7KPE | pdb_00007kpe

Dihydrodipicolinate synthase (DHDPS) from C.jejuni, E88Q mutant with pyruvate bound in the active site and R,R-bislysine at the allosteric site

PDB DOI: https://doi.org/10.2210/pdb7KPE/pdb

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

Deposited: 2020-11-11 Released: 2021-11-17
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: 2.06 Å
R-Value Free:
0.240 (Depositor), 0.220 (DCC)
R-Value Work:
0.200 (Depositor), 0.190 (DCC)
R-Value Observed:
0.202 (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

THE ALLOSTERIC SITE RESIDUE, E88 INTERACTS WITH THE INHIBITORS TO TRANSMIT THE ALLOSTERIC INHIBITION SIGNALS IN Cj.DHDPS BY FORMING A HYDROGEN BOND.

Saran, S., Majdi Yazdi, M., Chung, I., Sanders, D.A.R.

To be published.

Macromolecule Content

Total Structure Weight: 207.84 kDa
Atom Count: 14,821
Modeled Residue Count: 1,772
Deposited Residue Count: 1,860
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(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 AA [auth F] SDF format, chain K [auth B] SDF format, chain S [auth D] MOL2 format, chain AA [auth F] MOL2 format, chain K [auth B] MOL2 format, chain S [auth D] mmCIF format, chain AA [auth F] mmCIF format, chain K [auth B] mmCIF format, chain S [auth D]	AA [auth F], K [auth B], S [auth D]	(2R,5R)-2,5-diamino-2,5-bis(4-aminobutyl)hexanedioic acid C₁₄ H₃₀ N₄ O₄ XYUHPPVEDOOPDE-ZIAGYGMSSA-N		Interactions Focus chain AA [auth F] Focus chain K [auth B] Focus chain S [auth D] Interactions & Density Focus chain AA [auth F] Focus chain K [auth B] Focus chain S [auth D]
PGE (Subject of Investigation/LOI) Query on PGE Download Ideal Coordinates CCD File SDF format, chain Z [auth E] SDF format, chain M [auth B] SDF format, chain J [auth A] SDF format, chain GA [auth F] MOL2 format, chain Z [auth E] MOL2 format, chain M [auth B] MOL2 format, chain J [auth A] MOL2 format, chain GA [auth F] mmCIF format, chain Z [auth E] mmCIF format, chain M [auth B] mmCIF format, chain J [auth A] mmCIF format, chain GA [auth F]	GA [auth F], J [auth A], M [auth B], Z [auth E]	TRIETHYLENE GLYCOL C₆ H₁₄ O₄ ZIBGPFATKBEMQZ-UHFFFAOYSA-N		Interactions Focus chain GA [auth F] Focus chain J [auth A] Focus chain M [auth B] Focus chain Z [auth E] Interactions & Density Focus chain GA [auth F] Focus chain J [auth A] Focus chain M [auth B] Focus chain Z [auth E]
PEG (Subject of Investigation/LOI) Query on PEG Download Ideal Coordinates CCD File SDF format, chain V [auth D] SDF format, chain Q [auth C] SDF format, chain P [auth C] MOL2 format, chain V [auth D] MOL2 format, chain Q [auth C] MOL2 format, chain P [auth C] mmCIF format, chain V [auth D] mmCIF format, chain Q [auth C] mmCIF format, chain P [auth C]	P [auth C], Q [auth C], V [auth D]	DI(HYDROXYETHYL)ETHER C₄ H₁₀ O₃ MTHSVFCYNBDYFN-UHFFFAOYSA-N		Interactions Focus chain P [auth C] Focus chain Q [auth C] Focus chain V [auth D] Interactions & Density Focus chain P [auth C] Focus chain Q [auth C] Focus chain V [auth D]
GOL (Subject of Investigation/LOI) Query on GOL Download Ideal Coordinates CCD File SDF format, chain HA [auth F] MOL2 format, chain HA [auth F] mmCIF format, chain HA [auth F]	HA [auth F]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain HA [auth F] Interactions & Density Focus chain HA [auth F]
EDO (Subject of Investigation/LOI) Query on EDO Download Ideal Coordinates CCD File SDF format, chain I [auth A] SDF format, chain FA [auth F] SDF format, chain EA [auth F] MOL2 format, chain I [auth A] MOL2 format, chain FA [auth F] MOL2 format, chain EA [auth F] mmCIF format, chain I [auth A] mmCIF format, chain FA [auth F] mmCIF format, chain EA [auth F]	EA [auth F], FA [auth F], I [auth A]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain EA [auth F] Focus chain FA [auth F] Focus chain I [auth A] Interactions & Density Focus chain EA [auth F] Focus chain FA [auth F] Focus chain I [auth A]
ACT (Subject of Investigation/LOI) Query on ACT Download Ideal Coordinates CCD File SDF format, chain Y [auth E] SDF format, chain W [auth D] SDF format, chain R [auth C] SDF format, chain H [auth A] SDF format, chain DA [auth F] SDF format, chain CA [auth F] SDF format, chain BA [auth F] MOL2 format, chain Y [auth E] MOL2 format, chain W [auth D] MOL2 format, chain R [auth C] MOL2 format, chain H [auth A] MOL2 format, chain DA [auth F] MOL2 format, chain CA [auth F] MOL2 format, chain BA [auth F] mmCIF format, chain Y [auth E] mmCIF format, chain W [auth D] mmCIF format, chain R [auth C] mmCIF format, chain H [auth A] mmCIF format, chain DA [auth F] mmCIF format, chain CA [auth F] mmCIF format, chain BA [auth F]	BA [auth F] CA [auth F] DA [auth F] H [auth A] R [auth C] BA [auth F], CA [auth F], DA [auth F], H [auth A], R [auth C], W [auth D], Y [auth E]	ACETATE ION C₂ H₃ O₂ QTBSBXVTEAMEQO-UHFFFAOYSA-M		Interactions Focus chain BA [auth F] Focus chain CA [auth F] Focus chain DA [auth F] Focus chain H [auth A] Focus chain R [auth C] Focus chain W [auth D] Focus chain Y [auth E] Interactions & Density Focus chain BA [auth F] Focus chain CA [auth F] Focus chain DA [auth F] Focus chain H [auth A] Focus chain R [auth C] Focus chain W [auth D] Focus chain Y [auth E]
MG (Subject of Investigation/LOI) Query on MG Download Ideal Coordinates CCD File SDF format, chain X [auth E] SDF format, chain U [auth D] SDF format, chain T [auth D] SDF format, chain O [auth C] SDF format, chain N [auth C] SDF format, chain L [auth B] SDF format, chain G [auth A] MOL2 format, chain X [auth E] MOL2 format, chain U [auth D] MOL2 format, chain T [auth D] MOL2 format, chain O [auth C] MOL2 format, chain N [auth C] MOL2 format, chain L [auth B] MOL2 format, chain G [auth A] mmCIF format, chain X [auth E] mmCIF format, chain U [auth D] mmCIF format, chain T [auth D] mmCIF format, chain O [auth C] mmCIF format, chain N [auth C] mmCIF format, chain L [auth B] mmCIF format, chain G [auth A]	G [auth A] L [auth B] N [auth C] O [auth C] T [auth D] G [auth A], L [auth B], N [auth C], O [auth C], T [auth D], U [auth D], X [auth E]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain G [auth A] Focus chain L [auth B] Focus chain N [auth C] Focus chain O [auth C] Focus chain T [auth D] Focus chain U [auth D] Focus chain X [auth E] Interactions & Density Focus chain G [auth A] Focus chain L [auth B] Focus chain N [auth C] Focus chain O [auth C] Focus chain T [auth D] Focus chain U [auth D] Focus chain X [auth E]