7KWF | pdb_00007kwf

Dihydrodipicolinate synthase (DHDPS) from C.jejuni, H56N mutant with pyruvate bound in the active site and R,R-bislysine bound at the allosteric site

PDB DOI: https://doi.org/10.2210/pdb7KWF/pdb

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

Deposited: 2020-11-30 Released: 2021-12-08
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: 2.82 Å
R-Value Free:
0.334 (Depositor), 0.334 (DCC)
R-Value Work:
0.275 (Depositor), 0.277 (DCC)
R-Value Observed:
0.278 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.2 of the entry. See complete history.

Literature

ALLOSTERIC SITE RESIDUE 'H56' CAPS THE INHIBITOR AT THE TIGHT DIMER INTERFACE FOR TRANSMITTING THE ALLOSTERIC INHIBITION SIGNALS IN Cj.DHDPS

Saran, S., Skovpen, Y., Yazdi, M.M., Palmer, D.R.J., Sanders, D.A.R.

To be published.

Macromolecule Content

Total Structure Weight: 206.35 kDa
Atom Count: 13,867
Modeled Residue Count: 1,793
Deposited Residue Count: 1,860
Unique protein chains: 2

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
4-hydroxy-tetrahydrodipicolinate synthase	A, B, 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% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q9PPB4
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

| 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
4-hydroxy-tetrahydrodipicolinate synthase	C, D, E	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 4 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 G [auth B] SDF format, chain L [auth E] SDF format, chain I [auth C] MOL2 format, chain G [auth B] MOL2 format, chain L [auth E] MOL2 format, chain I [auth C] mmCIF format, chain G [auth B] mmCIF format, chain L [auth E] mmCIF format, chain I [auth C]	G [auth B], I [auth C], L [auth E]	(2R,5R)-2,5-diamino-2,5-bis(4-aminobutyl)hexanedioic acid C₁₄ H₃₀ N₄ O₄ XYUHPPVEDOOPDE-ZIAGYGMSSA-N		Interactions Focus chain G [auth B] Focus chain I [auth C] Focus chain L [auth E] Interactions & Density Focus chain G [auth B] Focus chain I [auth C] Focus chain L [auth E]
PGE (Subject of Investigation/LOI) Query on PGE Download:Ideal Coordinates CCD File SDF format, chain M [auth E] SDF format, chain O [auth F] MOL2 format, chain M [auth E] MOL2 format, chain O [auth F] mmCIF format, chain M [auth E] mmCIF format, chain O [auth F]	M [auth E], O [auth F]	TRIETHYLENE GLYCOL C₆ H₁₄ O₄ ZIBGPFATKBEMQZ-UHFFFAOYSA-N		Interactions Focus chain M [auth E] Focus chain O [auth F] Interactions & Density Focus chain M [auth E] Focus chain O [auth F]
PEG (Subject of Investigation/LOI) Query on PEG Download:Ideal Coordinates CCD File SDF format, chain J [auth C] SDF format, chain K [auth D] MOL2 format, chain J [auth C] MOL2 format, chain K [auth D] mmCIF format, chain J [auth C] mmCIF format, chain K [auth D]	J [auth C], K [auth D]	DI(HYDROXYETHYL)ETHER C₄ H₁₀ O₃ MTHSVFCYNBDYFN-UHFFFAOYSA-N		Interactions Focus chain J [auth C] Focus chain K [auth D] Interactions & Density Focus chain J [auth C] Focus chain K [auth D]
ACT (Subject of Investigation/LOI) Query on ACT Download:Ideal Coordinates CCD File SDF format, chain H [auth B] SDF format, chain N [auth F] MOL2 format, chain H [auth B] MOL2 format, chain N [auth F] mmCIF format, chain H [auth B] mmCIF format, chain N [auth F]	H [auth B], N [auth F]	ACETATE ION C₂ H₃ O₂ QTBSBXVTEAMEQO-UHFFFAOYSA-M		Interactions Focus chain H [auth B] Focus chain N [auth F] Interactions & Density Focus chain H [auth B] Focus chain N [auth F]