6WDU

The external aldimine form of the Salmonella thypi wild-type tryptophan synthase in open conformation showing multiple side chain conformations for the residue beta Q114 and sodium ion at the metal coordination site. One of the beta-Q114 rotamer conformations allows a hydrogen bond to form with the PLP oxygen at the position 3 in the ring.

PDB DOI: https://doi.org/10.2210/pdb6WDU/pdb

Classification: LYASE/LYASE INHIBITOR
Organism(s): Salmonella enterica subsp. enterica serovar Typhimurium str. LT2
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2020-04-01 Released: 2021-03-10
Deposition Author(s): Hilario, E., Fan, L., Dunn, M.F., Mueller, L.J.
Funding Organization(s): National Institutes of Health/National Human Genome Research Institute (NIH/NHGRI)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.40 Å
R-Value Free: 0.195
R-Value Work: 0.162
R-Value Observed: 0.163

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

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

Literature

The external aldimine form of the Salmonella thypi wild-type tryptophan synthase in open conformation showing multiple side chain conformations for the residue beta Q114 and sodium ion at the metal coordination site. One of the beta-Q114 rotamer conformations allows a hydrogen bond to form with the PLP oxygen at the position 3 in the ring.

Hilario, E., Fan, L., Dunn, M.F., Mueller, L.J.

To be published.

Macromolecule Content

Total Structure Weight: 73.8 kDa
Atom Count: 6,094
Modelled Residue Count: 650
Deposited Residue Count: 665
Unique protein chains: 2

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Tryptophan synthase alpha chain	A	268	Salmonella enterica subsp. enterica serovar Typhimurium str. LT2	Mutation(s): 0 Gene Names: trpA, STM1727 EC: 4.2.1.20
UniProt
Find proteins for P00929 (Salmonella typhimurium (strain LT2 / SGSC1412 / ATCC 700720)) Explore P00929 Go to UniProtKB: P00929
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P00929
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Tryptophan synthase beta chain	B	397	Salmonella enterica subsp. enterica serovar Typhimurium str. LT2	Mutation(s): 0 Gene Names: trpB, STM1726 EC: 4.2.1.20
UniProt
Find proteins for P0A2K1 (Salmonella typhimurium (strain LT2 / SGSC1412 / ATCC 700720)) Explore P0A2K1 Go to UniProtKB: P0A2K1
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P0A2K1
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 5 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
KOU (Subject of Investigation/LOI) Query on KOU Download Ideal Coordinates CCD File SDF format, chain R [auth B] MOL2 format, chain R [auth B]	R [auth B]	(E)-N-({3-hydroxy-2-methyl-5-[(phosphonooxy)methyl]pyridin-4-yl}methylidene)-L-serine C₁₁ H₁₅ N₂ O₈ P ZTQZHYMXYBDMIL-BIMOUXMDSA-N		Interactions Focus chain R [auth B] Interactions & Density Focus chain R [auth B]
PEG Query on PEG Download Ideal Coordinates CCD File SDF format, chain I [auth B] SDF format, chain L [auth B] MOL2 format, chain I [auth B] MOL2 format, chain L [auth B]	I [auth B], L [auth B]	DI(HYDROXYETHYL)ETHER C₄ H₁₀ O₃ MTHSVFCYNBDYFN-UHFFFAOYSA-N		Interactions Focus chain I [auth B] Focus chain L [auth B] Interactions & Density Focus chain I [auth B] Focus chain L [auth B]
DMS Query on DMS Download Ideal Coordinates CCD File SDF format, chain F [auth A] SDF format, chain G [auth A] SDF format, chain V [auth B] SDF format, chain W [auth B] SDF format, chain Y [auth B] SDF format, chain Z [auth B] SDF format, chain AA [auth B] SDF format, chain BA [auth B] SDF format, chain CA [auth B] SDF format, chain H [auth A] SDF format, chain S [auth B] SDF format, chain T [auth B] SDF format, chain U [auth B] SDF format, chain X [auth B] MOL2 format, chain F [auth A] MOL2 format, chain G [auth A] MOL2 format, chain V [auth B] MOL2 format, chain W [auth B] MOL2 format, chain Y [auth B] MOL2 format, chain Z [auth B] MOL2 format, chain AA [auth B] MOL2 format, chain BA [auth B] MOL2 format, chain CA [auth B] MOL2 format, chain H [auth A] MOL2 format, chain S [auth B] MOL2 format, chain T [auth B] MOL2 format, chain U [auth B] MOL2 format, chain X [auth B]	AA [auth B] BA [auth B] CA [auth B] F [auth A] G [auth A] AA [auth B], BA [auth B], CA [auth B], F [auth A], G [auth A], H [auth A], S [auth B], T [auth B], U [auth B], V [auth B], W [auth B], X [auth B], Y [auth B], Z [auth B]	DIMETHYL SULFOXIDE C₂ H₆ O S IAZDPXIOMUYVGZ-UHFFFAOYSA-N		Interactions Focus chain AA [auth B] Focus chain BA [auth B] Focus chain CA [auth B] Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth A] Focus chain S [auth B] Focus chain T [auth B] Focus chain U [auth B] Focus chain V [auth B] Focus chain W [auth B] Focus chain X [auth B] Focus chain Y [auth B] Focus chain Z [auth B] Interactions & Density Focus chain AA [auth B] Focus chain BA [auth B] Focus chain CA [auth B] Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth A] Focus chain S [auth B] Focus chain T [auth B] Focus chain U [auth B] Focus chain V [auth B] Focus chain W [auth B] Focus chain X [auth B] Focus chain Y [auth B] Focus chain Z [auth B]
EDO Query on EDO Download Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain D [auth A] SDF format, chain E [auth A] SDF format, chain J [auth B] SDF format, chain K [auth B] SDF format, chain M [auth B] SDF format, chain N [auth B] SDF format, chain Q [auth B] MOL2 format, chain C [auth A] MOL2 format, chain D [auth A] MOL2 format, chain E [auth A] MOL2 format, chain J [auth B] MOL2 format, chain K [auth B] MOL2 format, chain M [auth B] MOL2 format, chain N [auth B] MOL2 format, chain Q [auth B]	C [auth A] D [auth A] E [auth A] J [auth B] K [auth B] C [auth A], D [auth A], E [auth A], J [auth B], K [auth B], M [auth B], N [auth B], Q [auth B]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Focus chain D [auth A] Focus chain E [auth A] Focus chain J [auth B] Focus chain K [auth B] Focus chain M [auth B] Focus chain N [auth B] Focus chain Q [auth B] Interactions & Density Focus chain C [auth A] Focus chain D [auth A] Focus chain E [auth A] Focus chain J [auth B] Focus chain K [auth B] Focus chain M [auth B] Focus chain N [auth B] Focus chain Q [auth B]
NA Query on NA Download Ideal Coordinates CCD File SDF format, chain O [auth B] SDF format, chain P [auth B] MOL2 format, chain O [auth B] MOL2 format, chain P [auth B]	O [auth B], P [auth B]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N		Interactions Focus chain O [auth B] Focus chain P [auth B] Interactions & Density Focus chain O [auth B] Focus chain P [auth B]