7KEL | pdb_00007kel

Dihydrodipicolinate synthase (DHDPS) from C.jejuni, H59K mutant with pyruvate bound in the active site

PDB DOI: https://doi.org/10.2210/pdb7KEL/pdb

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

Deposited: 2020-10-11 Released: 2021-10-13
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: 2.10 Å
R-Value Free:
0.253 (Depositor), 0.253 (DCC)
R-Value Work:
0.206 (Depositor), 0.207 (DCC)
R-Value Observed:
0.208 (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

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

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

To be published.

Macromolecule Content

Total Structure Weight: 417.27 kDa
Atom Count: 29,356
Modeled Residue Count: 3,547
Deposited Residue Count: 3,720
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, G, H, I, J, K, L	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% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q9PPB4
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 6 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 AB [auth E] SDF format, chain DC [auth I] SDF format, chain GA [auth C] SDF format, chain HA [auth C] SDF format, chain JB [auth F] SDF format, chain LC [auth J] SDF format, chain M [auth A] SDF format, chain WA [auth D] SDF format, chain WC [auth K] SDF format, chain ZC [auth L] MOL2 format, chain AB [auth E] MOL2 format, chain DC [auth I] MOL2 format, chain GA [auth C] MOL2 format, chain HA [auth C] MOL2 format, chain JB [auth F] MOL2 format, chain LC [auth J] MOL2 format, chain M [auth A] MOL2 format, chain WA [auth D] MOL2 format, chain WC [auth K] MOL2 format, chain ZC [auth L] mmCIF format, chain AB [auth E] mmCIF format, chain DC [auth I] mmCIF format, chain GA [auth C] mmCIF format, chain HA [auth C] mmCIF format, chain JB [auth F] mmCIF format, chain LC [auth J] mmCIF format, chain M [auth A] mmCIF format, chain WA [auth D] mmCIF format, chain WC [auth K] mmCIF format, chain ZC [auth L]	AB [auth E] DC [auth I] GA [auth C] HA [auth C] JB [auth F] AB [auth E], DC [auth I], GA [auth C], HA [auth C], JB [auth F], LC [auth J], M [auth A], WA [auth D], WC [auth K], ZC [auth L]	TRIETHYLENE GLYCOL C₆ H₁₄ O₄ ZIBGPFATKBEMQZ-UHFFFAOYSA-N		Interactions Focus chain AB [auth E] Focus chain DC [auth I] Focus chain GA [auth C] Focus chain HA [auth C] Focus chain JB [auth F] Focus chain LC [auth J] Focus chain M [auth A] Focus chain WA [auth D] Focus chain WC [auth K] Focus chain ZC [auth L] Interactions & Density Focus chain AB [auth E] Focus chain DC [auth I] Focus chain GA [auth C] Focus chain HA [auth C] Focus chain JB [auth F] Focus chain LC [auth J] Focus chain M [auth A] Focus chain WA [auth D] Focus chain WC [auth K] Focus chain ZC [auth L]
PEG (Subject of Investigation/LOI) Query on PEG Download:Ideal Coordinates CCD File SDF format, chain CC [auth H] SDF format, chain GD [auth L] SDF format, chain HD [auth L] SDF format, chain OB [auth F] SDF format, chain VC [auth J] SDF format, chain WB [auth G] MOL2 format, chain CC [auth H] MOL2 format, chain GD [auth L] MOL2 format, chain HD [auth L] MOL2 format, chain OB [auth F] MOL2 format, chain VC [auth J] MOL2 format, chain WB [auth G] mmCIF format, chain CC [auth H] mmCIF format, chain GD [auth L] mmCIF format, chain HD [auth L] mmCIF format, chain OB [auth F] mmCIF format, chain VC [auth J] mmCIF format, chain WB [auth G]	CC [auth H] GD [auth L] HD [auth L] OB [auth F] VC [auth J] CC [auth H], GD [auth L], HD [auth L], OB [auth F], VC [auth J], WB [auth G]	DI(HYDROXYETHYL)ETHER C₄ H₁₀ O₃ MTHSVFCYNBDYFN-UHFFFAOYSA-N		Interactions Focus chain CC [auth H] Focus chain GD [auth L] Focus chain HD [auth L] Focus chain OB [auth F] Focus chain VC [auth J] Focus chain WB [auth G] Interactions & Density Focus chain CC [auth H] Focus chain GD [auth L] Focus chain HD [auth L] Focus chain OB [auth F] Focus chain VC [auth J] Focus chain WB [auth G]
GOL (Subject of Investigation/LOI) Query on GOL Download:Ideal Coordinates CCD File SDF format, chain AD [auth L] SDF format, chain EC [auth I] SDF format, chain PB [auth G] MOL2 format, chain AD [auth L] MOL2 format, chain EC [auth I] MOL2 format, chain PB [auth G] mmCIF format, chain AD [auth L] mmCIF format, chain EC [auth I] mmCIF format, chain PB [auth G]	AD [auth L], EC [auth I], PB [auth G]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain AD [auth L] Focus chain EC [auth I] Focus chain PB [auth G] Interactions & Density Focus chain AD [auth L] Focus chain EC [auth I] Focus chain PB [auth G]
EDO (Subject of Investigation/LOI) Query on EDO Download:Ideal Coordinates CCD File SDF format, chain AA [auth B] SDF format, chain AC [auth H] SDF format, chain BA [auth B] SDF format, chain CA [auth B] SDF format, chain CD [auth L] SDF format, chain DA [auth B] SDF format, chain DD [auth L] SDF format, chain EA [auth B] SDF format, chain FA [auth B] SDF format, chain FB [auth E] SDF format, chain GB [auth E] SDF format, chain HB [auth E] SDF format, chain IB [auth E] SDF format, chain IC [auth I] SDF format, chain JC [auth I] SDF format, chain KC [auth I] SDF format, chain LA [auth C] SDF format, chain LB [auth F] SDF format, chain MA [auth C] SDF format, chain MB [auth F] SDF format, chain NA [auth C] SDF format, chain NB [auth F] SDF format, chain OA [auth C] SDF format, chain PA [auth C] SDF format, chain PC [auth J] SDF format, chain Q [auth A] SDF format, chain QB [auth G] SDF format, chain QC [auth J] SDF format, chain R [auth A] SDF format, chain RA [auth C] SDF format, chain RB [auth G] SDF format, chain S [auth A] SDF format, chain SA [auth C] SDF format, chain SB [auth G] SDF format, chain SC [auth J] SDF format, chain T [auth A] SDF format, chain TA [auth C] SDF format, chain TB [auth G] SDF format, chain TC [auth J] SDF format, chain U [auth A] SDF format, chain UA [auth C] SDF format, chain UB [auth G] SDF format, chain UC [auth J] SDF format, chain V [auth A] SDF format, chain VA [auth C] SDF format, chain VB [auth G] SDF format, chain XC [auth K] SDF format, chain YC [auth K] SDF format, chain Z [auth B] SDF format, chain ZA [auth D] SDF format, chain YA [auth D] SDF format, chain RC [auth J] SDF format, chain QA [auth C] SDF format, chain FD [auth L] SDF format, chain ED [auth L] SDF format, chain BC [auth H] MOL2 format, chain AA [auth B] MOL2 format, chain AC [auth H] MOL2 format, chain BA [auth B] MOL2 format, chain CA [auth B] MOL2 format, chain CD [auth L] MOL2 format, chain DA [auth B] MOL2 format, chain DD [auth L] MOL2 format, chain EA [auth B] MOL2 format, chain FA [auth B] MOL2 format, chain FB [auth E] MOL2 format, chain GB [auth E] MOL2 format, chain HB [auth E] MOL2 format, chain IB [auth E] MOL2 format, chain IC [auth I] MOL2 format, chain JC [auth I] MOL2 format, chain KC [auth I] MOL2 format, chain LA [auth C] MOL2 format, chain LB [auth F] MOL2 format, chain MA [auth C] MOL2 format, chain MB [auth F] MOL2 format, chain NA [auth C] MOL2 format, chain NB [auth F] MOL2 format, chain OA [auth C] MOL2 format, chain PA [auth C] MOL2 format, chain PC [auth J] MOL2 format, chain Q [auth A] MOL2 format, chain QB [auth G] MOL2 format, chain QC [auth J] MOL2 format, chain R [auth A] MOL2 format, chain RA [auth C] MOL2 format, chain RB [auth G] MOL2 format, chain S [auth A] MOL2 format, chain SA [auth C] MOL2 format, chain SB [auth G] MOL2 format, chain SC [auth J] MOL2 format, chain T [auth A] MOL2 format, chain TA [auth C] MOL2 format, chain TB [auth G] MOL2 format, chain TC [auth J] MOL2 format, chain U [auth A] MOL2 format, chain UA [auth C] MOL2 format, chain UB [auth G] MOL2 format, chain UC [auth J] MOL2 format, chain V [auth A] MOL2 format, chain VA [auth C] MOL2 format, chain VB [auth G] MOL2 format, chain XC [auth K] MOL2 format, chain YC [auth K] MOL2 format, chain Z [auth B] MOL2 format, chain ZA [auth D] MOL2 format, chain YA [auth D] MOL2 format, chain RC [auth J] MOL2 format, chain QA [auth C] MOL2 format, chain FD [auth L] MOL2 format, chain ED [auth L] MOL2 format, chain BC [auth H] mmCIF format, chain AA [auth B] mmCIF format, chain AC [auth H] mmCIF format, chain BA [auth B] mmCIF format, chain CA [auth B] mmCIF format, chain CD [auth L] mmCIF format, chain DA [auth B] mmCIF format, chain DD [auth L] mmCIF format, chain EA [auth B] mmCIF format, chain FA [auth B] mmCIF format, chain FB [auth E] mmCIF format, chain GB [auth E] mmCIF format, chain HB [auth E] mmCIF format, chain IB [auth E] mmCIF format, chain IC [auth I] mmCIF format, chain JC [auth I] mmCIF format, chain KC [auth I] mmCIF format, chain LA [auth C] mmCIF format, chain LB [auth F] mmCIF format, chain MA [auth C] mmCIF format, chain MB [auth F] mmCIF format, chain NA [auth C] mmCIF format, chain NB [auth F] mmCIF format, chain OA [auth C] mmCIF format, chain PA [auth C] mmCIF format, chain PC [auth J] mmCIF format, chain Q [auth A] mmCIF format, chain QB [auth G] mmCIF format, chain QC [auth J] mmCIF format, chain R [auth A] mmCIF format, chain RA [auth C] mmCIF format, chain RB [auth G] mmCIF format, chain S [auth A] mmCIF format, chain SA [auth C] mmCIF format, chain SB [auth G] mmCIF format, chain SC [auth J] mmCIF format, chain T [auth A] mmCIF format, chain TA [auth C] mmCIF format, chain TB [auth G] mmCIF format, chain TC [auth J] mmCIF format, chain U [auth A] mmCIF format, chain UA [auth C] mmCIF format, chain UB [auth G] mmCIF format, chain UC [auth J] mmCIF format, chain V [auth A] mmCIF format, chain VA [auth C] mmCIF format, chain VB [auth G] mmCIF format, chain XC [auth K] mmCIF format, chain YC [auth K] mmCIF format, chain Z [auth B] mmCIF format, chain ZA [auth D] mmCIF format, chain YA [auth D] mmCIF format, chain RC [auth J] mmCIF format, chain QA [auth C] mmCIF format, chain FD [auth L] mmCIF format, chain ED [auth L] mmCIF format, chain BC [auth H]	AA [auth B] AC [auth H] BA [auth B] BC [auth H] CA [auth B] AA [auth B], AC [auth H], BA [auth B], BC [auth H], CA [auth B], CD [auth L], DA [auth B], DD [auth L], EA [auth B], ED [auth L], FA [auth B], FB [auth E], FD [auth L], GB [auth E], HB [auth E], IB [auth E], IC [auth I], JC [auth I], KC [auth I], LA [auth C], LB [auth F], MA [auth C], MB [auth F], NA [auth C], NB [auth F], OA [auth C], PA [auth C], PC [auth J], Q [auth A], QA [auth C], QB [auth G], QC [auth J], R [auth A], RA [auth C], RB [auth G], RC [auth J], S [auth A], SA [auth C], SB [auth G], SC [auth J], T [auth A], TA [auth C], TB [auth G], TC [auth J], U [auth A], UA [auth C], UB [auth G], UC [auth J], V [auth A], VA [auth C], VB [auth G], XC [auth K], YA [auth D], YC [auth K], Z [auth B], ZA [auth D]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain AA [auth B] Focus chain AC [auth H] Focus chain BA [auth B] Focus chain BC [auth H] Focus chain CA [auth B] Focus chain CD [auth L] Focus chain DA [auth B] Focus chain DD [auth L] Focus chain EA [auth B] Focus chain ED [auth L] Focus chain FA [auth B] Focus chain FB [auth E] Focus chain FD [auth L] Focus chain GB [auth E] Focus chain HB [auth E] Focus chain IB [auth E] Focus chain IC [auth I] Focus chain JC [auth I] Focus chain KC [auth I] Focus chain LA [auth C] Focus chain LB [auth F] Focus chain MA [auth C] Focus chain MB [auth F] Focus chain NA [auth C] Focus chain NB [auth F] Focus chain OA [auth C] Focus chain PA [auth C] Focus chain PC [auth J] Focus chain Q [auth A] Focus chain QA [auth C] Focus chain QB [auth G] Focus chain QC [auth J] Focus chain R [auth A] Focus chain RA [auth C] Focus chain RB [auth G] Focus chain RC [auth J] Focus chain S [auth A] Focus chain SA [auth C] Focus chain SB [auth G] Focus chain SC [auth J] Focus chain T [auth A] Focus chain TA [auth C] Focus chain TB [auth G] Focus chain TC [auth J] Focus chain U [auth A] Focus chain UA [auth C] Focus chain UB [auth G] Focus chain UC [auth J] Focus chain V [auth A] Focus chain VA [auth C] Focus chain VB [auth G] Focus chain XC [auth K] Focus chain YA [auth D] Focus chain YC [auth K] Focus chain Z [auth B] Focus chain ZA [auth D] Interactions & Density Focus chain AA [auth B] Focus chain AC [auth H] Focus chain BA [auth B] Focus chain BC [auth H] Focus chain CA [auth B] Focus chain CD [auth L] Focus chain DA [auth B] Focus chain DD [auth L] Focus chain EA [auth B] Focus chain ED [auth L] Focus chain FA [auth B] Focus chain FB [auth E] Focus chain FD [auth L] Focus chain GB [auth E] Focus chain HB [auth E] Focus chain IB [auth E] Focus chain IC [auth I] Focus chain JC [auth I] Focus chain KC [auth I] Focus chain LA [auth C] Focus chain LB [auth F] Focus chain MA [auth C] Focus chain MB [auth F] Focus chain NA [auth C] Focus chain NB [auth F] Focus chain OA [auth C] Focus chain PA [auth C] Focus chain PC [auth J] Focus chain Q [auth A] Focus chain QA [auth C] Focus chain QB [auth G] Focus chain QC [auth J] Focus chain R [auth A] Focus chain RA [auth C] Focus chain RB [auth G] Focus chain RC [auth J] Focus chain S [auth A] Focus chain SA [auth C] Focus chain SB [auth G] Focus chain SC [auth J] Focus chain T [auth A] Focus chain TA [auth C] Focus chain TB [auth G] Focus chain TC [auth J] Focus chain U [auth A] Focus chain UA [auth C] Focus chain UB [auth G] Focus chain UC [auth J] Focus chain V [auth A] Focus chain VA [auth C] Focus chain VB [auth G] Focus chain XC [auth K] Focus chain YA [auth D] Focus chain YC [auth K] 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 BB [auth E] SDF format, chain BD [auth L] SDF format, chain CB [auth E] SDF format, chain FC [auth I] SDF format, chain GC [auth I] SDF format, chain HC [auth I] SDF format, chain IA [auth C] SDF format, chain KB [auth F] SDF format, chain MC [auth J] SDF format, chain NC [auth J] SDF format, chain O [auth A] SDF format, chain OC [auth J] SDF format, chain W [auth B] SDF format, chain X [auth B] SDF format, chain XB [auth H] SDF format, chain Y [auth B] SDF format, chain YB [auth H] SDF format, chain ZB [auth H] SDF format, chain N [auth A] MOL2 format, chain BB [auth E] MOL2 format, chain BD [auth L] MOL2 format, chain CB [auth E] MOL2 format, chain FC [auth I] MOL2 format, chain GC [auth I] MOL2 format, chain HC [auth I] MOL2 format, chain IA [auth C] MOL2 format, chain KB [auth F] MOL2 format, chain MC [auth J] MOL2 format, chain NC [auth J] MOL2 format, chain O [auth A] MOL2 format, chain OC [auth J] MOL2 format, chain W [auth B] MOL2 format, chain X [auth B] MOL2 format, chain XB [auth H] MOL2 format, chain Y [auth B] MOL2 format, chain YB [auth H] MOL2 format, chain ZB [auth H] MOL2 format, chain N [auth A] mmCIF format, chain BB [auth E] mmCIF format, chain BD [auth L] mmCIF format, chain CB [auth E] mmCIF format, chain FC [auth I] mmCIF format, chain GC [auth I] mmCIF format, chain HC [auth I] mmCIF format, chain IA [auth C] mmCIF format, chain KB [auth F] mmCIF format, chain MC [auth J] mmCIF format, chain NC [auth J] mmCIF format, chain O [auth A] mmCIF format, chain OC [auth J] mmCIF format, chain W [auth B] mmCIF format, chain X [auth B] mmCIF format, chain XB [auth H] mmCIF format, chain Y [auth B] mmCIF format, chain YB [auth H] mmCIF format, chain ZB [auth H] mmCIF format, chain N [auth A]	BB [auth E] BD [auth L] CB [auth E] FC [auth I] GC [auth I] BB [auth E], BD [auth L], CB [auth E], FC [auth I], GC [auth I], HC [auth I], IA [auth C], KB [auth F], MC [auth J], N [auth A], NC [auth J], O [auth A], OC [auth J], W [auth B], X [auth B], XB [auth H], Y [auth B], YB [auth H], ZB [auth H]	ACETATE ION C₂ H₃ O₂ QTBSBXVTEAMEQO-UHFFFAOYSA-M		Interactions Focus chain BB [auth E] Focus chain BD [auth L] Focus chain CB [auth E] Focus chain FC [auth I] Focus chain GC [auth I] Focus chain HC [auth I] Focus chain IA [auth C] Focus chain KB [auth F] Focus chain MC [auth J] Focus chain N [auth A] Focus chain NC [auth J] Focus chain O [auth A] Focus chain OC [auth J] Focus chain W [auth B] Focus chain X [auth B] Focus chain XB [auth H] Focus chain Y [auth B] Focus chain YB [auth H] Focus chain ZB [auth H] Interactions & Density Focus chain BB [auth E] Focus chain BD [auth L] Focus chain CB [auth E] Focus chain FC [auth I] Focus chain GC [auth I] Focus chain HC [auth I] Focus chain IA [auth C] Focus chain KB [auth F] Focus chain MC [auth J] Focus chain N [auth A] Focus chain NC [auth J] Focus chain O [auth A] Focus chain OC [auth J] Focus chain W [auth B] Focus chain X [auth B] Focus chain XB [auth H] Focus chain Y [auth B] Focus chain YB [auth H] Focus chain ZB [auth H]
MG (Subject of Investigation/LOI) Query on MG Download:Ideal Coordinates CCD File SDF format, chain DB [auth E] SDF format, chain EB [auth E] SDF format, chain JA [auth C] SDF format, chain KA [auth C] SDF format, chain P [auth A] SDF format, chain XA [auth D] MOL2 format, chain DB [auth E] MOL2 format, chain EB [auth E] MOL2 format, chain JA [auth C] MOL2 format, chain KA [auth C] MOL2 format, chain P [auth A] MOL2 format, chain XA [auth D] mmCIF format, chain DB [auth E] mmCIF format, chain EB [auth E] mmCIF format, chain JA [auth C] mmCIF format, chain KA [auth C] mmCIF format, chain P [auth A] mmCIF format, chain XA [auth D]	DB [auth E] EB [auth E] JA [auth C] KA [auth C] P [auth A] DB [auth E], EB [auth E], JA [auth C], KA [auth C], P [auth A], XA [auth D]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain DB [auth E] Focus chain EB [auth E] Focus chain JA [auth C] Focus chain KA [auth C] Focus chain P [auth A] Focus chain XA [auth D] Interactions & Density Focus chain DB [auth E] Focus chain EB [auth E] Focus chain JA [auth C] Focus chain KA [auth C] Focus chain P [auth A] Focus chain XA [auth D]