7LBD

Dihydrodipicolinate synthase (DHDPS) from C.jejuni, H59K mutant with pyruvate bound in the active site in C2221 space group

PDB DOI: https://doi.org/10.2210/pdb7LBD/pdb

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

Deposited: 2021-01-07 Released: 2022-01-12
Deposition Author(s): Saran, S., Yazdi, M.M., Sanders, D.A.R.
Funding Organization(s): Natural Sciences and Engineering Research Council (NSERC, Canada)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.99 Å
R-Value Free: 0.221
R-Value Work: 0.191
R-Value Observed: 0.193

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

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

To be published.

Macromolecule Content

Total Structure Weight: 208.64 kDa
Atom Count: 14,581
Modelled Residue Count: 1,776
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 5 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 BA [auth C] SDF format, chain IA [auth D] SDF format, chain JA [auth D] SDF format, chain M [auth A] SDF format, chain QA [auth E] SDF format, chain V [auth B] MOL2 format, chain BA [auth C] MOL2 format, chain IA [auth D] MOL2 format, chain JA [auth D] MOL2 format, chain M [auth A] MOL2 format, chain QA [auth E] MOL2 format, chain V [auth B] mmCIF format, chain BA [auth C] mmCIF format, chain IA [auth D] mmCIF format, chain JA [auth D] mmCIF format, chain M [auth A] mmCIF format, chain QA [auth E] mmCIF format, chain V [auth B]	BA [auth C] IA [auth D] JA [auth D] M [auth A] QA [auth E] BA [auth C], IA [auth D], JA [auth D], M [auth A], QA [auth E], V [auth B]	TRIETHYLENE GLYCOL C₆ H₁₄ O₄ ZIBGPFATKBEMQZ-UHFFFAOYSA-N		Interactions Focus chain BA [auth C] Focus chain IA [auth D] Focus chain JA [auth D] Focus chain M [auth A] Focus chain QA [auth E] Focus chain V [auth B] Interactions & Density Focus chain BA [auth C] Focus chain IA [auth D] Focus chain JA [auth D] Focus chain M [auth A] Focus chain QA [auth E] Focus chain V [auth B]
PEG (Subject of Investigation/LOI) Query on PEG Download Ideal Coordinates CCD File SDF format, chain AB [auth F] SDF format, chain FA [auth C] SDF format, chain GA [auth C] SDF format, chain MA [auth D] SDF format, chain O [auth A] SDF format, chain P [auth A] SDF format, chain W [auth B] SDF format, chain YA [auth F] SDF format, chain ZA [auth F] MOL2 format, chain AB [auth F] MOL2 format, chain FA [auth C] MOL2 format, chain GA [auth C] MOL2 format, chain MA [auth D] MOL2 format, chain O [auth A] MOL2 format, chain P [auth A] MOL2 format, chain W [auth B] MOL2 format, chain YA [auth F] MOL2 format, chain ZA [auth F] mmCIF format, chain AB [auth F] mmCIF format, chain FA [auth C] mmCIF format, chain GA [auth C] mmCIF format, chain MA [auth D] mmCIF format, chain O [auth A] mmCIF format, chain P [auth A] mmCIF format, chain W [auth B] mmCIF format, chain YA [auth F] mmCIF format, chain ZA [auth F]	AB [auth F] FA [auth C] GA [auth C] MA [auth D] O [auth A] AB [auth F], FA [auth C], GA [auth C], MA [auth D], O [auth A], P [auth A], W [auth B], YA [auth F], ZA [auth F]	DI(HYDROXYETHYL)ETHER C₄ H₁₀ O₃ MTHSVFCYNBDYFN-UHFFFAOYSA-N		Interactions Focus chain AB [auth F] Focus chain FA [auth C] Focus chain GA [auth C] Focus chain MA [auth D] Focus chain O [auth A] Focus chain P [auth A] Focus chain W [auth B] Focus chain YA [auth F] Focus chain ZA [auth F] Interactions & Density Focus chain AB [auth F] Focus chain FA [auth C] Focus chain GA [auth C] Focus chain MA [auth D] Focus chain O [auth A] Focus chain P [auth A] Focus chain W [auth B] Focus chain YA [auth F] Focus chain ZA [auth F]
EDO (Subject of Investigation/LOI) Query on EDO Download Ideal Coordinates CCD File SDF format, chain AA [auth C] SDF format, chain HA [auth D] SDF format, chain I [auth A] SDF format, chain J [auth A] SDF format, chain K [auth A] SDF format, chain L [auth A] SDF format, chain NA [auth E] SDF format, chain OA [auth E] SDF format, chain PA [auth E] SDF format, chain S [auth B] SDF format, chain T [auth B] SDF format, chain U [auth B] SDF format, chain WA [auth F] SDF format, chain XA [auth F] SDF format, chain Y [auth C] SDF format, chain Z [auth C] MOL2 format, chain AA [auth C] MOL2 format, chain HA [auth D] MOL2 format, chain I [auth A] MOL2 format, chain J [auth A] MOL2 format, chain K [auth A] MOL2 format, chain L [auth A] MOL2 format, chain NA [auth E] MOL2 format, chain OA [auth E] MOL2 format, chain PA [auth E] MOL2 format, chain S [auth B] MOL2 format, chain T [auth B] MOL2 format, chain U [auth B] MOL2 format, chain WA [auth F] MOL2 format, chain XA [auth F] MOL2 format, chain Y [auth C] MOL2 format, chain Z [auth C] mmCIF format, chain AA [auth C] mmCIF format, chain HA [auth D] mmCIF format, chain I [auth A] mmCIF format, chain J [auth A] mmCIF format, chain K [auth A] mmCIF format, chain L [auth A] mmCIF format, chain NA [auth E] mmCIF format, chain OA [auth E] mmCIF format, chain PA [auth E] mmCIF format, chain S [auth B] mmCIF format, chain T [auth B] mmCIF format, chain U [auth B] mmCIF format, chain WA [auth F] mmCIF format, chain XA [auth F] mmCIF format, chain Y [auth C] mmCIF format, chain Z [auth C]	AA [auth C] HA [auth D] I [auth A] J [auth A] K [auth A] AA [auth C], HA [auth D], I [auth A], J [auth A], K [auth A], L [auth A], NA [auth E], OA [auth E], PA [auth E], S [auth B], T [auth B], U [auth B], WA [auth F], XA [auth F], Y [auth C], Z [auth C]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain AA [auth C] Focus chain HA [auth D] Focus chain I [auth A] Focus chain J [auth A] Focus chain K [auth A] Focus chain L [auth A] Focus chain NA [auth E] Focus chain OA [auth E] Focus chain PA [auth E] Focus chain S [auth B] Focus chain T [auth B] Focus chain U [auth B] Focus chain WA [auth F] Focus chain XA [auth F] Focus chain Y [auth C] Focus chain Z [auth C] Interactions & Density Focus chain AA [auth C] Focus chain HA [auth D] Focus chain I [auth A] Focus chain J [auth A] Focus chain K [auth A] Focus chain L [auth A] Focus chain NA [auth E] Focus chain OA [auth E] Focus chain PA [auth E] Focus chain S [auth B] Focus chain T [auth B] Focus chain U [auth B] Focus chain WA [auth F] Focus chain XA [auth F] 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 CA [auth C] SDF format, chain DA [auth C] SDF format, chain EA [auth C] SDF format, chain KA [auth D] SDF format, chain LA [auth D] SDF format, chain N [auth A] SDF format, chain RA [auth E] SDF format, chain SA [auth E] SDF format, chain TA [auth E] SDF format, chain UA [auth E] MOL2 format, chain CA [auth C] MOL2 format, chain DA [auth C] MOL2 format, chain EA [auth C] MOL2 format, chain KA [auth D] MOL2 format, chain LA [auth D] MOL2 format, chain N [auth A] MOL2 format, chain RA [auth E] MOL2 format, chain SA [auth E] MOL2 format, chain TA [auth E] MOL2 format, chain UA [auth E] mmCIF format, chain CA [auth C] mmCIF format, chain DA [auth C] mmCIF format, chain EA [auth C] mmCIF format, chain KA [auth D] mmCIF format, chain LA [auth D] mmCIF format, chain N [auth A] mmCIF format, chain RA [auth E] mmCIF format, chain SA [auth E] mmCIF format, chain TA [auth E] mmCIF format, chain UA [auth E]	CA [auth C] DA [auth C] EA [auth C] KA [auth D] LA [auth D] CA [auth C], DA [auth C], EA [auth C], KA [auth D], LA [auth D], N [auth A], RA [auth E], SA [auth E], TA [auth E], UA [auth E]	ACETATE ION C₂ H₃ O₂ QTBSBXVTEAMEQO-UHFFFAOYSA-M		Interactions Focus chain CA [auth C] Focus chain DA [auth C] Focus chain EA [auth C] Focus chain KA [auth D] Focus chain LA [auth D] Focus chain N [auth A] Focus chain RA [auth E] Focus chain SA [auth E] Focus chain TA [auth E] Focus chain UA [auth E] Interactions & Density Focus chain CA [auth C] Focus chain DA [auth C] Focus chain EA [auth C] Focus chain KA [auth D] Focus chain LA [auth D] Focus chain N [auth A] Focus chain RA [auth E] Focus chain SA [auth E] Focus chain TA [auth E] Focus chain UA [auth E]
MG (Subject of Investigation/LOI) Query on MG Download Ideal Coordinates CCD File SDF format, chain G [auth A] SDF format, chain H [auth A] SDF format, chain Q [auth B] SDF format, chain R [auth B] SDF format, chain VA [auth F] SDF format, chain X [auth C] MOL2 format, chain G [auth A] MOL2 format, chain H [auth A] MOL2 format, chain Q [auth B] MOL2 format, chain R [auth B] MOL2 format, chain VA [auth F] MOL2 format, chain X [auth C] mmCIF format, chain G [auth A] mmCIF format, chain H [auth A] mmCIF format, chain Q [auth B] mmCIF format, chain R [auth B] mmCIF format, chain VA [auth F] mmCIF format, chain X [auth C]	G [auth A] H [auth A] Q [auth B] R [auth B] VA [auth F] G [auth A], H [auth A], Q [auth B], R [auth B], VA [auth F], X [auth C]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain G [auth A] Focus chain H [auth A] Focus chain Q [auth B] Focus chain R [auth B] Focus chain VA [auth F] Focus chain X [auth C] Interactions & Density Focus chain G [auth A] Focus chain H [auth A] Focus chain Q [auth B] Focus chain R [auth B] Focus chain VA [auth F] Focus chain X [auth C]