6XE3

Salmonella typhimurium Tryptophan Synthase beta-S377A mutant in complex with inhibitor F9 at the enzyme alpha-site, cesium ion at the metal coordination site and carbanion III E(C3) at the enzyme beta-site.


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.55 Å
  • R-Value Free: 0.236 
  • R-Value Work: 0.174 
  • R-Value Observed: 0.177 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.1 of the entry. See complete history


Literature

Salmonella typhimurium Tryptophan Synthase beta-S377A mutant in complex with inhibitor F9 at the enzyme alpha-site, cesium ion at the metal coordination site and carbanion III E(C3) at the enzyme beta-site.

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

To be published.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Tryptophan synthase alpha chain268Salmonella enterica subsp. enterica serovar Typhimurium str. LT2Mutation(s): 0 
Gene Names: trpASTM1727
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 Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP00929
Sequence Annotations
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Tryptophan synthase beta chain397Salmonella enterica subsp. enterica serovar Typhimurium str. LT2Mutation(s): 1 
Gene Names: trpBSTM1726
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 Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP0A2K1
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 6 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
1D0 (Subject of Investigation/LOI)
Query on 1D0

Download Ideal Coordinates CCD File 
N [auth B](2E)-2-[({3-hydroxy-2-methyl-5-[(phosphonooxy)methyl]pyridin-4-yl}methyl)imino]-3-[(2-hydroxyphenyl)amino]propanoic acid
C17 H20 N3 O8 P
MKNJFLJOSVXALN-XMHGGMMESA-N
F9F (Subject of Investigation/LOI)
Query on F9F

Download Ideal Coordinates CCD File 
C [auth A]2-({[4-(TRIFLUOROMETHOXY)PHENYL]SULFONYL}AMINO)ETHYL DIHYDROGEN PHOSPHATE
C9 H11 F3 N O7 P S
JDDKDMFCTOZVCJ-UHFFFAOYSA-N
CS (Subject of Investigation/LOI)
Query on CS

Download Ideal Coordinates CCD File 
H [auth A],
W [auth B],
X [auth B],
Y [auth B]
CESIUM ION
Cs
NCMHKCKGHRPLCM-UHFFFAOYSA-N
DMS
Query on DMS

Download Ideal Coordinates CCD File 
E [auth A]
F [auth A]
J [auth A]
K [auth A]
L [auth A]
E [auth A],
F [auth A],
J [auth A],
K [auth A],
L [auth A],
M [auth A],
NA [auth B],
O [auth B],
OA [auth B],
P [auth B],
PA [auth B],
QA [auth B],
RA [auth B],
U [auth B]
DIMETHYL SULFOXIDE
C2 H6 O S
IAZDPXIOMUYVGZ-UHFFFAOYSA-N
EDO
Query on EDO

Download Ideal Coordinates CCD File 
D [auth A]
G [auth A]
Q [auth B]
R [auth B]
S [auth B]
D [auth A],
G [auth A],
Q [auth B],
R [auth B],
S [auth B],
SA [auth B],
T [auth B],
V [auth B]
1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
CL
Query on CL

Download Ideal Coordinates CCD File 
AA [auth B]
BA [auth B]
CA [auth B]
DA [auth B]
EA [auth B]
AA [auth B],
BA [auth B],
CA [auth B],
DA [auth B],
EA [auth B],
FA [auth B],
GA [auth B],
HA [auth B],
I [auth A],
IA [auth B],
JA [auth B],
KA [auth B],
LA [auth B],
MA [auth B],
Z [auth B]
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.55 Å
  • R-Value Free: 0.236 
  • R-Value Work: 0.174 
  • R-Value Observed: 0.177 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 181.517α = 90
b = 59.427β = 94.64
c = 67.063γ = 90
Software Package:
Software NamePurpose
xia2data reduction
SCALAdata scaling
MOLREPphasing
DMphasing
REFMACrefinement
PDB_EXTRACTdata extraction

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Human Genome Research Institute (NIH/NHGRI)United States2R01GM097569-06A1

Revision History  (Full details and data files)

  • Version 1.0: 2021-03-10
    Type: Initial release
  • Version 1.1: 2023-10-18
    Changes: Data collection, Database references, Refinement description