3VWN

Crystal structure of 6-aminohexanoate-dimer hydrolase G181D/R187G/H266N/D370Y mutant


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.20 Å
  • R-Value Free: 0.146 
  • R-Value Work: 0.130 
  • R-Value Observed: 0.130 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Structural, kinetic and theoretical analyses of hydrolase mutants altering in the directionality and equilibrium point of reversible amide-synthetic/hydrolytic reaction

Negoro, S.Kawashima, Y.Shibata, N.Shigeta, Y.Kobayashi, T.Nishiguchi, H.Matsui, T.Baba, T.Lee, Y.Kamiya, K.Kato, D.Takeo, M.Higuchi, Y.

To be published.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
6-aminohexanoate-dimer hydrolaseA [auth X]392Paenarthrobacter ureafaciensFlavobacterium sp. KI723T1
This entity is chimeric
Mutation(s): 4 
Gene Names: nylBnylB'
EC: 3.5.1.46
UniProt
Find proteins for P07062 (Paenarthrobacter ureafaciens)
Explore P07062 
Go to UniProtKB:  P07062
Find proteins for P07061 (Paenarthrobacter ureafaciens)
Explore P07061 
Go to UniProtKB:  P07061
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupsP07061P07062
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
MES
Query on MES

Download Ideal Coordinates CCD File 
G [auth X],
H [auth X],
I [auth X]
2-(N-MORPHOLINO)-ETHANESULFONIC ACID
C6 H13 N O4 S
SXGZJKUKBWWHRA-UHFFFAOYSA-N
SO4
Query on SO4

Download Ideal Coordinates CCD File 
J [auth X],
K [auth X],
L [auth X]
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
GOL
Query on GOL

Download Ideal Coordinates CCD File 
B [auth X],
C [auth X],
D [auth X],
E [auth X],
F [auth X]
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
NA
Query on NA

Download Ideal Coordinates CCD File 
M [auth X],
N [auth X],
O [auth X]
SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.20 Å
  • R-Value Free: 0.146 
  • R-Value Work: 0.130 
  • R-Value Observed: 0.130 
  • Space Group: P 32 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 96.64α = 90
b = 96.64β = 90
c = 112.996γ = 120
Software Package:
Software NamePurpose
SCALEPACKdata scaling
REFMACrefinement
PDB_EXTRACTdata extraction
HKL-2000data reduction

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2013-10-16
    Type: Initial release
  • Version 1.1: 2024-03-20
    Changes: Data collection, Database references, Derived calculations