4K9C

CRYSTAL STRUCTURE OF probable sugar kinase protein from Rhizobium etli CFN 42 complexed with N-(HYDROXYMETHYL)BENZAMIDE and 4-METHYL-3,4-DIHYDRO-2H-1,4-BENZOXAZINE-7-CARBOXYLIC ACID


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.50 Å
  • R-Value Free: 0.195 
  • R-Value Work: 0.173 
  • R-Value Observed: 0.174 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.0 of the entry. See complete history


Literature

CRYSTAL STRUCTURE OF probable sugar kinase protein from Rhizobium etli CFN 42 complexed with N-(HYDROXYMETHYL)BENZAMIDE and 4-METHYL-3,4-DIHYDRO-2H-1,4-BENZOXAZINE-7-CARBOXYLIC ACID

Malashkevich, V.N.Bhosle, R.Toro, R.Hillerich, B.Gizzi, A.Garforth, S.Kar, A.Chan, M.K.Lafluer, J.Patel, H.Matikainen, B.Chamala, S.Lim, S.Celikgil, A.Villegas, G.Evans, B.Love, J.Fiser, A.Khafizov, K.Seidel, R.Bonanno, J.B.Almo, S.C.

To be published.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
sugar kinaseA, B352Rhizobium etli CFN 42Mutation(s): 0 
Gene Names: RHE_CH00135
UniProt
Find proteins for Q2KDX6 (Rhizobium etli (strain CFN 42 / ATCC 51251))
Explore Q2KDX6 
Go to UniProtKB:  Q2KDX6
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ2KDX6
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 5 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ADN
Query on ADN

Download Ideal Coordinates CCD File 
C [auth A],
I [auth B]
ADENOSINE
C10 H13 N5 O4
OIRDTQYFTABQOQ-KQYNXXCUSA-N
 Ligand Interaction
C29
Query on C29

Download Ideal Coordinates CCD File 
D [auth A],
J [auth B]
4-methyl-3,4-dihydro-2H-1,4-benzoxazine-7-carboxylic acid
C10 H11 N O3
XWYHWMDBIRZPFG-UHFFFAOYSA-N
 Ligand Interaction
1Q8
Query on 1Q8

Download Ideal Coordinates CCD File 
G [auth A],
M [auth B]
N-(hydroxymethyl)benzamide
C8 H9 N O2
UOUBPDZUBVJZOQ-UHFFFAOYSA-N
 Ligand Interaction
DMS
Query on DMS

Download Ideal Coordinates CCD File 
E [auth A],
F [auth A],
K [auth B],
L [auth B]
DIMETHYL SULFOXIDE
C2 H6 O S
IAZDPXIOMUYVGZ-UHFFFAOYSA-N
 Ligand Interaction
K
Query on K

Download Ideal Coordinates CCD File 
H [auth A],
N [auth B]
POTASSIUM ION
K
NPYPAHLBTDXSSS-UHFFFAOYSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
MSE
Query on MSE
A, B L-PEPTIDE LINKINGC5 H11 N O2 SeMET
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.50 Å
  • R-Value Free: 0.195 
  • R-Value Work: 0.173 
  • R-Value Observed: 0.174 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 51.165α = 90
b = 81.355β = 98.08
c = 82.69γ = 90
Software Package:
Software NamePurpose
SCALEPACKdata scaling
PHASERphasing
REFMACrefinement
PDB_EXTRACTdata extraction

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History