7LCF | pdb_00007lcf

Dihydrodipicolinate synthase (DHDPS) from C.jejuni, with pyruvate bound in the active site and L-lysine bound at the allosteric site in C121 space group

PDB DOI: https://doi.org/10.2210/pdb7LCF/pdb

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

Deposited: 2021-01-10 Released: 2022-01-12
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: 2.69 Å
R-Value Free:
0.269 (Depositor), 0.270 (DCC)
R-Value Work:
0.227 (Depositor), 0.229 (DCC)
R-Value Observed:
0.229 (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-factors: L- lysine and R, R- bisLysine allosterically inhibit Cj. DHDPS Enzyme by decreasing its protein dynamics

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

To be published.

Macromolecule Content

Total Structure Weight: 412.01 kDa
Atom Count: 27,972
Modeled Residue Count: 3,553
Deposited Residue Count: 3,720
Unique protein chains: 1

Macromolecules

Find similar proteins by:

| 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 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
LYS (Subject of Investigation/LOI) Query on LYS Download:Ideal Coordinates CCD File SDF format, chain M [auth A] SDF format, chain O [auth C] SDF format, chain P [auth D] SDF format, chain Q [auth E] SDF format, chain S [auth G] SDF format, chain T [auth H] SDF format, chain V [auth I] SDF format, chain W [auth J] SDF format, chain Y [auth L] SDF format, chain X [auth K] SDF format, chain R [auth F] SDF format, chain N [auth B] MOL2 format, chain M [auth A] MOL2 format, chain O [auth C] MOL2 format, chain P [auth D] MOL2 format, chain Q [auth E] MOL2 format, chain S [auth G] MOL2 format, chain T [auth H] MOL2 format, chain V [auth I] MOL2 format, chain W [auth J] MOL2 format, chain Y [auth L] MOL2 format, chain X [auth K] MOL2 format, chain R [auth F] MOL2 format, chain N [auth B] mmCIF format, chain M [auth A] mmCIF format, chain O [auth C] mmCIF format, chain P [auth D] mmCIF format, chain Q [auth E] mmCIF format, chain S [auth G] mmCIF format, chain T [auth H] mmCIF format, chain V [auth I] mmCIF format, chain W [auth J] mmCIF format, chain Y [auth L] mmCIF format, chain X [auth K] mmCIF format, chain R [auth F] mmCIF format, chain N [auth B]	M [auth A] N [auth B] O [auth C] P [auth D] Q [auth E] M [auth A], N [auth B], O [auth C], P [auth D], Q [auth E], R [auth F], S [auth G], T [auth H], V [auth I], W [auth J], X [auth K], Y [auth L]	LYSINE C₆ H₁₅ N₂ O₂ KDXKERNSBIXSRK-YFKPBYRVSA-O		Interactions Focus chain M [auth A] Focus chain N [auth B] Focus chain O [auth C] Focus chain P [auth D] Focus chain Q [auth E] Focus chain R [auth F] Focus chain S [auth G] Focus chain T [auth H] Focus chain V [auth I] Focus chain W [auth J] Focus chain X [auth K] Focus chain Y [auth L] Interactions & Density Focus chain M [auth A] Focus chain N [auth B] Focus chain O [auth C] Focus chain P [auth D] Focus chain Q [auth E] Focus chain R [auth F] Focus chain S [auth G] Focus chain T [auth H] Focus chain V [auth I] Focus chain W [auth J] Focus chain X [auth K] Focus chain Y [auth L]
MG (Subject of Investigation/LOI) Query on MG Download:Ideal Coordinates CCD File SDF format, chain U [auth H] MOL2 format, chain U [auth H] mmCIF format, chain U [auth H]	U [auth H]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain U [auth H] Interactions & Density Focus chain U [auth H]