7L4B | pdb_00007l4b

Dihydrodipicolinate synthase (DHDPS) from C.jejuni with pyruvate bound in the active site in P1211 space group

PDB DOI: https://doi.org/10.2210/pdb7L4B/pdb

Classification: LYASE
Organism(s): Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2020-12-18 Released: 2021-12-22
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: 2.42 Å
R-Value Free:
0.268 (Depositor), 0.269 (DCC)
R-Value Work:
0.225 (Depositor), 0.229 (DCC)
R-Value Observed:
0.227 (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

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: 412.73 kDa
Atom Count: 27,966
Modeled Residue Count: 3,550
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 subsp. jejuni NCTC 11168 = ATCC 700819	Mutation(s): 0 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 4 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 CA [auth G] SDF format, chain DA [auth H] SDF format, chain EA [auth I] SDF format, chain FA [auth J] SDF format, chain IA [auth K] SDF format, chain JA [auth L] SDF format, chain M [auth A] SDF format, chain O [auth B] SDF format, chain P [auth C] SDF format, chain Q [auth C] SDF format, chain U [auth D] SDF format, chain W [auth E] SDF format, chain X [auth E] SDF format, chain Z [auth F] MOL2 format, chain CA [auth G] MOL2 format, chain DA [auth H] MOL2 format, chain EA [auth I] MOL2 format, chain FA [auth J] MOL2 format, chain IA [auth K] MOL2 format, chain JA [auth L] MOL2 format, chain M [auth A] MOL2 format, chain O [auth B] MOL2 format, chain P [auth C] MOL2 format, chain Q [auth C] MOL2 format, chain U [auth D] MOL2 format, chain W [auth E] MOL2 format, chain X [auth E] MOL2 format, chain Z [auth F] mmCIF format, chain CA [auth G] mmCIF format, chain DA [auth H] mmCIF format, chain EA [auth I] mmCIF format, chain FA [auth J] mmCIF format, chain IA [auth K] mmCIF format, chain JA [auth L] mmCIF format, chain M [auth A] mmCIF format, chain O [auth B] mmCIF format, chain P [auth C] mmCIF format, chain Q [auth C] mmCIF format, chain U [auth D] mmCIF format, chain W [auth E] mmCIF format, chain X [auth E] mmCIF format, chain Z [auth F]	CA [auth G] DA [auth H] EA [auth I] FA [auth J] IA [auth K] CA [auth G], DA [auth H], EA [auth I], FA [auth J], IA [auth K], JA [auth L], M [auth A], O [auth B], P [auth C], Q [auth C], U [auth D], W [auth E], X [auth E], Z [auth F]	TRIETHYLENE GLYCOL C₆ H₁₄ O₄ ZIBGPFATKBEMQZ-UHFFFAOYSA-N		Interactions Focus chain CA [auth G] Focus chain DA [auth H] Focus chain EA [auth I] Focus chain FA [auth J] Focus chain IA [auth K] Focus chain JA [auth L] Focus chain M [auth A] Focus chain O [auth B] Focus chain P [auth C] Focus chain Q [auth C] Focus chain U [auth D] Focus chain W [auth E] Focus chain X [auth E] Focus chain Z [auth F] Interactions & Density Focus chain CA [auth G] Focus chain DA [auth H] Focus chain EA [auth I] Focus chain FA [auth J] Focus chain IA [auth K] Focus chain JA [auth L] Focus chain M [auth A] Focus chain O [auth B] Focus chain P [auth C] Focus chain Q [auth C] Focus chain U [auth D] Focus chain W [auth E] Focus chain X [auth E] Focus chain Z [auth F]
EDO (Subject of Investigation/LOI) Query on EDO Download:Ideal Coordinates CCD File SDF format, chain HA [auth J] MOL2 format, chain HA [auth J] mmCIF format, chain HA [auth J]	HA [auth J]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain HA [auth J] Interactions & Density Focus chain HA [auth J]
ACT (Subject of Investigation/LOI) Query on ACT Download:Ideal Coordinates CCD File SDF format, chain BA [auth F] SDF format, chain KA [auth L] SDF format, chain T [auth C] MOL2 format, chain BA [auth F] MOL2 format, chain KA [auth L] MOL2 format, chain T [auth C] mmCIF format, chain BA [auth F] mmCIF format, chain KA [auth L] mmCIF format, chain T [auth C]	BA [auth F], KA [auth L], T [auth C]	ACETATE ION C₂ H₃ O₂ QTBSBXVTEAMEQO-UHFFFAOYSA-M		Interactions Focus chain BA [auth F] Focus chain KA [auth L] Focus chain T [auth C] Interactions & Density Focus chain BA [auth F] Focus chain KA [auth L] Focus chain T [auth C]
MG (Subject of Investigation/LOI) Query on MG Download:Ideal Coordinates CCD File SDF format, chain AA [auth F] SDF format, chain GA [auth J] SDF format, chain N [auth A] SDF format, chain R [auth C] SDF format, chain S [auth C] SDF format, chain V [auth D] SDF format, chain Y [auth E] MOL2 format, chain AA [auth F] MOL2 format, chain GA [auth J] MOL2 format, chain N [auth A] MOL2 format, chain R [auth C] MOL2 format, chain S [auth C] MOL2 format, chain V [auth D] MOL2 format, chain Y [auth E] mmCIF format, chain AA [auth F] mmCIF format, chain GA [auth J] mmCIF format, chain N [auth A] mmCIF format, chain R [auth C] mmCIF format, chain S [auth C] mmCIF format, chain V [auth D] mmCIF format, chain Y [auth E]	AA [auth F] GA [auth J] N [auth A] R [auth C] S [auth C] AA [auth F], GA [auth J], N [auth A], R [auth C], S [auth C], V [auth D], Y [auth E]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain AA [auth F] Focus chain GA [auth J] Focus chain N [auth A] Focus chain R [auth C] Focus chain S [auth C] Focus chain V [auth D] Focus chain Y [auth E] Interactions & Density Focus chain AA [auth F] Focus chain GA [auth J] Focus chain N [auth A] Focus chain R [auth C] Focus chain S [auth C] Focus chain V [auth D] Focus chain Y [auth E]