7M06 | pdb_00007m06

Dihydrodipicolinate synthase (DHDPS) from C.jejuni, Y110F mutant with R,R-bislysine bound at the allosteric site at 2.7 Angstrom

PDB DOI: https://doi.org/10.2210/pdb7M06/pdb

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

Deposited: 2021-03-10 Released: 2022-03-16
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: 2.70 Å
R-Value Free:
0.242 (Depositor), 0.230 (DCC)
R-Value Work:
0.194 (Depositor)
R-Value Observed:
0.196 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.1 of the entry. See complete history.

Literature

B-FACTOR ANALYSIS SUGGEST THAT L-LYSINE AND R, R-BISLYSINE ALLOSTERICALLY INHIBIT Cj.DHDPS ENZYME BY DECREASING PROTEIN DYNAMICS

Saran, S., Sanders, D.A.R.

To be published.

Macromolecule Content

Total Structure Weight: 138.13 kDa
Atom Count: 9,256
Modeled Residue Count: 1,185
Deposited Residue Count: 1,240
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	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% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q9PPB4
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 5 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 L [auth C] SDF format, chain H [auth B] MOL2 format, chain L [auth C] MOL2 format, chain H [auth B] mmCIF format, chain L [auth C] mmCIF format, chain H [auth B]	H [auth B], L [auth C]	(2R,5R)-2,5-diamino-2,5-bis(4-aminobutyl)hexanedioic acid C₁₄ H₃₀ N₄ O₄ XYUHPPVEDOOPDE-ZIAGYGMSSA-N		Interactions Focus chain H [auth B] Focus chain L [auth C] Interactions & Density Focus chain H [auth B] Focus chain L [auth C]
PGE (Subject of Investigation/LOI) Query on PGE Download:Ideal Coordinates CCD File SDF format, chain G [auth A] SDF format, chain J [auth B] SDF format, chain T [auth D] SDF format, chain Q [auth C] MOL2 format, chain G [auth A] MOL2 format, chain J [auth B] MOL2 format, chain T [auth D] MOL2 format, chain Q [auth C] mmCIF format, chain G [auth A] mmCIF format, chain J [auth B] mmCIF format, chain T [auth D] mmCIF format, chain Q [auth C]	G [auth A], J [auth B], Q [auth C], T [auth D]	TRIETHYLENE GLYCOL C₆ H₁₄ O₄ ZIBGPFATKBEMQZ-UHFFFAOYSA-N		Interactions Focus chain G [auth A] Focus chain J [auth B] Focus chain Q [auth C] Focus chain T [auth D] Interactions & Density Focus chain G [auth A] Focus chain J [auth B] Focus chain Q [auth C] Focus chain T [auth D]
PEG (Subject of Investigation/LOI) Query on PEG Download:Ideal Coordinates CCD File SDF format, chain K [auth B] SDF format, chain U [auth D] MOL2 format, chain K [auth B] MOL2 format, chain U [auth D] mmCIF format, chain K [auth B] mmCIF format, chain U [auth D]	K [auth B], U [auth D]	DI(HYDROXYETHYL)ETHER C₄ H₁₀ O₃ MTHSVFCYNBDYFN-UHFFFAOYSA-N		Interactions Focus chain K [auth B] Focus chain U [auth D] Interactions & Density Focus chain K [auth B] Focus chain U [auth D]
EDO (Subject of Investigation/LOI) Query on EDO Download:Ideal Coordinates CCD File SDF format, chain V [auth D] MOL2 format, chain V [auth D] mmCIF format, chain V [auth D]	V [auth D]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain V [auth D] Interactions & Density Focus chain V [auth D]
MG (Subject of Investigation/LOI) Query on MG Download:Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain M [auth C] SDF format, chain N [auth C] SDF format, chain O [auth C] SDF format, chain R [auth D] SDF format, chain S [auth D] SDF format, chain P [auth C] SDF format, chain I [auth B] SDF format, chain F [auth A] MOL2 format, chain E [auth A] MOL2 format, chain M [auth C] MOL2 format, chain N [auth C] MOL2 format, chain O [auth C] MOL2 format, chain R [auth D] MOL2 format, chain S [auth D] MOL2 format, chain P [auth C] MOL2 format, chain I [auth B] MOL2 format, chain F [auth A] mmCIF format, chain E [auth A] mmCIF format, chain M [auth C] mmCIF format, chain N [auth C] mmCIF format, chain O [auth C] mmCIF format, chain R [auth D] mmCIF format, chain S [auth D] mmCIF format, chain P [auth C] mmCIF format, chain I [auth B] mmCIF format, chain F [auth A]	E [auth A] F [auth A] I [auth B] M [auth C] N [auth C] E [auth A], F [auth A], I [auth B], M [auth C], N [auth C], O [auth C], P [auth C], R [auth D], S [auth D]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Focus chain F [auth A] Focus chain I [auth B] Focus chain M [auth C] Focus chain N [auth C] Focus chain O [auth C] Focus chain P [auth C] Focus chain R [auth D] Focus chain S [auth D] Interactions & Density Focus chain E [auth A] Focus chain F [auth A] Focus chain I [auth B] Focus chain M [auth C] Focus chain N [auth C] Focus chain O [auth C] Focus chain P [auth C] Focus chain R [auth D] Focus chain S [auth D]