3ST8 | pdb_00003st8

Crystal structure of GlmU from Mycobacterium tuberculosis in complex with COENZYME A, GLUCOSAMINE 1-PHOSPHATE and URIDINE-DIPHOSPHATE-N-ACETYLGLUCOSAMINE

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.98 Å
  • R-Value Free: 
    0.202 (Depositor), 0.203 (DCC) 
  • R-Value Work: 
    0.167 (Depositor), 0.169 (DCC) 
  • R-Value Observed: 
    0.168 (Depositor) 

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Ligand Structure Quality Assessment 


This is version 2.1 of the entry. See complete history. 

Literature

Structure of Mycobacterium tuberculosis GlmU in complex with Acetyl CoA

Jagtap, P.A., Prakash, B.

To be published.

Macromolecule Content 

  • Total Structure Weight: 54.2 kDa 
  • Atom Count: 4,115 
  • Modeled Residue Count: 475 
  • Deposited Residue Count: 501 
  • Unique protein chains: 1

Macromolecules

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|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Bifunctional protein glmU501Mycobacterium tuberculosis H37RvMutation(s): 0 
Gene Names: glmU, MT1046, Rv1018c
EC: 2.7.7.23 (PDB Primary Data), 2.3.1.157 (PDB Primary Data)
UniProt
Find proteins for P9WMN3 (Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv))
Explore P9WMN3 
Go to UniProtKB:  P9WMN3
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP9WMN3
Sequence Annotations
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Reference Sequence

Small Molecules

Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
COA

Query on COA


Download:Ideal Coordinates CCD File
D [auth A]COENZYME A
C21 H36 N7 O16 P3 S
RGJOEKWQDUBAIZ-IBOSZNHHSA-N
UD1

Query on UD1


Download:Ideal Coordinates CCD File
H [auth A]URIDINE-DIPHOSPHATE-N-ACETYLGLUCOSAMINE
C17 H27 N3 O17 P2
LFTYTUAZOPRMMI-CFRASDGPSA-N
GP1

Query on GP1


Download:Ideal Coordinates CCD File
E [auth A]2-amino-2-deoxy-1-O-phosphono-alpha-D-glucopyranose
C6 H14 N O8 P
YMJBYRVFGYXULK-QZABAPFNSA-N
MG

Query on MG


Download:Ideal Coordinates CCD File
B [auth A],
C [auth A],
F [auth A],
G [auth A]		MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.98 Å
  • R-Value Free:  0.202 (Depositor), 0.203 (DCC) 
  • R-Value Work:  0.167 (Depositor), 0.169 (DCC) 
  • R-Value Observed: 0.168 (Depositor) 
Space Group: H 3 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 110.312α = 90
b = 110.312β = 90
c = 360.537γ = 120
Software Package:
Software NamePurpose
XSCALEdata scaling
REFMACrefinement
PDB_EXTRACTdata extraction

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2012-08-08
    Type: Initial release
  • Version 2.0: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Atomic model, Data collection, Database references, Derived calculations, Structure summary
  • Version 2.1: 2024-03-20
    Changes: Data collection, Database references, Structure summary