain FA [auth D] Focus chain GA [auth D] Focus chain HA [auth D] Focus chain IA [auth D] Focus chain M [auth A] Focus chain N [auth A] Focus chain NA [auth E] Focus chain U [auth B] Focus chain WA [auth F]
MG (Subject of Investigation/LOI) Query on MG Download Ideal Coordinates CCD File SDF format, chain OA [auth E] MOL2 format, chain OA [auth E] mmCIF format, chain OA [auth E]	OA [auth E]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain OA [auth E] Interactions & Density Focus chain OA [auth E]