7KG2

Dihydrodipicolinate synthase (DHDPS) from C.jejuni, H59K mutant with pyruvate bound in the active site and L-histidine bound at the allosteric site

PDB DOI: https://doi.org/10.2210/pdb7KG2/pdb

Classification: LYASE
Organism(s): Campylobacter jejuni
Expression System: Escherichia coli
Mutation(s): Yes

Deposited: 2020-10-15 Released: 2021-10-20
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: 1.89 Å
R-Value Free: 0.207
R-Value Work: 0.170
R-Value Observed: 0.171

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

Reversing the roles of a crucial hydrogen-bonding pair: a lysine-insensitive mutant of Campylobacter jejuni dihydrodipicolinate synthase, H59K, binds histidine in its allosteric site

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

To be published.

Macromolecule Content

Total Structure Weight: 211.51 kDa
Atom Count: 14,872
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	Mutation(s): 1 Gene Names: dapA 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
PG4 (Subject of Investigation/LOI) Query on PG4 Download Ideal Coordinates CCD File SDF format, chain KB [auth D] MOL2 format, chain KB [auth D] mmCIF format, chain KB [auth D]	KB [auth D]	TETRAETHYLENE GLYCOL C₈ H₁₈ O₅ UWHCKJMYHZGTIT-UHFFFAOYSA-N		Interactions Focus chain KB [auth D] Interactions & Density Focus chain KB [auth D]
HIS (Subject of Investigation/LOI) Query on HIS Download Ideal Coordinates CCD File SDF format, chain FC [auth E] SDF format, chain JA [auth B] SDF format, chain OB [auth D] SDF format, chain OC [auth F] SDF format, chain TA [auth C] SDF format, chain W [auth A] MOL2 format, chain FC [auth E] MOL2 format, chain JA [auth B] MOL2 format, chain OB [auth D] MOL2 format, chain OC [auth F] MOL2 format, chain TA [auth C] MOL2 format, chain W [auth A] mmCIF format, chain FC [auth E] mmCIF format, chain JA [auth B] mmCIF format, chain OB [auth D] mmCIF format, chain OC [auth F] mmCIF format, chain TA [auth C] mmCIF format, chain W [auth A]	FC [auth E] JA [auth B] OB [auth D] OC [auth F] TA [auth C] FC [auth E], JA [auth B], OB [auth D], OC [auth F], TA [auth C], W [auth A]	HISTIDINE C₆ H₁₀ N₃ O₂ HNDVDQJCIGZPNO-YFKPBYRVSA-O		Interactions Focus chain FC [auth E] Focus chain JA [auth B] Focus chain OB [auth D] Focus chain OC [auth F] Focus chain TA [auth C] Focus chain W [auth A] Interactions & Density Focus chain FC [auth E] Focus chain JA [auth B] Focus chain OB [auth D] Focus chain OC [auth F] Focus chain TA [auth C] Focus chain W [auth A]
PGE (Subject of Investigation/LOI) Query on PGE Download Ideal Coordinates CCD File SDF format, chain AC [auth E] SDF format, chain BC [auth E] SDF format, chain CC [auth E] SDF format, chain HA [auth B] SDF format, chain IA [auth B] SDF format, chain JB [auth D] SDF format, chain SA [auth C] SDF format, chain V [auth A] MOL2 format, chain AC [auth E] MOL2 format, chain BC [auth E] MOL2 format, chain CC [auth E] MOL2 format, chain HA [auth B] MOL2 format, chain IA [auth B] MOL2 format, chain JB [auth D] MOL2 format, chain SA [auth C] MOL2 format, chain V [auth A] mmCIF format, chain AC [auth E] mmCIF format, chain BC [auth E] mmCIF format, chain CC [auth E] mmCIF format, chain HA [auth B] mmCIF format, chain IA [auth B] mmCIF format, chain JB [auth D] mmCIF format, chain SA [auth C] mmCIF format, chain V [auth A]	AC [auth E] BC [auth E] CC [auth E] HA [auth B] IA [auth B] AC [auth E], BC [auth E], CC [auth E], HA [auth B], IA [auth B], JB [auth D], SA [auth C], V [auth A]	TRIETHYLENE GLYCOL C₆ H₁₄ O₄ ZIBGPFATKBEMQZ-UHFFFAOYSA-N		Interactions Focus chain AC [auth E] Focus chain BC [auth E] Focus chain CC [auth E] Focus chain HA [auth B] Focus chain IA [auth B] Focus chain JB [auth D] Focus chain SA [auth C] Focus chain V [auth A] Interactions & Density Focus chain AC [auth E] Focus chain BC [auth E] Focus chain CC [auth E] Focus chain HA [auth B] Focus chain IA [auth B] Focus chain JB [auth D] Focus chain SA [auth C] Focus chain V [auth A]
PEG (Subject of Investigation/LOI) Query on PEG Download Ideal Coordinates CCD File SDF format, chain DC [auth E] SDF format, chain EC [auth E] SDF format, chain LB [auth D] SDF format, chain MB [auth D] SDF format, chain NB [auth D] MOL2 format, chain DC [auth E] MOL2 format, chain EC [auth E] MOL2 format, chain LB [auth D] MOL2 format, chain MB [auth D] MOL2 format, chain NB [auth D] mmCIF format, chain DC [auth E] mmCIF format, chain EC [auth E] mmCIF format, chain LB [auth D] mmCIF format, chain MB [auth D] mmCIF format, chain NB [auth D]	DC [auth E], EC [auth E], LB [auth D], MB [auth D], NB [auth D]	DI(HYDROXYETHYL)ETHER C₄ H₁₀ O₃ MTHSVFCYNBDYFN-UHFFFAOYSA-N		Interactions Focus chain DC [auth E] Focus chain EC [auth E] Focus chain LB [auth D] Focus chain MB [auth D] Focus chain NB [auth D] Interactions & Density Focus chain DC [auth E] Focus chain EC [auth E] Focus chain LB [auth D] Focus chain MB [auth D] Focus chain NB [auth D]
EDO (Subject of Investigation/LOI) Query on EDO Download Ideal Coordinates CCD File SDF format, chain AA [auth B] SDF format, chain AB [auth D] SDF format, chain BA [auth B] SDF format, chain BB [auth D] SDF format, chain CB [auth D] SDF format, chain G [auth A] SDF format, chain GC [auth F] SDF format, chain H [auth A] SDF format, chain HC [auth F] SDF format, chain I [auth A] SDF format, chain IC [auth F] SDF format, chain J [auth A] SDF format, chain JC [auth F] SDF format, chain K [auth A] SDF format, chain KA [auth C] SDF format, chain L [auth A] SDF format, chain LA [auth C] SDF format, chain M [auth A] SDF format, chain MA [auth C] SDF format, chain NA [auth C] SDF format, chain OA [auth C] SDF format, chain PA [auth C] SDF format, chain PB [auth E] SDF format, chain QB [auth E] SDF format, chain RB [auth E] SDF format, chain SB [auth E] SDF format, chain TB [auth E] SDF format, chain UA [auth D] SDF format, chain UB [auth E] SDF format, chain VA [auth D] SDF format, chain VB [auth E] SDF format, chain WA [auth D] SDF format, chain X [auth B] SDF format, chain XA [auth D] SDF format, chain Y [auth B] SDF format, chain YA [auth D] SDF format, chain Z [auth B] SDF format, chain ZA [auth D] MOL2 format, chain AA [auth B] MOL2 format, chain AB [auth D] MOL2 format, chain BA [auth B] MOL2 format, chain BB [auth D] MOL2 format, chain CB [auth D] MOL2 format, chain G [auth A] MOL2 format, chain GC [auth F] MOL2 format, chain H [auth A] MOL2 format, chain HC [auth F] MOL2 format, chain I [auth A] MOL2 format, chain IC [auth F] MOL2 format, chain J [auth A] MOL2 format, chain JC [auth F] MOL2 format, chain K [auth A] MOL2 format, chain KA [auth C] MOL2 format, chain L [auth A] MOL2 format, chain LA [auth C] MOL2 format, chain M [auth A] MOL2 format, chain MA [auth C] MOL2 format, chain NA [auth C] MOL2 format, chain OA [auth C] MOL2 format, chain PA [auth C] MOL2 format, chain PB [auth E] MOL2 format, chain QB [auth E] MOL2 format, chain RB [auth E] MOL2 format, chain SB [auth E] MOL2 format, chain TB [auth E] MOL2 format, chain UA [auth D] MOL2 format, chain UB [auth E] MOL2 format, chain VA [auth D] MOL2 format, chain VB [auth E] MOL2 format, chain WA [auth D] MOL2 format, chain X [auth B] MOL2 format, chain XA [auth D] MOL2 format, chain Y [auth B] MOL2 format, chain YA [auth D] MOL2 format, chain Z [auth B] MOL2 format, chain ZA [auth D] mmCIF format, chain AA [auth B] mmCIF format, chain AB [auth D] mmCIF format, chain BA [auth B] mmCIF format, chain BB [auth D] mmCIF format, chain CB [auth D] mmCIF format, chain G [auth A] mmCIF format, chain GC [auth F] mmCIF format, chain H [auth A] mmCIF format, chain HC [auth F] mmCIF format, chain I [auth A] mmCIF format, chain IC [auth F] mmCIF format, chain J [auth A] mmCIF format, chain JC [auth F] mmCIF format, chain K [auth A] mmCIF format, chain KA [auth C] mmCIF format, chain L [auth A] mmCIF format, chain LA [auth C] mmCIF format, chain M [auth A] mmCIF format, chain MA [auth C] mmCIF format, chain NA [auth C] mmCIF format, chain OA [auth C] mmCIF format, chain PA [auth C] mmCIF format, chain PB [auth E] mmCIF format, chain QB [auth E] mmCIF format, chain RB [auth E] mmCIF format, chain SB [auth E] mmCIF format, chain TB [auth E] mmCIF format, chain UA [auth D] mmCIF format, chain UB [auth E] mmCIF format, chain VA [auth D] mmCIF format, chain VB [auth E] mmCIF format, chain WA [auth D] mmCIF format, chain X [auth B] mmCIF format, chain XA [auth D] mmCIF format, chain Y [auth B] mmCIF format, chain YA [auth D] mmCIF format, chain Z [auth B] mmCIF format, chain ZA [auth D]	AA [auth B] AB [auth D] BA [auth B] BB [auth D] CB [auth D] AA [auth B], AB [auth D], BA [auth B], BB [auth D], CB [auth D], G [auth A], GC [auth F], H [auth A], HC [auth F], I [auth A], IC [auth F], J [auth A], JC [auth F], K [auth A], KA [auth C], L [auth A], LA [auth C], M [auth A], MA [auth C], NA [auth C], OA [auth C], PA [auth C], PB [auth E], QB [auth E], RB [auth E], SB [auth E], TB [auth E], UA [auth D], UB [auth E], VA [auth D], VB [auth E], WA [auth D], X [auth B], XA [auth D], Y [auth B], YA [auth D], Z [auth B], ZA [auth D]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain AA [auth B] Focus chain AB [auth D] Focus chain BA [auth B] Focus chain BB [auth D] Focus chain CB [auth D] Focus chain G [auth A] Focus chain GC [auth F] Focus chain H [auth A] Focus chain HC [auth F] Focus chain I [auth A] Focus chain IC [auth F] Focus chain J [auth A] Focus chain JC [auth F] Focus chain K [auth A] Focus chain KA [auth C] Focus chain L [auth A] Focus chain LA [auth C] Focus chain M [auth A] Focus chain MA [auth C] Focus chain NA [auth C] Focus chain OA [auth C] Focus chain PA [auth C] Focus chain PB [auth E] Focus chain QB [auth E] Focus chain RB [auth E] Focus chain SB [auth E] Focus chain TB [auth E] Focus chain UA [auth D] Focus chain UB [auth E] Focus chain VA [auth D] Focus chain VB [auth E] 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] Focus chain ZA [auth D] Interactions & Density Focus chain AA [auth B] Focus chain AB [auth D] Focus chain BA [auth B] Focus chain BB [auth D] Focus chain CB [auth D] Focus chain G [auth A] Focus chain GC [auth F] Focus chain H [auth A] Focus chain HC [auth F] Focus chain I [auth A] Focus chain IC [auth F] Focus chain J [auth A] Focus chain JC [auth F] Focus chain K [auth A] Focus chain KA [auth C] Focus chain L [auth A] Focus chain LA [auth C] Focus chain M [auth A] Focus chain MA [auth C] Focus chain NA [auth C] Focus chain OA [auth C] Focus chain PA [auth C] Focus chain PB [auth E] Focus chain QB [auth E] Focus chain RB [auth E] Focus chain SB [auth E] Focus chain TB [auth E] Focus chain UA [auth D] Focus chain UB [auth E] Focus chain VA [auth D] Focus chain VB [auth E] 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] Focus chain ZA [auth D]
ACT (Subject of Investigation/LOI) Query on ACT Download Ideal Coordinates CCD File SDF format, chain EA [auth B] SDF format, chain FA [auth B] SDF format, chain GA [auth B] SDF format, chain GB [auth D] SDF format, chain HB [auth D] SDF format, chain IB [auth D] SDF format, chain LC [auth F] SDF format, chain MC [auth F] SDF format, chain NC [auth F] SDF format, chain RA [auth C] SDF format, chain S [auth A] SDF format, chain T [auth A] SDF format, chain U [auth A] SDF format, chain YB [auth E] SDF format, chain ZB [auth E] MOL2 format, chain EA [auth B] MOL2 format, chain FA [auth B] MOL2 format, chain GA [auth B] MOL2 format, chain GB [auth D] MOL2 format, chain HB [auth D] MOL2 format, chain IB [auth D] MOL2 format, chain LC [auth F] MOL2 format, chain MC [auth F] MOL2 format, chain NC [auth F] MOL2 format, chain RA [auth C] MOL2 format, chain S [auth A] MOL2 format, chain T [auth A] MOL2 format, chain U [auth A] MOL2 format, chain YB [auth E] MOL2 format, chain ZB [auth E] mmCIF format, chain EA [auth B] mmCIF format, chain FA [auth B] mmCIF format, chain GA [auth B] mmCIF format, chain GB [auth D] mmCIF format, chain HB [auth D] mmCIF format, chain IB [auth D] mmCIF format, chain LC [auth F] mmCIF format, chain MC [auth F] mmCIF format, chain NC [auth F] mmCIF format, chain RA [auth C] mmCIF format, chain S [auth A] mmCIF format, chain T [auth A] mmCIF format, chain U [auth A] mmCIF format, chain YB [auth E] mmCIF format, chain ZB [auth E]	EA [auth B] FA [auth B] GA [auth B] GB [auth D] HB [auth D] EA [auth B], FA [auth B], GA [auth B], GB [auth D], HB [auth D], IB [auth D], LC [auth F], MC [auth F], NC [auth F], RA [auth C], S [auth A], T [auth A], U [auth A], YB [auth E], ZB [auth E]	ACETATE ION C₂ H₃ O₂ QTBSBXVTEAMEQO-UHFFFAOYSA-M		Interactions Focus chain EA [auth B] Focus chain FA [auth B] Focus chain GA [auth B] Focus chain GB [auth D] Focus chain HB [auth D] Focus chain IB [auth D] Focus chain LC [auth F] Focus chain MC [auth F] Focus chain NC [auth F] Focus chain RA [auth C] Focus chain S [auth A] Focus chain T [auth A] Focus chain U [auth A] Focus chain YB [auth E] Focus chain ZB [auth E] Interactions & Density Focus chain EA [auth B] Focus chain FA [auth B] Focus chain GA [auth B] Focus chain GB [auth D] Focus chain HB [auth D] Focus chain IB [auth D] Focus chain LC [auth F] Focus chain MC [auth F] Focus chain NC [auth F] Focus chain RA [auth C] Focus chain S [auth A] Focus chain T [auth A] Focus chain U [auth A] Focus chain YB [auth E] Focus chain ZB [auth E]
MG (Subject of Investigation/LOI) Query on MG Download Ideal Coordinates CCD File SDF format, chain CA [auth B] SDF format, chain DA [auth B] SDF format, chain DB [auth D] SDF format, chain EB [auth D] SDF format, chain FB [auth D] SDF format, chain KC [auth F] SDF format, chain N [auth A] SDF format, chain O [auth A] SDF format, chain P [auth A] SDF format, chain Q [auth A] SDF format, chain QA [auth C] SDF format, chain R [auth A] SDF format, chain WB [auth E] SDF format, chain XB [auth E] MOL2 format, chain CA [auth B] MOL2 format, chain DA [auth B] MOL2 format, chain DB [auth D] MOL2 format, chain EB [auth D] MOL2 format, chain FB [auth D] MOL2 format, chain KC [auth F] MOL2 format, chain N [auth A] MOL2 format, chain O [auth A] MOL2 format, chain P [auth A] MOL2 format, chain Q [auth A] MOL2 format, chain QA [auth C] MOL2 format, chain R [auth A] MOL2 format, chain WB [auth E] MOL2 format, chain XB [auth E] mmCIF format, chain CA [auth B] mmCIF format, chain DA [auth B] mmCIF format, chain DB [auth D] mmCIF format, chain EB [auth D] mmCIF format, chain FB [auth D] mmCIF format, chain KC [auth F] mmCIF format, chain N [auth A] mmCIF format, chain O [auth A] mmCIF format, chain P [auth A] mmCIF format, chain Q [auth A] mmCIF format, chain QA [auth C] mmCIF format, chain R [auth A] mmCIF format, chain WB [auth E] mmCIF format, chain XB [auth E]	CA [auth B] DA [auth B] DB [auth D] EB [auth D] FB [auth D] CA [auth B], DA [auth B], DB [auth D], EB [auth D], FB [auth D], KC [auth F], N [auth A], O [auth A], P [auth A], Q [auth A], QA [auth C], R [auth A], WB [auth E], XB [auth E]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain CA [auth B] Focus chain DA [auth B] Focus chain DB [auth D] Focus chain EB [auth D] Focus chain FB [auth D] Focus chain KC [auth F] Focus chain N [auth A] Focus chain O [auth A] Focus chain P [auth A] Focus chain Q [auth A] Focus chain QA [auth C] Focus chain R [auth A] Focus chain WB [auth E] Focus chain XB [auth E] Interactions & Density Focus chain CA [auth B] Focus chain DA [auth B] Focus chain DB [auth D] Focus chain EB [auth D] Focus chain FB [auth D] Focus chain KC [auth F] Focus chain N [auth A] Focus chain O [auth A] Focus chain P [auth A] Focus chain Q [auth A] Focus chain QA [auth C] Focus chain R [auth A] Focus chain WB [auth E] Focus chain XB [auth E]