4YB4

Crystal structure of homoisocitrate dehydrogenase from Thermus thermophilus in complex with homoisocitrate, magnesium ion (II) and NADH


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.50 Å
  • R-Value Free: 0.205 
  • R-Value Work: 0.150 
  • R-Value Observed: 0.153 

Starting Model: experimental
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Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history


Literature

Structure of homoisocitrate dehydrogenase from Thermus thermophilus in complex with homoisocitrate, magnesium(II) and NADH

Takahashi, K.Tomita, T.Kuzuyama, T.Nishiyama, M.

To be published.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Homoisocitrate dehydrogenase
A, B, C, D
334Thermus thermophilus HB27Mutation(s): 0 
Gene Names: hicdhdhhicdhTT_C1012
EC: 1.1.1.87 (PDB Primary Data), 1.1.1.286 (UniProt)
UniProt
Find proteins for Q72IW9 (Thermus thermophilus (strain ATCC BAA-163 / DSM 7039 / HB27))
Explore Q72IW9 
Go to UniProtKB:  Q72IW9
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ72IW9
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 5 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
NAI
Query on NAI

Download Ideal Coordinates CCD File 
G [auth A],
GB [auth D],
LA [auth C],
U [auth B]
1,4-DIHYDRONICOTINAMIDE ADENINE DINUCLEOTIDE
C21 H29 N7 O14 P2
BOPGDPNILDQYTO-NNYOXOHSSA-N
48Y
Query on 48Y

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F [auth A],
FB [auth D],
KA [auth C],
T [auth B]
(1R,2S)-1-hydroxybutane-1,2,4-tricarboxylic acid
C7 H10 O7
OEJZZCGRGVFWHK-WVZVXSGGSA-N
SO4
Query on SO4

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AB [auth C]
BA [auth B]
BB [auth C]
CA [auth B]
CB [auth C]
AB [auth C],
BA [auth B],
BB [auth C],
CA [auth B],
CB [auth C],
DA [auth B],
DB [auth C],
EA [auth B],
EB [auth C],
FA [auth B],
GA [auth B],
HA [auth B],
IA [auth B],
M [auth A],
N [auth A],
NB [auth D],
O [auth A],
OB [auth D],
P [auth A],
PB [auth D],
Q [auth A],
QB [auth D],
R [auth A],
RB [auth D],
S [auth A],
VA [auth C],
WA [auth C],
XA [auth C],
YA [auth C],
ZA [auth C]
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
GOL
Query on GOL

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AA [auth B]
HB [auth D]
I [auth A]
IB [auth D]
J [auth A]
AA [auth B],
HB [auth D],
I [auth A],
IB [auth D],
J [auth A],
JB [auth D],
K [auth A],
KB [auth D],
L [auth A],
LB [auth D],
MB [auth D],
NA [auth C],
OA [auth C],
PA [auth C],
QA [auth C],
RA [auth C],
SA [auth C],
TA [auth C],
UA [auth C],
V [auth B],
W [auth B],
X [auth B],
Y [auth B],
Z [auth B]
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
MG
Query on MG

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E [auth A],
H [auth A],
JA [auth C],
MA [auth C]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.50 Å
  • R-Value Free: 0.205 
  • R-Value Work: 0.150 
  • R-Value Observed: 0.153 
  • Space Group: P 43 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 159.663α = 90
b = 159.663β = 90
c = 148.517γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
Cootrefinement
HKL-2000data scaling
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2016-03-09
    Type: Initial release
  • Version 1.1: 2020-02-05
    Changes: Data collection, Derived calculations
  • Version 1.2: 2023-11-08
    Changes: Data collection, Database references, Derived calculations, Refinement description