7KZ2 | pdb_00007kz2

Dihydrodipicolinate synthase (DHDPS) from C.jejuni, Y110F mutant with pyruvate bound in the active site and L-lysine bound at the allosteric site in C2221 space group

PDB DOI: https://doi.org/10.2210/pdb7KZ2/pdb

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

Deposited: 2020-12-09 Released: 2021-12-15
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: 1.90 Å
R-Value Free:
0.218 (Depositor), 0.230 (DCC)
R-Value Work:
0.186 (Depositor), 0.200 (DCC)
R-Value Observed:
0.188 (Depositor)

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

This is version 1.2 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: 209.69 kDa
Atom Count: 15,048
Modeled 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 6 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
PGE Query on PGE Download Ideal Coordinates CCD File SDF format, chain WA [auth E] SDF format, chain U [auth A] SDF format, chain RA [auth D] SDF format, chain OA [auth C] SDF format, chain EA [auth B] SDF format, chain DB [auth F] SDF format, chain CB [auth F] MOL2 format, chain WA [auth E] MOL2 format, chain U [auth A] MOL2 format, chain RA [auth D] MOL2 format, chain OA [auth C] MOL2 format, chain EA [auth B] MOL2 format, chain DB [auth F] MOL2 format, chain CB [auth F] mmCIF format, chain WA [auth E] mmCIF format, chain U [auth A] mmCIF format, chain RA [auth D] mmCIF format, chain OA [auth C] mmCIF format, chain EA [auth B] mmCIF format, chain DB [auth F] mmCIF format, chain CB [auth F]	CB [auth F] DB [auth F] EA [auth B] OA [auth C] RA [auth D] CB [auth F], DB [auth F], EA [auth B], OA [auth C], RA [auth D], U [auth A], WA [auth E]	TRIETHYLENE GLYCOL C₆ H₁₄ O₄ ZIBGPFATKBEMQZ-UHFFFAOYSA-N		Interactions Focus chain CB [auth F] Focus chain DB [auth F] Focus chain EA [auth B] Focus chain OA [auth C] Focus chain RA [auth D] Focus chain U [auth A] Focus chain WA [auth E] Interactions & Density Focus chain CB [auth F] Focus chain DB [auth F] Focus chain EA [auth B] Focus chain OA [auth C] Focus chain RA [auth D] Focus chain U [auth A] Focus chain WA [auth E]
LYS Query on LYS Download Ideal Coordinates CCD File SDF format, chain FA [auth C] SDF format, chain G [auth A] SDF format, chain PA [auth D] SDF format, chain SA [auth E] SDF format, chain V [auth B] SDF format, chain XA [auth F] MOL2 format, chain FA [auth C] MOL2 format, chain G [auth A] MOL2 format, chain PA [auth D] MOL2 format, chain SA [auth E] MOL2 format, chain V [auth B] MOL2 format, chain XA [auth F] mmCIF format, chain FA [auth C] mmCIF format, chain G [auth A] mmCIF format, chain PA [auth D] mmCIF format, chain SA [auth E] mmCIF format, chain V [auth B] mmCIF format, chain XA [auth F]	FA [auth C] G [auth A] PA [auth D] SA [auth E] V [auth B] FA [auth C], G [auth A], PA [auth D], SA [auth E], V [auth B], XA [auth F]	LYSINE C₆ H₁₅ N₂ O₂ KDXKERNSBIXSRK-YFKPBYRVSA-O		Interactions Focus chain FA [auth C] Focus chain G [auth A] Focus chain PA [auth D] Focus chain SA [auth E] Focus chain V [auth B] Focus chain XA [auth F] Interactions & Density Focus chain FA [auth C] Focus chain G [auth A] Focus chain PA [auth D] Focus chain SA [auth E] Focus chain V [auth B] Focus chain XA [auth F]
PEG Query on PEG Download Ideal Coordinates CCD File SDF format, chain ZA [auth F] SDF format, chain YA [auth F] SDF format, chain W [auth B] SDF format, chain UA [auth E] SDF format, chain TA [auth E] SDF format, chain M [auth A] SDF format, chain L [auth A] SDF format, chain K [auth A] SDF format, chain J [auth A] SDF format, chain I [auth A] SDF format, chain HA [auth C] SDF format, chain H [auth A] SDF format, chain GA [auth C] MOL2 format, chain ZA [auth F] MOL2 format, chain YA [auth F] MOL2 format, chain W [auth B] MOL2 format, chain UA [auth E] MOL2 format, chain TA [auth E] MOL2 format, chain M [auth A] MOL2 format, chain L [auth A] MOL2 format, chain K [auth A] MOL2 format, chain J [auth A] MOL2 format, chain I [auth A] MOL2 format, chain HA [auth C] MOL2 format, chain H [auth A] MOL2 format, chain GA [auth C] mmCIF format, chain ZA [auth F] mmCIF format, chain YA [auth F] mmCIF format, chain W [auth B] mmCIF format, chain UA [auth E] mmCIF format, chain TA [auth E] mmCIF format, chain M [auth A] mmCIF format, chain L [auth A] mmCIF format, chain K [auth A] mmCIF format, chain J [auth A] mmCIF format, chain I [auth A] mmCIF format, chain HA [auth C] mmCIF format, chain H [auth A] mmCIF format, chain GA [auth C]	GA [auth C] H [auth A] HA [auth C] I [auth A] J [auth A] GA [auth C], H [auth A], HA [auth C], I [auth A], J [auth A], K [auth A], L [auth A], M [auth A], TA [auth E], UA [auth E], W [auth B], YA [auth F], ZA [auth F]	DI(HYDROXYETHYL)ETHER C₄ H₁₀ O₃ MTHSVFCYNBDYFN-UHFFFAOYSA-N		Interactions Focus chain GA [auth C] Focus chain H [auth A] Focus chain HA [auth C] Focus chain I [auth A] Focus chain J [auth A] Focus chain K [auth A] Focus chain L [auth A] Focus chain M [auth A] Focus chain TA [auth E] Focus chain UA [auth E] Focus chain W [auth B] Focus chain YA [auth F] Focus chain ZA [auth F] Interactions & Density Focus chain GA [auth C] Focus chain H [auth A] Focus chain HA [auth C] Focus chain I [auth A] Focus chain J [auth A] Focus chain K [auth A] Focus chain L [auth A] Focus chain M [auth A] Focus chain TA [auth E] Focus chain UA [auth E] Focus chain W [auth B] Focus chain YA [auth F] Focus chain ZA [auth F]
EDO Query on EDO Download Ideal Coordinates CCD File SDF format, chain Z [auth B] SDF format, chain Y [auth B] SDF format, chain X [auth B] SDF format, chain VA [auth E] SDF format, chain R [auth A] SDF format, chain QA [auth D] SDF format, chain Q [auth A] SDF format, chain P [auth A] SDF format, chain O [auth A] SDF format, chain N [auth A] SDF format, chain MA [auth C] SDF format, chain LA [auth C] SDF format, chain KA [auth C] SDF format, chain JA [auth C] SDF format, chain IA [auth C] SDF format, chain AB [auth F] SDF format, chain AA [auth B] MOL2 format, chain Z [auth B] MOL2 format, chain Y [auth B] MOL2 format, chain X [auth B] MOL2 format, chain VA [auth E] MOL2 format, chain R [auth A] MOL2 format, chain QA [auth D] MOL2 format, chain Q [auth A] MOL2 format, chain P [auth A] MOL2 format, chain O [auth A] MOL2 format, chain N [auth A] MOL2 format, chain MA [auth C] MOL2 format, chain LA [auth C] MOL2 format, chain KA [auth C] MOL2 format, chain JA [auth C] MOL2 format, chain IA [auth C] MOL2 format, chain AB [auth F] MOL2 format, chain AA [auth B] mmCIF format, chain Z [auth B] mmCIF format, chain Y [auth B] mmCIF format, chain X [auth B] mmCIF format, chain VA [auth E] mmCIF format, chain R [auth A] mmCIF format, chain QA [auth D] mmCIF format, chain Q [auth A] mmCIF format, chain P [auth A] mmCIF format, chain O [auth A] mmCIF format, chain N [auth A] mmCIF format, chain MA [auth C] mmCIF format, chain LA [auth C] mmCIF format, chain KA [auth C] mmCIF format, chain JA [auth C] mmCIF format, chain IA [auth C] mmCIF format, chain AB [auth F] mmCIF format, chain AA [auth B]	AA [auth B] AB [auth F] IA [auth C] JA [auth C] KA [auth C] AA [auth B], AB [auth F], IA [auth C], JA [auth C], KA [auth C], LA [auth C], MA [auth C], N [auth A], O [auth A], P [auth A], Q [auth A], QA [auth D], R [auth A], VA [auth E], X [auth B], Y [auth B], Z [auth B]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain AA [auth B] Focus chain AB [auth F] Focus chain IA [auth C] Focus chain JA [auth C] Focus chain KA [auth C] Focus chain LA [auth C] Focus chain MA [auth C] Focus chain N [auth A] Focus chain O [auth A] Focus chain P [auth A] Focus chain Q [auth A] Focus chain QA [auth D] Focus chain R [auth A] Focus chain VA [auth E] Focus chain X [auth B] Focus chain Y [auth B] Focus chain Z [auth B] Interactions & Density Focus chain AA [auth B] Focus chain AB [auth F] Focus chain IA [auth C] Focus chain JA [auth C] Focus chain KA [auth C] Focus chain LA [auth C] Focus chain MA [auth C] Focus chain N [auth A] Focus chain O [auth A] Focus chain P [auth A] Focus chain Q [auth A] Focus chain QA [auth D] Focus chain R [auth A] Focus chain VA [auth E] Focus chain X [auth B] Focus chain Y [auth B] Focus chain Z [auth B]
ACT Query on ACT Download Ideal Coordinates CCD File SDF format, chain T [auth A] SDF format, chain S [auth A] SDF format, chain DA [auth B] SDF format, chain BB [auth F] MOL2 format, chain T [auth A] MOL2 format, chain S [auth A] MOL2 format, chain DA [auth B] MOL2 format, chain BB [auth F] mmCIF format, chain T [auth A] mmCIF format, chain S [auth A] mmCIF format, chain DA [auth B] mmCIF format, chain BB [auth F]	BB [auth F], DA [auth B], S [auth A], T [auth A]	ACETATE ION C₂ H₃ O₂ QTBSBXVTEAMEQO-UHFFFAOYSA-M		Interactions Focus chain BB [auth F] Focus chain DA [auth B] Focus chain S [auth A] Focus chain T [auth A] Interactions & Density Focus chain BB [auth F] Focus chain DA [auth B] Focus chain S [auth A] Focus chain T [auth A]
MG Query on MG Download Ideal Coordinates CCD File SDF format, chain NA [auth C] SDF format, chain CA [auth B] SDF format, chain BA [auth B] MOL2 format, chain NA [auth C] MOL2 format, chain CA [auth B] MOL2 format, chain BA [auth B] mmCIF format, chain NA [auth C] mmCIF format, chain CA [auth B] mmCIF format, chain BA [auth B]	BA [auth B], CA [auth B], NA [auth C]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain BA [auth B] Focus chain CA [auth B] Focus chain NA [auth C] Interactions & Density Focus chain BA [auth B] Focus chain CA [auth B] Focus chain NA [auth C]