3ADP | pdb_00003adp

Crystal Structure of the Rabbit L-Gulonate 3-Dehydrogenase (NADH Form)

• PDB DOI: https://doi.org/10.2210/pdb3ADP/pdb
• Entry: 3ADP supersedes: 3A97

• Classification: OXIDOREDUCTASE
• Organism(s): Oryctolagus cuniculus
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2010-01-26 Released: 2010-02-09 
• Deposition Author(s): Asada, Y., Hara, A., Kunishima, N., RIKEN Structural Genomics/Proteomics Initiative (RSGI)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.85 Å
• R-Value Free: 
  0.200 (Depositor), 0.190 (DCC) 
• R-Value Work: 
  0.166 (Depositor), 0.160 (DCC) 
• R-Value Observed: 
  0.168 (Depositor) 

Starting Model: experimental

Literature

Crystal Structure of the Rabbit L-Gulonate 3-Dehydrogenase

Asada, Y., Hara, A., 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: 35.91 kDa 
• Atom Count: 2,889 
• Modeled Residue Count: 310 
• Deposited Residue Count: 319 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Lambda-crystallin	A	319	Oryctolagus cuniculus	Mutation(s): 0  Gene Names: CRYL1, GUL3DH EC: 1.1.1.45
UniProt
Find proteins for P14755 (Oryctolagus cuniculus) Explore P14755  Go to UniProtKB:  P14755

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NAI	B [auth A]	1,4-DIHYDRONICOTINAMIDE ADENINE DINUCLEOTIDE C21 H29 N7 O14 P2 BOPGDPNILDQYTO-NNYOXOHSSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.85 Å
• R-Value Free:  0.200 (Depositor), 0.190 (DCC) 
• R-Value Work:  0.166 (Depositor), 0.160 (DCC) 
• R-Value Observed: 0.168 (Depositor) 

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 72.016	α = 90
b = 69.517	β = 102.7
c = 65.096	γ = 90

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Released Date: 2010-02-09 
Deposition Author(s): Asada, Y., Hara, A., Kunishima, N., RIKEN Structural Genomics/Proteomics Initiative (RSGI)
• This entry supersedes: 3A97

Revision History  

• Version 1.0: 2010-02-09
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2023-11-01
  Changes: Data collection, Database references, Derived calculations, Refinement description