5HKO

Crystal structure of ABC transporter Solute Binding Protein MSMEG_3598 from Mycobacterium smegmatis str. MC2 155, target EFI-510969, in complex with L-sorbitol


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.20 Å
  • R-Value Free: 0.178 
  • R-Value Work: 0.156 
  • R-Value Observed: 0.157 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.3 of the entry. See complete history


Literature

Crystal structure of ABC transporter Solute Binding Protein MSMEG_3598 from Mycobacterium smegmatis str. MC2 155, target EFI-510969, in complex with L-sorbitol

Roth, Y.Vetting, M.W.Al Obaidi, N.F.Toro, R.Morisco, L.L.Benach, J.Koss, J.Wasserman, S.R.Gerlt, J.A.Almo, S.C.Enzyme Function Initiative (EFI)

To be published.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
ABC transporter, carbohydrate uptake transporter-2 (CUT2) family, periplasmic sugar-binding protein348Mycolicibacterium smegmatis MC2 155Mutation(s): 0 
Gene Names: MSMEG_3598MSMEI_3515
EC: 3.6.3.17
UniProt
Find proteins for A0QYB3 (Mycolicibacterium smegmatis (strain ATCC 700084 / mc(2)155))
Explore A0QYB3 
Go to UniProtKB:  A0QYB3
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0QYB3
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 5 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
62W
Query on 62W

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Z [auth A]L-glucitol
C6 H14 O6
FBPFZTCFMRRESA-FSIIMWSLSA-N
IMD
Query on IMD

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AA [auth A],
BA [auth A],
CA [auth A],
DA [auth A],
EA [auth A]
IMIDAZOLE
C3 H5 N2
RAXXELZNTBOGNW-UHFFFAOYSA-O
ZN
Query on ZN

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B [auth A]
C [auth A]
D [auth A]
E [auth A]
F [auth A]
B [auth A],
C [auth A],
D [auth A],
E [auth A],
F [auth A],
G [auth A],
H [auth A],
I [auth A],
J [auth A],
K [auth A],
L [auth A],
M [auth A],
N [auth A],
O [auth A],
P [auth A]
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
ACT
Query on ACT

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FA [auth A],
GA [auth A],
HA [auth A]
ACETATE ION
C2 H3 O2
QTBSBXVTEAMEQO-UHFFFAOYSA-M
CL
Query on CL

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Q [auth A]
R [auth A]
S [auth A]
T [auth A]
U [auth A]
Q [auth A],
R [auth A],
S [auth A],
T [auth A],
U [auth A],
V [auth A],
W [auth A],
X [auth A],
Y [auth A]
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.20 Å
  • R-Value Free: 0.178 
  • R-Value Work: 0.156 
  • R-Value Observed: 0.157 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 62.947α = 90
b = 62.94β = 90
c = 73.153γ = 90
Software Package:
Software NamePurpose
HKL-3000data scaling
REFMACrefinement
PDB_EXTRACTdata extraction
HKL-3000data reduction
MOLREPphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesGM093342

Revision History  (Full details and data files)

  • Version 1.0: 2016-02-03
    Type: Initial release
  • Version 1.1: 2017-09-27
    Changes: Author supporting evidence, Derived calculations
  • Version 1.2: 2019-12-25
    Changes: Author supporting evidence
  • Version 1.3: 2023-09-27
    Changes: Data collection, Database references, Derived calculations, Refinement description