6UAP

Crystal structure of tryptophan synthase from M. tuberculosis - open form with BRD6309 bound


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.75 Å
  • R-Value Free: 0.211 
  • R-Value Work: 0.171 
  • R-Value Observed: 0.172 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


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Literature

Crystal structure of tryptophan synthase from M. tuberculosis - open form with BRD6309 bound

Chang, C.Michalska, K.Maltseva, N.I.Jedrzejczak, R.McCarren, P.Nag, P.P.Joachimiak, A.Satchell, K.

To be published.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Tryptophan synthase alpha chainA, C, E, G276Mycobacterium tuberculosis H37RvMutation(s): 0 
Gene Names: trpARv1613MTCY01B2.05
EC: 4.2.1.20
UniProt
Find proteins for P9WFY1 (Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv))
Explore P9WFY1 
Go to UniProtKB:  P9WFY1
Protein Feature View
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Tryptophan synthase beta chainB, D, F, H410Mycobacterium tuberculosis H37RvMutation(s): 0 
Gene Names: trpBRv1612MTCY01B2.04
EC: 4.2.1.20
UniProt
Find proteins for P9WFX9 (Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv))
Explore P9WFX9 
Go to UniProtKB:  P9WFX9
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 6 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
H9V (Subject of Investigation/LOI)
Query on H9V

Download Ideal Coordinates CCD File 
KA [auth F], L [auth B], UA [auth H], W [auth D](2R,3S,4R)-3-(4'-chloro-2',6'-difluoro[1,1'-biphenyl]-4-yl)-4-(fluoromethyl)azetidine-2-carbonitrile
C17 H12 Cl F3 N2
XHUZEPHBFHVYMY-YQQAZPJKSA-N
 Ligand Interaction
MLT
Query on MLT

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FA [auth D], GA [auth D], P [auth B], QA [auth F], WA [auth H]D-MALATE
C4 H6 O5
BJEPYKJPYRNKOW-UWTATZPHSA-N
 Ligand Interaction
MLA
Query on MLA

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O [auth B], PA [auth F], U [auth C]MALONIC ACID
C3 H4 O4
OFOBLEOULBTSOW-UHFFFAOYSA-N
 Ligand Interaction
EDO
Query on EDO

Download Ideal Coordinates CCD File 
HA [auth D], K [auth A]1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
 Ligand Interaction
ACT
Query on ACT

Download Ideal Coordinates CCD File 
IA [auth D], JA [auth D], TA [auth G], X [auth D], XA [auth H], Y [auth D]ACETATE ION
C2 H3 O2
QTBSBXVTEAMEQO-UHFFFAOYSA-M
 Ligand Interaction
FMT
Query on FMT

Download Ideal Coordinates CCD File 
AA [auth D] , BA [auth D] , CA [auth D] , DA [auth D] , EA [auth D] , I [auth A] , J [auth A] , LA [auth F] , 
AA [auth D], BA [auth D], CA [auth D], DA [auth D], EA [auth D], I [auth A], J [auth A], LA [auth F], M [auth B], MA [auth F], N [auth B], NA [auth F], OA [auth F], Q [auth B], R [auth B], RA [auth F], S [auth B], SA [auth G], T [auth C], V [auth C], VA [auth H], YA [auth H], Z [auth D]
FORMIC ACID
C H2 O2
BDAGIHXWWSANSR-UHFFFAOYSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
LLP
Query on LLP
B, D, F, HL-PEPTIDE LINKINGC14 H22 N3 O7 PLYS
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.75 Å
  • R-Value Free: 0.211 
  • R-Value Work: 0.171 
  • R-Value Observed: 0.172 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 134.777α = 90
b = 157.877β = 90
c = 166.69γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
SCALEPACKdata scaling
PDB_EXTRACTdata extraction
HKL-3000data reduction
HKL-3000phasing

Structure Validation

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Ligand Structure Quality Assessment  



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Structure-guided Drug Discovery CoalitionCanada--

Revision History  (Full details and data files)

  • Version 1.0: 2019-10-30
    Type: Initial release