4I6V

The crystal structure of an amidohydrolase 2 from Planctomyces limnophilus DSM 3776


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.137 Å
  • R-Value Free: 0.218 
  • R-Value Work: 0.168 

wwPDB Validation 3D Report Full Report


This is version 1.0 of the entry. See complete history

Literature

The crystal structure of an amidohydrolase 2 from Planctomyces limnophilus DSM 3776

Fan, Y.Tan, K.Wu, R.Bearden, J.Joachimiak, A.

To be published.

Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Amidohydrolase 2
A, B, C
434Planctopirus limnophila (strain ATCC 43296 / DSM 3776 / IFAM 1008 / 290)EC: 5.3.1.12
Find proteins for D5SMT1 (Planctopirus limnophila (strain ATCC 43296 / DSM 3776 / IFAM 1008 / 290))
Go to UniProtKB:  D5SMT1
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN

Download SDF File 
Download CCD File 
A, B, C
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
ACT
Query on ACT

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Download CCD File 
A
ACETATE ION
C2 H3 O2
QTBSBXVTEAMEQO-UHFFFAOYSA-M
 Ligand Interaction
GOL
Query on GOL

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Download CCD File 
A, B, C
GLYCEROL
GLYCERIN; PROPANE-1,2,3-TRIOL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
MSE
Query on MSE
A, B, C
L-PEPTIDE LINKINGC5 H11 N O2 SeMET
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.137 Å
  • R-Value Free: 0.218 
  • R-Value Work: 0.168 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 81.224α = 90.00
b = 111.245β = 90.00
c = 147.148γ = 90.00
Software Package:
Software NamePurpose
MLPHAREphasing
PHENIXrefinement
HKL-3000data scaling
ARPmodel building
DMphasing
DMmodel building
WARPmodel building
SBC-Collectdata collection
HKL-3000phasing
SHELXDphasing
HKL-3000data reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2013-02-06
    Type: Initial release