4F7I

Structure of Isopropylmalate dehydrogenase from Thermus thermophilus in complex with IPM, Mn and NADH


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2 Å
  • R-Value Free: 0.196 
  • R-Value Work: 0.152 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

Structural and energetic basis of isopropylmalate dehydrogenase enzyme catalysis.

Pallo, A.Olah, J.Graczer, E.Merli, A.Zavodszky, P.Weiss, M.S.Vas, M.

(2014) Febs J. 281: 5063-5076


Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
3-isopropylmalate dehydrogenase
A, B, C, D
359Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)Mutation(s): 0 
Gene Names: leuB
EC: 1.1.1.85
Find proteins for Q5SIY4 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
Go to UniProtKB:  Q5SIY4
Small Molecules
Ligands 7 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
K
Query on K

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Download CCD File 
A, B, C, D
POTASSIUM ION
K
NPYPAHLBTDXSSS-UHFFFAOYSA-N
 Ligand Interaction
MN
Query on MN

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Download CCD File 
A, B, C, D
MANGANESE (II) ION
Mn
WAEMQWOKJMHJLA-UHFFFAOYSA-N
 Ligand Interaction
GOL
Query on GOL

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A, B, C, D
GLYCEROL
GLYCERIN; PROPANE-1,2,3-TRIOL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
MPO
Query on MPO

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Download CCD File 
A, C, D
3[N-MORPHOLINO]PROPANE SULFONIC ACID
C7 H15 N O4 S
DVLFYONBTKHTER-UHFFFAOYSA-N
 Ligand Interaction
NAD
Query on NAD

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Download CCD File 
A, B, C, D
NICOTINAMIDE-ADENINE-DINUCLEOTIDE
C21 H27 N7 O14 P2
BAWFJGJZGIEFAR-NNYOXOHSSA-N
 Ligand Interaction
IPM
Query on IPM

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Download CCD File 
A, B, C, D
3-ISOPROPYLMALIC ACID
C7 H12 O5
RNQHMTFBUSSBJQ-CRCLSJGQSA-N
 Ligand Interaction
EOH
Query on EOH

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Download CCD File 
A, B, C, D
ETHANOL
C2 H6 O
LFQSCWFLJHTTHZ-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2 Å
  • R-Value Free: 0.196 
  • R-Value Work: 0.152 
  • Space Group: C 1 2 1
Unit Cell:
Length (Å)Angle (°)
a = 148.380α = 90.00
b = 50.720β = 93.09
c = 178.240γ = 90.00
Software Package:
Software NamePurpose
XDSdata reduction
MOLREPphasing
XSCALEdata scaling
REFMACrefinement
MAR345dtbdata collection

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2012-06-13
    Type: Initial release
  • Version 1.1: 2014-10-22
    Type: Database references
  • Version 1.2: 2014-11-12
    Type: Database references
  • Version 1.3: 2014-11-26
    Type: Database references