5U4S | pdb_00005u4s

Crystal structure of a Short chain dehydrogenase from Burkholderia cenocepacia J2315 in complex with NADP.

• PDB DOI: https://doi.org/10.2210/pdb5U4S/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): Burkholderia cenocepacia J2315
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2016-12-06 Released: 2017-01-18 
• Deposition Author(s): Seattle Structural Genomics Center for Infectious Disease (SSGCID)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.40 Å
• R-Value Free: 
  0.166 (Depositor), 0.170 (DCC) 
• R-Value Work: 
  0.148 (Depositor), 0.150 (DCC) 
• R-Value Observed: 
  0.149 (Depositor) 

Literature

Crystal structure of a short-chain dehydrogenase from Burkholderia cenocepacia J2315 in complex with NADP+ and benzoic acid

Belfon, K.K.J., Beyer, O., Abendroth, J., Dranow, D.M., Lorimer, D.D., Abramov, A., Latimore, Y., Hamilton, C., Dawkins, A., Hinojosa, I., Martinez, X., Mirabel, S., Duncan, M., Womack, R., Hicks, L., Turlington, Z.R., Edwards, T.E., Torelli, A.T., Hicks, K.A., French, J.B.

(2024) Acta Crystallogr F Struct Biol Commun 80

• DOI: https://doi.org/10.1107/S2053230X24011282

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 53.87 kDa 
• Atom Count: 4,038 
• Modeled Residue Count: 467 
• Deposited Residue Count: 490 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Putative short chain dehydrogenase	A, B	245	Burkholderia cenocepacia J2315	Mutation(s): 0  Gene Names: BCAM2128
UniProt
Find proteins for B4EFS5 (Burkholderia cenocepacia (strain ATCC BAA-245 / DSM 16553 / LMG 16656 / NCTC 13227 / J2315 / CF5610)) Explore B4EFS5  Go to UniProtKB:  B4EFS5

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NAP	C [auth A], F [auth B]	NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE C21 H28 N7 O17 P3 XJLXINKUBYWONI-NNYOXOHSSA-N
BEZ	D [auth A], G [auth B]	BENZOIC ACID C7 H6 O2 WPYMKLBDIGXBTP-UHFFFAOYSA-N
PO4	E [auth A]	PHOSPHATE ION O4 P NBIIXXVUZAFLBC-UHFFFAOYSA-K

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.40 Å
• R-Value Free:  0.166 (Depositor), 0.170 (DCC) 
• R-Value Work:  0.148 (Depositor), 0.150 (DCC) 
• R-Value Observed: 0.149 (Depositor) 

Diffraction Data: https://doi.org/10.18430/M35U4S

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 39.27	α = 90
b = 75.66	β = 90
c = 146.01	γ = 90

Software Package:

Software Name	Purpose
XDS	data reduction
XSCALE	data scaling
PHASER	phasing
ARP	model building
Coot	model building
PHENIX	refinement
PDB_EXTRACT	data extraction

Structure Validation

Entry History 

Deposition Data

• Released Date: 2017-01-18 
Deposition Author(s): Seattle Structural Genomics Center for Infectious Disease (SSGCID)

Revision History  

• Version 1.0: 2017-01-18
  Type: Initial release
  
• Version 1.1: 2024-03-06
  Changes: Data collection, Database references
• Version 1.2: 2025-11-12
  Changes: Database references, Structure summary