4R16 | pdb_00004r16

Structure of UDP-D-MAnNAc dehdrogeanse from Pyrococcus horikoshii

• PDB DOI: https://doi.org/10.2210/pdb4R16/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): Pyrococcus horikoshii OT3
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2014-08-04 Released: 2015-10-14 
• Deposition Author(s): Pampa, K.J., Lokanath, N.K., Rai, R.V., Kunishima, N.

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.55 Å
• R-Value Free: 
  0.251 (Depositor), 0.251 (DCC) 
• R-Value Work: 
  0.224 (Depositor), 0.224 (DCC) 

Literature

Structure of UDP-D-MAnNAc dehdrogeanse from Pyrococcus horikoshii

Pampa, K.J., Lokanath, N.K., Rai, R.V., Kunishima, N.

To be published.

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: 94.48 kDa 
• Atom Count: 7,590 
• Modeled Residue Count: 836 
• Deposited Residue Count: 836 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
418aa long hypothetical UDP-N-acetyl-D-mannosaminuronic acid dehydrogenase	A, B	418	Pyrococcus horikoshii OT3	Mutation(s): 0  Gene Names: PH1618 EC: 1.1.1.336
UniProt
Find proteins for O59284 (Pyrococcus horikoshii (strain ATCC 700860 / DSM 12428 / JCM 9974 / NBRC 100139 / OT-3)) Explore O59284  Go to UniProtKB:  O59284

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SAJ	C [auth A], D [auth B]	(2S,3S,4R,5S,6R)-5-acetamido-6-[[[(2R,3S,4R,5R)-5-[2,4-bis(oxidanylidene)pyrimidin-1-yl]-3,4-bis(oxidanyl)oxolan-2-yl]methoxy-oxidanyl-phosphoryl]oxy-oxidanyl-phosphoryl]oxy-3,4-bis(oxidanyl)oxane-2-carboxylic acid C17 H25 N3 O18 P2 DZOGQXKQLXAPND-XHUKORKBSA-N

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE	A, B	L-PEPTIDE LINKING	C5 H11 N O2 Se		MET

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.55 Å
• R-Value Free:  0.251 (Depositor), 0.251 (DCC) 
• R-Value Work:  0.224 (Depositor), 0.224 (DCC) 

Space Group: P 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 54.03	α = 66.2
b = 74.65	β = 70.4
c = 73.56	γ = 75.2

Software Package:

Software Name	Purpose
HKL-2000	data collection
SOLVE	phasing
CNS	refinement
HKL-2000	data reduction
SCALEPACK	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2015-10-14 
Deposition Author(s): Pampa, K.J., Lokanath, N.K., Rai, R.V., Kunishima, N.

Revision History  

• Version 1.0: 2015-10-14
  Type: Initial release
  
• Version 1.1: 2024-11-20
  Changes: Data collection, Database references, Derived calculations, Structure summary