4I9D

X-ray structure of NikA in complex with Fe-N,N'-Bis(2-pyridylmethyl)-N-carboxymethyl-N'-methyl

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.70 Å
  • R-Value Free: 0.195 
  • R-Value Work: 0.152 
  • R-Value Observed: 0.154 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.0 of the entry. See complete history. 


Literature

An artificial oxygenase built from scratch: substrate binding site identified using a docking approach.

Esmieu, C., Cherrier, M.V., Amara, P., Girgenti, E., Marchi-Delapierre, C., Oddon, F., Iannello, M., Jorge-Robin, A., Cavazza, C., Menage, S.

(2013) Angew Chem Int Ed Engl 52: 3922-3925


Macromolecules
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(by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Nickel-binding periplasmic proteinA, B502Escherichia coli BL21(DE3)Mutation(s): 0 
Gene Names: b3476, JW3441, nikA
EC: 3.6.3.24
UniProt
Find proteins for P33590 (Escherichia coli (strain K12))
Explore P33590 
Go to UniProtKB:  P33590
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP33590
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
L4D
Query on L4D
Download Ideal Coordinates CCD File 
GA [auth A],
WA [auth B]		{(S)-N-(2-{methyl[(pyridin-2-yl-kappaN)methyl]amino-kappaN}ethyl)-N-[(pyridin-2-yl-kappaN)methyl]glycinato-kappa~2~N,O}iron(2+)
C17 H21 Fe N4 O2
KEGLXUIHTNIIAB-UHFFFAOYSA-M		 Ligand Interaction
SO4
Query on SO4
Download Ideal Coordinates CCD File 
F [auth A],
G [auth A]		SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L		 Ligand Interaction
GOL
Query on GOL
Download Ideal Coordinates CCD File 
BA [auth A],
E [auth A],
H [auth A],
HA [auth A],
IA [auth A],
BA [auth A],
E [auth A],
H [auth A],
HA [auth A],
IA [auth A],
J [auth A],
JA [auth A],
K [auth A],
KA [auth B],
L [auth A],
LA [auth B],
N [auth A],
NA [auth B],
P [auth A],
PA [auth B],
TA [auth B],
U [auth A],
UA [auth B],
X [auth A],
XA [auth B],
ZA [auth B]
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N		 Ligand Interaction
ACT
Query on ACT
Download Ideal Coordinates CCD File 
AA [auth A],
C [auth A],
CA [auth A],
D [auth A],
DA [auth A],
AA [auth A],
C [auth A],
CA [auth A],
D [auth A],
DA [auth A],
EA [auth A],
FA [auth A],
I [auth A],
M [auth A],
MA [auth B],
O [auth A],
OA [auth B],
Q [auth A],
QA [auth B],
R [auth A],
RA [auth B],
S [auth A],
SA [auth B],
T [auth A],
V [auth A],
VA [auth B],
W [auth A],
Y [auth A],
YA [auth B],
Z [auth A]
ACETATE ION
C2 H3 O2
QTBSBXVTEAMEQO-UHFFFAOYSA-M		 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.70 Å
  • R-Value Free: 0.195 
  • R-Value Work: 0.152 
  • R-Value Observed: 0.154 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 86.67α = 90
b = 94.73β = 90
c = 124.87γ = 90
Software Package:
Software NamePurpose
XSCALEdata scaling
PHENIXrefinement
PDB_EXTRACTdata extraction
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 


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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2013-04-17
    Type: Initial release