5YSH

Diol dehydratase - alpha/T172A mutant complexed with AdoCbl, aerobically-prepared crystal


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.9 Å
  • R-Value Free: 0.191 
  • R-Value Work: 0.164 

wwPDB Validation 3D Report Full Report


This is version 1.0 of the entry. See complete history

Literature

Direct Participation of a Peripheral Side Chain of a Corrin Ring in Coenzyme B12Catalysis.

Shibata, N.Sueyoshi, Y.Higuchi, Y.Toraya, T.

(2018) Angew. Chem. Int. Ed. Engl. 57: 7830-7835


Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Diol dehydrase alpha subunit
A, D, G, J
554Klebsiella oxytocaMutation(s): 1 
Gene Names: pddA (pduC)
EC: 4.2.1.28
Find proteins for Q59470 (Klebsiella oxytoca)
Go to UniProtKB:  Q59470
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Diol dehydrase beta subunit
B, E, H, K
200Klebsiella oxytocaMutation(s): 0 
Gene Names: pddB (pduD)
EC: 4.2.1.28
Find proteins for Q59471 (Klebsiella oxytoca)
Go to UniProtKB:  Q59471
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
Diol dehydrase gamma subunit
C, F, I, L
137Klebsiella oxytocaMutation(s): 0 
Gene Names: pddC (pduE)
EC: 4.2.1.28
Find proteins for Q59472 (Klebsiella oxytoca)
Go to UniProtKB:  Q59472
Small Molecules
Ligands 5 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
K
Query on K

Download SDF File 
Download CCD File 
A, D, G, J
POTASSIUM ION
K
NPYPAHLBTDXSSS-UHFFFAOYSA-N
 Ligand Interaction
CA
Query on CA

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Download CCD File 
A, D, G, J
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
 Ligand Interaction
5AD
Query on 5AD

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Download CCD File 
A, D, G, J
5'-DEOXYADENOSINE
C10 H13 N5 O3
XGYIMTFOTBMPFP-KQYNXXCUSA-N
 Ligand Interaction
B12
Query on B12

Download SDF File 
Download CCD File 
B, E, H, K
COBALAMIN
C62 H89 Co N13 O14 P
LKVIQTCSMMVGFU-DWSMJLPVSA-N
 Ligand Interaction
PGO
Query on PGO

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Download CCD File 
A, D, G, J
S-1,2-PROPANEDIOL
C3 H8 O2
DNIAPMSPPWPWGF-VKHMYHEASA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.9 Å
  • R-Value Free: 0.191 
  • R-Value Work: 0.164 
  • Space Group: P 1
Unit Cell:
Length (Å)Angle (°)
a = 70.330α = 92.69
b = 110.490β = 95.97
c = 115.480γ = 105.44
Software Package:
Software NamePurpose
PHASERphasing
PHENIXrefinement
XDSdata reduction
XDSdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

  • Deposited Date: 2017-11-14 
  • Released Date: 2018-09-19 
  • Deposition Author(s): Shibata, N.

Revision History 

  • Version 1.0: 2018-09-19
    Type: Initial release